Sandor Vajda | Profiles RNS

Sandor Vajda, PhD

Professor

Boston University College of Engineering

Biomedical Engineering

PhD, Hungarian Academy of Sciences
MS, Gupkin State Academy of Oil and Gas
BS, Eotvos University

Websites

	LinkedIn
	Google Scholar
	ResearchGate
	BU Center for Molecular Discovery
	College of Engineering Faculty
	BU BioMolecular Engineering Research Center
	BU Center for Information & Systems Engineering

ORCID : 0000-0003-1540-8220

Sandor Vajda received M.S. in Electrical Engineering in Moscow, Russia, and M.S. in Applied Mathematics and Ph.D. in Chemistry, both in Budapest, Hungary. He held research positions in the Department of Engineering, University of Warwick, England, and the Department of Chemistry, Princeton University. He was on the faculty of the Eotvos Lorand University, Budapest, Hungary and the Mount Sinai School of Medicine, New York, NY. Currently he is Professor of Biomedical Engineering and Chemistry at Boston University. He also directs the Biomolecular Engineering Research Center at BU. Dr. Vajda has been active in method development for modeling of biological macromolecules, with focus on two problems. The first is the analysis of protein-protein interactions, including protein docking, antibody maturation, and protein aggregation. The second broad area includes the characterization of protein binding sites, target identification, druggability assessment, and the development of computational methods for fragment based drug discovery. In 2004 he and his graduate students founded SolMap Pharmaceuticals, a start-up company focusing on fragment-based drug design. SolMap was acquired by Forma Therapeutics, Cambridge, MA, in 2008. He is currently the CSO of another drug discovery software development startup, Acpharis Inc.

Professor
Boston University College of Arts and Sciences
Chemistry

BU Research
NIH RePORTER Research

Analysis and Prediction of Molecular Interactions
06/01/2021 - 03/31/2026 (PI)
NIH/National Institute of General Medical Sciences
5R35GM118078-09

Optimization and Learning Strategies for Protein Docking
09/20/2019 - 08/31/2023 (Co-Investigator)
NIH/National Institute of General Medical Sciences
5R01GM135930-03

Collaborative Research: ABI Development: The next stage in protein-protein docking
06/01/2018 - 05/31/2022 (PI)
National Science Foundation
DBI-1759472

Analysis and Prediction of Molecular Interactions
04/06/2016 - 05/31/2021 (PI)
NIH/National Institute of General Medical Sciences
5R35GM118078-05

ABI development: Utilization of diverse data in exploring pprotein-protein interactions
06/01/2015 - 05/31/2019 (PI)
National Science Foundation
DBI-1458509

AF: Small: Manifold Optimization Algorithms for Protein-Protein Docking
07/01/2016 - 08/30/2018 (Subcontract PI)
The Research Foundation for the State University of New York National Science Fdn
CCF-1645512

Computational mapping of proteins for the binding of ligands
04/01/2015 - 03/31/2017 (PI)
NIH/National Institute of General Medical Sciences
2R01GM064700-13

A MULTISTAGE APPROACH TO PROTEIN-PROTEIN DOCKING
03/01/2016 - 02/28/2017 (PI)
NIH/National Institute of General Medical Sciences
4R01GM061867-15

ABI Development: Refinement Algorithms and Server for Protein Docking
06/01/2012 - 05/31/2016 (PI)
National Science Foundation
DBI-1147082

A MULTISTAGE APPROACH TO PROTEIN-PROTEIN DOCKING
03/01/2013 - 02/29/2016 (PI)
NIH/National Institute of General Medical Sciences
5R01GM061867-14

Showing 10 of 16 results. Show All Results

Title

Yr	Title	Project-Sub Proj	Pubs
2024	Analysis and Prediction of Molecular Interactions	3R35GM118078-09S1
2024	Analysis and Prediction of Molecular Interactions	5R35GM118078-09
2023	Analysis and Prediction of Molecular Interactions	5R35GM118078-08
2022	Analysis and Prediction of Molecular Interactions	5R35GM118078-07
2021	Analysis and Prediction of Molecular Interactions	2R35GM118078-06	25
2020	Analysis and prediction of molecular interactions	5R35GM118078-05	25
2019	Analysis and prediction of molecular interactions	5R35GM118078-04	25
2018	Analysis and prediction of molecular interactions	5R35GM118078-03	25
2018	Analysis and prediction of molecular interactions	3R35GM118078-03S1	25
2017	Analysis and prediction of molecular interactions	5R35GM118078-02	25

Showing 10 of 56 results. Show All Results

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

iCite Analysis Copy PMIDs To Clipboard

Sándor M, Vitale DS, Nagy ZA, Ibrahim SY, Abu-El-Haija M, Lazou M, Vajda S, Sahin-Tóth M. Misfolding PRSS1 variant p.Ala61Val in a case of suspected intrauterine pancreatitis. Pancreatology. 2024 Dec 24. PMID: 39734120

Lazou M, Khan O, Nguyen T, Padhorny D, Kozakov D, Joseph-McCarthy D, Vajda S. Predicting multiple conformations of ligand binding sites in proteins suggests that AlphaFold2 may remember too much. Proc Natl Acad Sci U S A. 2024 Nov 26; 121(48):e2412719121.View Related Profiles.

Joseph-McCarthy, Diane
Vajda, Sandor

PMID: 39565312

Lazou M, Bekar-Cesaretli AA, Vajda S, Joseph-McCarthy D. Identification and Ranking of Binding Sites from Structural Ensembles: Application to SARS-CoV-2. Viruses. 2024 Oct 22; 16(11).View Related Profiles.

Joseph-McCarthy, Diane
Vajda, Sandor

PMID: 39599762; PMCID: PMC11599001; DOI: 10.3390/v16111647;

Lazou M, Kozakov D, Joseph-McCarthy D, Vajda S. Which cryptic sites are feasible drug targets? Drug Discov Today. 2024 Nov; 29(11):104197.View Related Profiles.

Joseph-McCarthy, Diane
Vajda, Sandor

PMID: 39368697; PMCID: PMC11568903; DOI: 10.1016/j.drudis.2024.104197;

Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Patsahan T, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction. Biophys J. 2024 Sep 03; 123(17):2902-2909. PMID: 38751115; PMCID: PMC11393670; DOI: 10.1016/j.bpj.2024.05.011;

Khan O, Jones G, Lazou M, Joseph-McCarthy D, Kozakov D, Beglov D, Vajda S. Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. J Chem Inf Model. 2024 Mar 25; 64(6):2084-2100.View Related Profiles.

Joseph-McCarthy, Diane
Beglov, Dmitri
Vajda, Sandor

PMID: 38456842; PMCID: PMC11694573; DOI: 10.1021/acs.jcim.3c01969;

Bekar-Cesaretli AA, Khan O, Nguyen T, Kozakov D, Joseph-Mccarthy D, Vajda S. Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. J Chem Inf Model. 2024 Feb 12; 64(3):960-973.View Related Profiles.

Joseph-McCarthy, Diane
Vajda, Sandor

PMID: 38253327; PMCID: PMC10922769; DOI: 10.1021/acs.jcim.3c01761;

Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction. bioRxiv. 2023 Dec 14. PMID: 38077000; PMCID: PMC10705405; DOI: 10.1101/2023.11.29.569310;

Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez-Lumbreras LA, Fernandez-Recio J, Harmalkar A, Chu LS, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang SY, Roel-Touris J, Jimenez-Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Velankar S, Wodak SJ. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins. 2023 Dec; 91(12):1658-1683.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 37905971; PMCID: PMC10841881; DOI: 10.1002/prot.26609;

Kotelnikov S, Ashizawa R, Popov KI, Khan O, Ignatov M, Li SX, Hassan M, Coutsias EA, Poda G, Padhorny D, Tropsha A, Vajda S, Kozakov D. Accurate ligand-protein docking in CASP15 using the ClusPro LigTBM server. Proteins. 2023 Dec; 91(12):1822-1828. PMID: 37697630; PMCID: PMC10947245; DOI: 10.1002/prot.26587;

Showing 10 of 268 results. Show More

Hashemi N, Hao B, Ignatov M, Paschalidis IC, Vakili P, Vajda S, Kozakov D. Improved prediction of MHC-peptide binding using protein language models. Front Bioinform. 2023; 3:1207380.View Related Profiles.

Paschalidis, Ioannis
Vajda, Sandor

PMID: 37663788; PMCID: PMC10469926; DOI: 10.3389/fbinf.2023.1207380;

Desta IT, Kotelnikov S, Jones G, Ghani U, Abyzov M, Kholodov Y, Standley DM, Beglov D, Vajda S, Kozakov D. The ClusPro AbEMap web server for the prediction of antibody epitopes. Nat Protoc. 2023 Jun; 18(6):1814-1840.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 37188806; PMCID: PMC10898366; DOI: 10.1038/s41596-023-00826-7;

Ignatov M, Jindal A, Kotelnikov S, Beglov D, Posternak G, Tang X, Maisonneuve P, Poda G, Batey RA, Sicheri F, Whitty A, Tonge PJ, Vajda S, Kozakov D. High Accuracy Prediction of PROTAC Complex Structures. J Am Chem Soc. 2023 Apr 05; 145(13):7123-7135.View Related Profiles.

Whitty, Adrian
Beglov, Dmitri
Vajda, Sandor

PMID: 36961978; PMCID: PMC10240388; DOI: 10.1021/jacs.2c09387;

Whitty, Adrian
Beglov, Dmitri
Vajda, Sandor

PMID: 36961978; PMCID: PMC10240388; DOI: 10.1021/jacs.2c09387;

Wodak SJ, Vajda S, Lensink MF, Kozakov D, Bates PA. Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes. Annu Rev Biophys. 2023 May 09; 52:183-206. PMID: 36626764; PMCID: PMC10885158; DOI: 10.1146/annurev-biophys-102622-084607;

Sándor M, Thiel FG, Schmid M, Demcsák A, Morales Granda NC, Németh BC, Vajda S, Hoerning A, Sahin-Tóth M. Novel p.G250A Mutation Associated with Chronic Pancreatitis Highlights Misfolding-Prone Region in Carboxypeptidase A1 (CPA1). Int J Mol Sci. 2022 Dec 07; 23(24). PMID: 36555104; PMCID: PMC9779553; DOI: 10.3390/ijms232415463;

Pesei ZG, Jancsó Z, Demcsák A, Németh BC, Vajda S, Sahin-Tóth M. Preclinical testing of dabigatran in trypsin-dependent pancreatitis. JCI Insight. 2022 Nov 08; 7(21). PMID: 36136430; PMCID: PMC9675574; DOI: 10.1172/jci.insight.161145;

Wakefield AE, Bajusz D, Kozakov D, Keseru GM, Vajda S. Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors. J Chem Inf Model. 2022 Oct 24; 62(20):4937-4954. PMID: 36195573; PMCID: PMC9847135; DOI: 10.1021/acs.jcim.2c00209;

Desta IT, Kotelnikov S, Jones G, Ghani U, Abyzov M, Kholodov Y, Standley DM, Sabitova M, Beglov D, Vajda S, Kozakov D. Mapping of antibody epitopes based on docking and homology modeling. Proteins. 2023 Feb; 91(2):171-182.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 36088633; PMCID: PMC9822860; DOI: 10.1002/prot.26420;

Ma S, Sun Z, Jing Y, McGann M, Vajda S, Enyedy IJ. Use of Solvent Mapping for Characterizing the Binding Site and for Predicting the Inhibition of the Human Ether-á-Go-Go-Related K+ Channel. Chem Res Toxicol. 2022 Aug 15; 35(8):1359-1369. PMID: 35895844; PMCID: PMC9805671; DOI: 10.1021/acs.chemrestox.2c00036;

Jones G, Wakefield AE, Triplett J, Idrissa K, Goebel J, Kozakov D, Vajda S. API Development Increases Access to Shared Computing Resources at Boston University. J Softw Eng Appl. 2022 Jun; 15(6):197-207. PMID: 36568682; PMCID: PMC9779984; DOI: 10.4236/jsea.2022.156011;

Wakefield AE, Kozakov D, Vajda S. Mapping the binding sites of challenging drug targets. Curr Opin Struct Biol. 2022 Aug; 75:102396. PMID: 35636004; PMCID: PMC9790766; DOI: 10.1016/j.sbi.2022.102396;

Jones G, Jindal A, Ghani U, Kotelnikov S, Egbert M, Hashemi N, Vajda S, Padhorny D, Kozakov D. Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap. Acta Crystallogr D Struct Biol. 2022 Jun 01; 78(Pt 6):690-697. PMID: 35647916; PMCID: PMC9159284; DOI: 10.1107/S2059798322002741;

Egbert M, Jones G, Collins MR, Kozakov D, Vajda S. FTMove: A Web Server for Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures. J Mol Biol. 2022 Jun 15; 434(11):167587. PMID: 35662465; PMCID: PMC9789685; DOI: 10.1016/j.jmb.2022.167587;

Jindal A, Kotelnikov S, Padhorny D, Kozakov D, Zhu Y, Chowdhury R, Vajda S. Side-chain Packing Using SE(3)-Transformer. Pac Symp Biocomput. 2022; 27:46-55. PMID: 34890135; PMCID: PMC8887833

Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A, Czaplewski C, Gieldon A, Kogut M, Lipska AG, Liwo A, Lubecka EA, Maszota-Zieleniak M, Sieradzan AK, Slusarz R, Wesolowski PA, Zieba K, Del Carpio Muñoz CA, Ichiishi E, Harmalkar A, Gray JJ, Bonvin AMJJ, Ambrosetti F, Vargas Honorato R, Jandova Z, Jiménez-García B, Koukos PI, Van Keulen S, Van Noort CW, Réau M, Roel-Touris J, Kotelnikov S, Padhorny D, Porter KA, Alekseenko A, Ignatov M, Desta I, Ashizawa R, Sun Z, Ghani U, Hashemi N, Vajda S, Kozakov D, Rosell M, Rodríguez-Lumbreras LA, Fernandez-Recio J, Karczynska A, Grudinin S, Yan Y, Li H, Lin P, Huang SY, Christoffer C, Terashi G, Verburgt J, Sarkar D, Aderinwale T, Wang X, Kihara D, Nakamura T, Hanazono Y, Gowthaman R, Guest JD, Yin R, Taherzadeh G, Pierce BG, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Sun Y, Zhu S, Shen Y, Park T, Woo H, Yang J, Kwon S, Won J, Seok C, Kiyota Y, Kobayashi S, Harada Y, Takeda-Shitaka M, Kundrotas PJ, Singh A, Vakser IA, Dapkunas J, Olechnovic K, Venclovas C, Duan R, Qiu L, Xu X, Zhang S, Zou X, Wodak SJ. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins. 2021 12; 89(12):1800-1823. PMID: 34453465; PMCID: PMC8616814; DOI: 10.1002/prot.26222;

Egbert M, Ghani U, Ashizawa R, Kotelnikov S, Nguyen T, Desta I, Hashemi N, Padhorny D, Kozakov D, Vajda S. Assessing the binding properties of CASP14 targets and models. Proteins. 2021 12; 89(12):1922-1939. PMID: 34368994; PMCID: PMC8616776; DOI: 10.1002/prot.26209;

Liu Y, Halder A, Seifert S, Marcella N, Vajda S, Frenkel AI. Probing Active Sites in CuxPdy Cluster Catalysts by Machine-Learning-Assisted X-ray Absorption Spectroscopy. ACS Appl Mater Interfaces. 2021 Nov 17; 13(45):53363-53374. PMID: 34255469; DOI: 10.1021/acsami.1c06714;

Bajusz D, Wade WS, Satala G, Bojarski AJ, Ilaš J, Ebner J, Grebien F, Papp H, Jakab F, Douangamath A, Fearon D, von Delft F, Schuller M, Ahel I, Wakefield A, Vajda S, Gerencsér J, Pallai P, Keseru GM. Exploring protein hotspots by optimized fragment pharmacophores. Nat Commun. 2021 05 27; 12(1):3201. PMID: 34045440; PMCID: PMC8159961; DOI: 10.1038/s41467-021-23443-y;

Egbert M, Porter KA, Ghani U, Kotelnikov S, Nguyen T, Ashizawa R, Kozakov D, Vajda S. Conservation of binding properties in protein models. Comput Struct Biotechnol J. 2021; 19:2549-2566. PMID: 34025942; PMCID: PMC8114079; DOI: 10.1016/j.csbj.2021.04.048;

Sotudian S, Desta IT, Hashemi N, Zarbafian S, Kozakov D, Vakili P, Vajda S, Paschalidis IC. Improved cluster ranking in protein-protein docking using a regression approach. Comput Struct Biotechnol J. 2021; 19:2269-2278.View Related Profiles.

Paschalidis, Ioannis
Vajda, Sandor

PMID: 33995918; PMCID: PMC8102165; DOI: 10.1016/j.csbj.2021.04.028;

Vajda S, Porter KA, Kozakov D. Progress toward improved understanding of antibody maturation. Curr Opin Struct Biol. 2021 04; 67:226-231. PMID: 33610066; PMCID: PMC8177482; DOI: 10.1016/j.sbi.2020.11.008;

Wakefield AE, Yueh C, Beglov D, Castilho MS, Kozakov D, Keseru GM, Whitty A, Vajda S. Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. J Chem Inf Model. 2020 12 28; 60(12):6612-6623.View Related Profiles.

Whitty, Adrian
Beglov, Dmitri
Vajda, Sandor

PMID: 33291870; PMCID: PMC8200320; DOI: 10.1021/acs.jcim.0c00877;

Desta IT, Porter KA, Xia B, Kozakov D, Vajda S. Performance and Its Limits in Rigid Body Protein-Protein Docking. Structure. 2020 09 01; 28(9):1071-1081.e3. PMID: 32649857; PMCID: PMC7484347; DOI: 10.1016/j.str.2020.06.006;

Campbell CT, López N, Vajda S. Catalytic properties of model supported nanoparticles. J Chem Phys. 2020 04 14; 152(14):140401. PMID: 32295369; DOI: 10.1063/5.0007579;

Padhorny D, Porter KA, Ignatov M, Alekseenko A, Beglov D, Kotelnikov S, Ashizawa R, Desta I, Alam N, Sun Z, Brini E, Dill K, Schueler-Furman O, Vajda S, Kozakov D. ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking. Proteins. 2020 08; 88(8):1082-1090.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 32142178; PMCID: PMC7874234; DOI: 10.1002/prot.25887;

Halder A, Lee S, Yang B, Pellin MJ, Vajda S, Li Z, Yang Y, Farha OK, Hupp JT. Structural reversibility of Cu doped NU-1000 MOFs under hydrogenation conditions. J Chem Phys. 2020 Feb 28; 152(8):084703. PMID: 32113354; DOI: 10.1063/1.5130600;

Khramushin A, Marcu O, Alam N, Shimony O, Padhorny D, Brini E, Dill KA, Vajda S, Kozakov D, Schueler-Furman O. Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45. Proteins. 2020 08; 88(8):1037-1049. PMID: 31891416; PMCID: PMC7539656; DOI: 10.1002/prot.25871;

Zhong M, Lynch A, Muellers SN, Jehle S, Luo L, Hall DR, Iwase R, Carolan JP, Egbert M, Wakefield A, Streu K, Harvey CM, Ortet PC, Kozakov D, Vajda S, Allen KN, Whitty A. Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2). Biochemistry. 2020 02 04; 59(4):563-581.View Related Profiles.

Whitty, Adrian
Vajda, Sandor

PMID: 31851823; PMCID: PMC8177486; DOI: 10.1021/acs.biochem.9b00943;

Alekseenko A, Kotelnikov S, Ignatov M, Egbert M, Kholodov Y, Vajda S, Kozakov D. ClusPro LigTBM: Automated Template-based Small Molecule Docking. J Mol Biol. 2020 05 15; 432(11):3404-3410. PMID: 31863748; PMCID: PMC7890944; DOI: 10.1016/j.jmb.2019.12.011;

Sun Z, Wakefield AE, Kolossvary I, Beglov D, Vajda S. Structure-Based Analysis of Cryptic-Site Opening. Structure. 2020 02 04; 28(2):223-235.e2.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 31810712; PMCID: PMC7004864; DOI: 10.1016/j.str.2019.11.007;

Halder A, Ngo AT, Luo X, Wang HH, Wen JG, Abbasi P, Asadi M, Zhang C, Miller D, Zhang D, Lu J, Redfern PC, Lau KC, Amine R, Assary RS, Lee YJ, Salehi-Khojin A, Vajda S, Amine K, Curtiss LA. In Situ Formed Ir3Li Nanoparticles as Active Cathode Material in Li-Oxygen Batteries. J Phys Chem A. 2019 Nov 21; 123(46):10047-10056. PMID: 31657929; DOI: 10.1021/acs.jpca.9b06875;

Liu Y, Marcella N, Timoshenko J, Halder A, Yang B, Kolipaka L, Pellin MJ, Seifert S, Vajda S, Liu P, Frenkel AI. Mapping XANES spectra on structural descriptors of copper oxide clusters using supervised machine learning. J Chem Phys. 2019 Oct 28; 151(16):164201. PMID: 31675887; DOI: 10.1063/1.5126597;

Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon L, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subraman SR, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, Chauvot de Beauchêne I, Maigret B, Devignes MD, Ruiz Echartea ME, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkunas J, Olechnovic K, Venclovas C, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Ryan Merideth B, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Honorato RV, Bonvin AMJJ, Wodak SJ. Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. Proteins. 2019 12; 87(12):1200-1221.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 31612567; PMCID: PMC7274794; DOI: 10.1002/prot.25838;

Porter KA, Padhorny D, Desta I, Ignatov M, Beglov D, Kotelnikov S, Sun Z, Alekseenko A, Anishchenko I, Cong Q, Ovchinnikov S, Baker D, Vajda S, Kozakov D. Template-based modeling by ClusPro in CASP13 and the potential for using co-evolutionary information in docking. Proteins. 2019 12; 87(12):1241-1248.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 31444975; PMCID: PMC8200321; DOI: 10.1002/prot.25808;

Chu J, Zhang W, Cencic R, Devine WG, Beglov D, Henkel T, Brown LE, Vajda S, Porco JA, Pelletier J. Amidino-Rocaglates: A Potent Class of eIF4A Inhibitors. Cell Chem Biol. 2019 11 21; 26(11):1586-1593.e3.View Related Profiles.

Beglov, Dmitri
Porco, John
Brown, Lauren
Vajda, Sandor

PMID: 31519508; PMCID: PMC6874763; DOI: 10.1016/j.chembiol.2019.08.008;

Vajda S, Emili A. Mapping global protein contacts. Science. 2019 07 12; 365(6449):120-121.View Related Profiles.

Emili, Andrew
Vajda, Sandor

PMID: 31296755; PMCID: PMC7299175; DOI: 10.1126/science.aay1440;

Yueh C, Rettenmaier J, Xia B, Hall DR, Alekseenko A, Porter KA, Barkovich K, Keseru G, Whitty A, Wells JA, Vajda S, Kozakov D. Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases. J Med Chem. 2019 07 25; 62(14):6512-6524.View Related Profiles.

Whitty, Adrian
Vajda, Sandor

PMID: 31274316; PMCID: PMC7019049; DOI: 10.1021/acs.jmedchem.9b00089;

Egbert M, Whitty A, Keseru GM, Vajda S. Why Some Targets Benefit from beyond Rule of Five Drugs. J Med Chem. 2019 11 27; 62(22):10005-10025.View Related Profiles.

Whitty, Adrian
Vajda, Sandor

PMID: 31188592; PMCID: PMC7102492; DOI: 10.1021/acs.jmedchem.8b01732;

Wakefield AE, Mason JS, Vajda S, Keseru GM. Analysis of tractable allosteric sites in G protein-coupled receptors. Sci Rep. 2019 04 16; 9(1):6180. PMID: 30992500; PMCID: PMC6467999; DOI: 10.1038/s41598-019-42618-8;

Halder A, Kioseoglou J, Yang B, Kolipaka KL, Seifert S, Ilavsky J, Pellin M, Sowwan M, Grammatikopoulos P, Vajda S. Nanoassemblies of ultrasmall clusters with remarkable activity in carbon dioxide conversion into C1 fuels. Nanoscale. 2019 Mar 14; 11(11):4683-4687. PMID: 30783643; DOI: 10.1039/c8nr06664g;

Lee S, Halder A, Ferguson GA, Seifert S, Winans RE, Teschner D, Schlögl R, Papaefthimiou V, Greeley J, Curtiss LA, Vajda S. Subnanometer cobalt oxide clusters as selective low temperature oxidative dehydrogenation catalysts. Nat Commun. 2019 02 27; 10(1):954. PMID: 30814524; PMCID: PMC6393513; DOI: 10.1038/s41467-019-08819-5;

Trilles R, Beglov D, Chen Q, He H, Wireman R, Reed A, Chennamadhavuni S, Panek JS, Brown LE, Vajda S, Porco JA, Kelley MR, Georgiadis MM. Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1. J Med Chem. 2019 02 28; 62(4):1971-1988.View Related Profiles.

Beglov, Dmitri
Panek, James
Porco, John
Brown, Lauren
Vajda, Sandor

PMID: 30653918; PMCID: PMC6583781; DOI: 10.1021/acs.jmedchem.8b01529;

Porter KA, Desta I, Kozakov D, Vajda S. What method to use for protein-protein docking? Curr Opin Struct Biol. 2019 04; 55:1-7. PMID: 30711743; PMCID: PMC6669123; DOI: 10.1016/j.sbi.2018.12.010;

Mammen N, Spanu L, Tyo EC, Yang B, Halder A, Seifert S, Pellin MJ, Vajda S, Narasimhan S. Using first principles calculations to interpret XANES experiments: extracting the size-dependence of the (p?, T) phase diagram of sub-nanometer Cu clusters in an O2 environment. J Phys Condens Matter. 2019 Apr 10; 31(14):144002. PMID: 30625421; DOI: 10.1088/1361-648X/aafcf9;

Froes TQ, Baldini RL, Vajda S, Castilho MS. Structure-based Druggability Assessment of Anti-virulence Targets from Pseudomonas aeruginosa. Curr Protein Pept Sci. 2019; 20(12):1189-1203. PMID: 31038064; PMCID: PMC7067568; DOI: 10.2174/1389203720666190417120758;

Vajda S, Karargyris A, Jaeger S, Santosh KC, Candemir S, Xue Z, Antani S, Thoma G. Feature Selection for Automatic Tuberculosis Screening in Frontal Chest Radiographs. J Med Syst. 2018 Jun 29; 42(8):146. PMID: 29959539; DOI: 10.1007/s10916-018-0991-9;

Vajda S, Beglov D, Wakefield AE, Egbert M, Whitty A. Cryptic binding sites on proteins: definition, detection, and druggability. Curr Opin Chem Biol. 2018 06; 44:1-8.View Related Profiles.

Whitty, Adrian
Beglov, Dmitri
Vajda, Sandor

PMID: 29800865; PMCID: PMC6088748; DOI: 10.1016/j.cbpa.2018.05.003;

Zarbafian S, Moghadasi M, Roshandelpoor A, Nan F, Li K, Vakli P, Vajda S, Kozakov D, Paschalidis IC. Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes. Sci Rep. 2018 04 12; 8(1):5896.View Related Profiles.

Paschalidis, Ioannis
Vajda, Sandor

PMID: 29650980; PMCID: PMC5955889; DOI: 10.1038/s41598-018-23982-3;

Beglov D, Hall DR, Wakefield AE, Luo L, Allen KN, Kozakov D, Whitty A, Vajda S. Exploring the structural origins of cryptic sites on proteins. Proc Natl Acad Sci U S A. 2018 04 10; 115(15):E3416-E3425.View Related Profiles.

Whitty, Adrian
Beglov, Dmitri
Allen, Karen
Vajda, Sandor

PMID: 29581267; PMCID: PMC5899430; DOI: 10.1073/pnas.1711490115;

Halder A, Curtiss LA, Fortunelli A, Vajda S. Perspective: Size selected clusters for catalysis and electrochemistry. J Chem Phys. 2018 Mar 21; 148(11):110901. PMID: 29566496; DOI: 10.1063/1.5020301;

Suchomel P, Kvitek L, Prucek R, Panacek A, Halder A, Vajda S, Zboril R. Simple size-controlled synthesis of Au nanoparticles and their size-dependent catalytic activity. Sci Rep. 2018 03 15; 8(1):4589. PMID: 29545580; PMCID: PMC5854582; DOI: 10.1038/s41598-018-22976-5;

Negreiros FR, Halder A, Yin C, Singh A, Barcaro G, Sementa L, Tyo EC, Pellin MJ, Bartling S, Meiwes-Broer KH, Seifert S, Sen P, Nigam S, Majumder C, Fukui N, Yasumatsu H, Vajda S, Fortunelli A. Bimetallic Ag-Pt Sub-nanometer Supported Clusters as Highly Efficient and Robust Oxidation Catalysts. Angew Chem Int Ed Engl. 2018 01 26; 57(5):1209-1213. PMID: 29239093; DOI: 10.1002/anie.201709784;

Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S. The ClusPro web server for protein-protein docking. Nat Protoc. 2017 Feb; 12(2):255-278.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 28079879; PMCID: PMC5540229; DOI: 10.1038/nprot.2016.169;

Vajda S, Yueh C, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Kozakov D. New additions to the ClusPro server motivated by CAPRI. Proteins. 2017 03; 85(3):435-444.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 27936493; PMCID: PMC5313348; DOI: 10.1002/prot.25219;

Park SD, Baranov D, Ryu J, Cho B, Halder A, Seifert S, Vajda S, Jonas DM. Bandgap Inhomogeneity of a PbSe Quantum Dot Ensemble from Two-Dimensional Spectroscopy and Comparison to Size Inhomogeneity from Electron Microscopy. Nano Lett. 2017 02 08; 17(2):762-771. PMID: 28045274; DOI: 10.1021/acs.nanolett.6b03874;

Bohnuud T, Luo L, Wodak SJ, Bonvin AM, Weng Z, Vajda S, Schueler-Furman O, Kozakov D. A benchmark testing ground for integrating homology modeling and protein docking. Proteins. 2017 01; 85(1):10-16. PMID: 27172383; PMCID: PMC5817996; DOI: 10.1002/prot.25063;

Yueh C, Hall DR, Xia B, Padhorny D, Kozakov D, Vajda S. ClusPro-DC: Dimer Classification by the Cluspro Server for Protein-Protein Docking. J Mol Biol. 2017 02 03; 429(3):372-381. PMID: 27771482; PMCID: PMC5538892; DOI: 10.1016/j.jmb.2016.10.019;

Pellin MJ, Riha SC, Tyo EC, Kwon G, Libera JA, Elam JW, Seifert S, Lee S, Vajda S. Water Oxidation by Size-Selected Co27 Clusters Supported on Fe2 O3. ChemSusChem. 2016 Oct 20; 9(20):3005-3011. PMID: 27717160; DOI: 10.1002/cssc.201600982;

Padhorny D, Kazennov A, Zerbe BS, Porter KA, Xia B, Mottarella SE, Kholodov Y, Ritchie DW, Vajda S, Kozakov D. Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds. Proc Natl Acad Sci U S A. 2016 07 26; 113(30):E4286-93. PMID: 27412858; PMCID: PMC4968711; DOI: 10.1073/pnas.1603929113;

Xia B, Vajda S, Kozakov D. Accounting for pairwise distance restraints in FFT-based protein-protein docking. Bioinformatics. 2016 11 01; 32(21):3342-3344. PMID: 27357172; PMCID: PMC6095118; DOI: 10.1093/bioinformatics/btw306;

Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins. 2016 09; 84 Suppl 1:323-48.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 27122118; PMCID: PMC5030136; DOI: 10.1002/prot.25007;

Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA. Challenges in structural approaches to cell modeling. J Mol Biol. 2016 07 31; 428(15):2943-64. PMID: 27255863; PMCID: PMC4976022; DOI: 10.1016/j.jmb.2016.05.024;

Santosh KC, Vajda S, Antani S, Thoma GR. Edge map analysis in chest X-rays for automatic pulmonary abnormality screening. Int J Comput Assist Radiol Surg. 2016 Sep; 11(9):1637-46. PMID: 26995600; DOI: 10.1007/s11548-016-1359-6;

Whitty A, Zhong M, Viarengo L, Beglov D, Hall DR, Vajda S. Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs. Drug Discov Today. 2016 May; 21(5):712-7.View Related Profiles.

Whitty, Adrian
Beglov, Dmitri
Vajda, Sandor

PMID: 26891978; PMCID: PMC5821503; DOI: 10.1016/j.drudis.2016.02.005;

Mamonov AB, Moghadasi M, Mirzaei H, Zarbafian S, Grove LE, Bohnuud T, Vakili P, Ch Paschalidis I, Vajda S, Kozakov D. Focused grid-based resampling for protein docking and mapping. J Comput Chem. 2016 Apr 30; 37(11):961-70. PMID: 26837000; PMCID: PMC4814242; DOI: 10.1002/jcc.24273;

Lukose V, Luo L, Kozakov D, Vajda S, Allen KN, Imperiali B. Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identify the Functional Catalytic Core. Biochemistry. 2015 Dec 22; 54(50):7326-34.View Related Profiles.

Allen, Karen
Vajda, Sandor

PMID: 26600273; PMCID: PMC5483379; DOI: 10.1021/acs.biochem.5b01086;

Hall DR, Kozakov D, Whitty A, Vajda S. Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery. Trends Pharmacol Sci. 2015 Nov; 36(11):724-36.View Related Profiles.

Whitty, Adrian
Vajda, Sandor

PMID: 26538314; PMCID: PMC4640985; DOI: 10.1016/j.tips.2015.08.003;

Kozakov D, Hall DR, Napoleon RL, Yueh C, Whitty A, Vajda S. New Frontiers in Druggability. J Med Chem. 2015 Dec 10; 58(23):9063-88.View Related Profiles.

Whitty, Adrian
Vajda, Sandor

PMID: 26230724; PMCID: PMC4762776; DOI: 10.1021/acs.jmedchem.5b00586;

Vajda S, Whitty A, Kozakov D. Fragments and hot spots in drug discovery. Oncotarget. 2015 Aug 7; 6(22):18740-1.View Related Profiles.

Whitty, Adrian
Vajda, Sandor

PMID: 26300051; PMCID: PMC4662450; DOI: 10.18632/oncotarget.4968;

Liu C, Yang B, Tyo E, Seifert S, DeBartolo J, von Issendorff B, Zapol P, Vajda S, Curtiss LA. Carbon Dioxide Conversion to Methanol over Size-Selected Cu4 Clusters at Low Pressures. J Am Chem Soc. 2015 Jul 15; 137(27):8676-9. PMID: 26115184; DOI: 10.1021/jacs.5b03668;

Tyo EC, Vajda S. Catalysis by clusters with precise numbers of atoms. Nat Nanotechnol. 2015 Jul; 10(7):577-88. PMID: 26139144; DOI: 10.1038/nnano.2015.140;

Karargyris A, Siegelman J, Tzortzis D, Jaeger S, Candemir S, Xue Z, Santosh KC, Vajda S, Antani S, Folio L, Thoma GR. Combination of texture and shape features to detect pulmonary abnormalities in digital chest X-rays. Int J Comput Assist Radiol Surg. 2016 Jan; 11(1):99-106. PMID: 26092662; DOI: 10.1007/s11548-015-1242-x;

Xia B, Mamonov A, Leysen S, Allen KN, Strelkov SV, Paschalidis ICh, Vajda S, Kozakov D. Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro. J Comput Chem. 2015 Jul 30; 36(20):1568-72.View Related Profiles.

Paschalidis, Ioannis
Allen, Karen
Vajda, Sandor

PMID: 26095982; PMCID: PMC4485579; DOI: 10.1002/jcc.23952;

Bartling S, Yin C, Barke I, Oldenburg K, Hartmann H, von Oeynhausen V, Pohl MM, Houben K, Tyo EC, Seifert S, Lievens P, Meiwes-Broer KH, Vajda S. Pronounced Size Dependence in Structure and Morphology of Gas-Phase Produced, Partially Oxidized Cobalt Nanoparticles under Catalytic Reaction Conditions. ACS Nano. 2015 Jun 23; 9(6):5984-98. PMID: 26027910; DOI: 10.1021/acsnano.5b00791;

Vajda S, Rangoni Y, Cecotti H. Semi-automatic ground truth generation using unsupervised clustering and limited manual labeling: Application to handwritten character recognition. Pattern Recognit Lett. 2015 Jun 01; 58:23-28. PMID: 25870463; PMCID: PMC4392711; DOI: 10.1016/j.patrec.2015.02.001;

Kozakov D, Hall DR, Jehle S, Jehle S, Luo L, Ochiana SO, Jones EV, Pollastri M, Allen KN, Whitty A, Vajda S. Ligand deconstruction: Why some fragment binding positions are conserved and others are not. Proc Natl Acad Sci U S A. 2015 May 19; 112(20):E2585-94.View Related Profiles.

Whitty, Adrian
Allen, Karen
Vajda, Sandor

PMID: 25918377; PMCID: PMC4443342; DOI: 10.1073/pnas.1501567112;

Kozakov D, Grove LE, Hall DR, Bohnuud T, Mottarella SE, Luo L, Xia B, Beglov D, Vajda S. The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins. Nat Protoc. 2015 May; 10(5):733-55.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 25855957; PMCID: PMC4762777; DOI: 10.1038/nprot.2015.043;

Moghadasi M, Mirzaei H, Mamonov A, Vakili P, Vajda S, Paschalidis ICh, Kozakov D. The impact of side-chain packing on protein docking refinement. J Chem Inf Model. 2015 Apr 27; 55(4):872-81.View Related Profiles.

Paschalidis, Ioannis
Vajda, Sandor

PMID: 25714358; PMCID: PMC4734134; DOI: 10.1021/ci500380a;

Mirzaei H, Zarbafian S, Villar E, Mottarella S, Beglov D, Vajda S, Paschalidis ICh, Vakili P, Kozakov D. Energy Minimization on Manifolds for Docking Flexible Molecules. J Chem Theory Comput. 2015 Mar 10; 11(3):1063-76.View Related Profiles.

Beglov, Dmitri
Paschalidis, Ioannis
Vajda, Sandor

PMID: 26478722; PMCID: PMC4606885; DOI: 10.1021/ct500155t;

Mao BH, Chang R, Shi L, Zhuo QQ, Rani S, Liu XS, Tyo EC, Vajda S, Wang SD, Liu Z. A near ambient pressure XPS study of subnanometer silver clusters on Al2O3 and TiO2 ultrathin film supports. Phys Chem Chem Phys. 2014 Dec 28; 16(48):26645-52. PMID: 25372410; DOI: 10.1039/c4cp02325k;

van Bokhoven JA, Vajda S. Size selected clusters and particles: from physical chemistry and chemical physics to catalysis. Phys Chem Chem Phys. 2014 Dec 28; 16(48):26418-20. PMID: 25373845; DOI: 10.1039/c4cp90163k;

Nan F, Moghadasi M, Vakili P, Vajda S, Kozakov D, Ch Paschalidis I. A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking. Proc IEEE Conf Decis Control. 2014 Dec; 2014:4623-4628. PMID: 25914440; PMCID: PMC4405505; DOI: 10.1109/CDC.2014.7040111;

Vakili P, Mirzaei H, Zarbafian S, Paschalidis IC, Kozakov D, Vajda S. Optimization on the space of rigid and flexible motions: an alternative manifold optimization approach. Proc IEEE Conf Decis Control. 2014 Dec; 2014:5825-5830.View Related Profiles.

Paschalidis, Ioannis
Vajda, Sandor

PMID: 25774073; PMCID: PMC4357846; DOI: 10.1109/CDC.2014.7040301;

Bohnuud T, Kozakov D, Vajda S. Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces. PLoS Comput Biol. 2014 Oct; 10(10):e1003872. PMID: 25275445; PMCID: PMC4183424; DOI: 10.1371/journal.pcbi.1003872;

Lu J, Cheng L, Lau KC, Tyo E, Luo X, Wen J, Miller D, Assary RS, Wang HH, Redfern P, Wu H, Park JB, Sun YK, Vajda S, Amine K, Curtiss LA. Effect of the size-selective silver clusters on lithium peroxide morphology in lithium-oxygen batteries. Nat Commun. 2014 Sep 12; 5:4895. PMID: 25215517; DOI: 10.1038/ncomms5895;

Chowdhury R, Beglov D, Moghadasi M, Paschalidis IC, Vakili P, Vajda S, Bajaj C, Kozakov D. Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations. J Chem Theory Comput. 2014 Oct 14; 10(10):4449-4454.View Related Profiles.

Beglov, Dmitri
Paschalidis, Ioannis
Vajda, Sandor

PMID: 25328494; PMCID: PMC4196749; DOI: 10.1021/ct400474w;

Heard CJ, Heiles S, Vajda S, Johnston RL. Pd(n)Ag(4-n) and Pd(n)Pt(4-n) clusters on MgO (100): a density functional surface genetic algorithm investigation. Nanoscale. 2014 Oct 21; 6(20):11777-88. PMID: 25158024; DOI: 10.1039/c4nr03363a;

Parks AJ, Pollastri MP, Hahn ME, Stanford EA, Novikov O, Franks DG, Haigh SE, Narasimhan S, Ashton TD, Hopper TG, Kozakov D, Beglov D, Vajda S, Schlezinger JJ, Sherr DH. In silico identification of an aryl hydrocarbon receptor antagonist with biological activity in vitro and in vivo. Mol Pharmacol. 2014 Nov; 86(5):593-608.View Related Profiles.

Sherr, David
Beglov, Dmitri
Stanford, Elizabeth
Schlezinger, Jennifer
Novikov, Olga
Vajda, Sandor

PMID: 25159092; PMCID: PMC4201140; DOI: 10.1124/mol.114.093369;

Pillai HK, Fang M, Beglov D, Kozakov D, Vajda S, Stapleton HM, Webster TF, Schlezinger JJ. Ligand binding and activation of PPAR? by Firemaster® 550: effects on adipogenesis and osteogenesis in vitro. Environ Health Perspect. 2014 Nov; 122(11):1225-32.View Related Profiles.

Beglov, Dmitri
Schlezinger, Jennifer
Vajda, Sandor
Webster, Thomas

PMID: 25062436; PMCID: PMC4216168; DOI: 10.1289/ehp.1408111;

Villar EA, Beglov D, Chennamadhavuni S, Porco JA, Kozakov D, Vajda S, Whitty A. How proteins bind macrocycles. Nat Chem Biol. 2014 Sep; 10(9):723-31.View Related Profiles.

Whitty, Adrian
Beglov, Dmitri
Porco, John
Vajda, Sandor

PMID: 25038790; PMCID: PMC4417626; DOI: 10.1038/nchembio.1584;

Mottarella SE, Beglov D, Beglova N, Nugent MA, Kozakov D, Vajda S. Docking server for the identification of heparin binding sites on proteins. J Chem Inf Model. 2014 Jul 28; 54(7):2068-78.View Related Profiles.

Beglov, Dmitri
Nugent, Matthew
Vajda, Sandor

PMID: 24974889; PMCID: PMC4184157; DOI: 10.1021/ci500115j;

Yin C, Zheng F, Lee S, Guo J, Wang WC, Kwon G, Vajda V, Wang HH, Lee B, DeBartolo J, Seifert S, Winans RE, Vajda S. Size- and support-dependent evolution of the oxidation state and structure by oxidation of subnanometer cobalt clusters. J Phys Chem A. 2014 Sep 18; 118(37):8477-84. PMID: 24922443; DOI: 10.1021/jp501817u;

Bogorad AM, Xia B, Sandor DG, Mamonov AB, Cafarella TR, Jehle S, Vajda S, Kozakov D, Marintchev A. Insights into the architecture of the eIF2Ba/ß/d regulatory subcomplex. Biochemistry. 2014 Jun 3; 53(21):3432-45.View Related Profiles.

Bogorad, Andrew
Marintchev, Assen
Sandor, Dana
Vajda, Sandor

PMID: 24811713; PMCID: PMC4045321; DOI: 10.1021/bi500346u;

Yin C, Tyo E, Kuchta K, von Issendorff B, Vajda S. Atomically precise (catalytic) particles synthesized by a novel cluster deposition instrument. J Chem Phys. 2014 May 07; 140(17):174201. PMID: 24811634; DOI: 10.1063/1.4871799;

Kozakov D, Li K, Hall DR, Beglov D, Zheng J, Vakili P, Schueler-Furman O, Paschalidis ICh, Clore GM, Vajda S. Encounter complexes and dimensionality reduction in protein-protein association. Elife. 2014 Apr 08; 3:e01370.View Related Profiles.

Beglov, Dmitri
Paschalidis, Ioannis
Vajda, Sandor

PMID: 24714491; PMCID: PMC3978769; DOI: 10.7554/eLife.01370;

Shin U, Williams DE, Kozakov D, Hall DR, Beglov D, Vajda S, Andersen RJ, Pelletier J. Stimulators of translation identified during a small molecule screening campaign. Anal Biochem. 2014 Feb 15; 447:6-14.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 24513115; PMCID: PMC3943918; DOI: 10.1016/j.ab.2013.10.026;

Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ. Blind prediction of interfacial water positions in CAPRI. Proteins. 2014 Apr; 82(4):620-32. PMID: 24155158; PMCID: PMC4582081; DOI: 10.1002/prot.24439;

Kozakov D, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Vajda S. How good is automated protein docking? Proteins. 2013 Dec; 81(12):2159-66.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 23996272; PMCID: PMC3934018; DOI: 10.1002/prot.24403;

Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 2013 Nov; 81(11):1980-7.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 23843247; DOI: 10.1002/prot.24356;

Vajda S, Hall DR, Kozakov D. Sampling and scoring: a marriage made in heaven. Proteins. 2013 Nov; 81(11):1874-84. PMID: 23775627; PMCID: PMC3942495; DOI: 10.1002/prot.24343;

Kwon G, Ferguson GA, Heard CJ, Tyo EC, Yin C, DeBartolo J, Seifert S, Winans RE, Kropf AJ, Greeley J, Johnston RL, Curtiss LA, Pellin MJ, Vajda S. Size-dependent subnanometer Pd cluster (Pd4, Pd6, and Pd17) water oxidation electrocatalysis. ACS Nano. 2013 Jul 23; 7(7):5808-17. PMID: 23799858; DOI: 10.1021/nn400772s;

Mao BH, Chang R, Lee S, Axnanda S, Crumlin E, Grass ME, Wang SD, Vajda S, Liu Z. Oxidation and reduction of size-selected subnanometer Pd clusters on Al2O3 surface. J Chem Phys. 2013 Jun 07; 138(21):214304. PMID: 23758368; DOI: 10.1063/1.4807488;

Golden MS, Cote SM, Sayeg M, Zerbe BS, Villar EA, Beglov D, Sazinsky SL, Georgiadis RM, Vajda S, Kozakov D, Whitty A. Comprehensive experimental and computational analysis of binding energy hot spots at the NF-?B essential modulator/IKKß protein-protein interface. J Am Chem Soc. 2013 Apr 24; 135(16):6242-56.View Related Profiles.

Whitty, Adrian
Beglov, Dmitri
Georgiadis, Rosina
Vajda, Sandor

PMID: 23506214; PMCID: PMC3680600; DOI: 10.1021/ja400914z;

Grove LE, Hall DR, Beglov D, Vajda S, Kozakov D. FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. Bioinformatics. 2013 May 01; 29(9):1218-9.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 23476022; PMCID: PMC3634182; DOI: 10.1093/bioinformatics/btt102;

Riha SC, Klahr BM, Tyo EC, Seifert S, Vajda S, Pellin MJ, Hamann TW, Martinson AB. Atomic layer deposition of a submonolayer catalyst for the enhanced photoelectrochemical performance of water oxidation with hematite. ACS Nano. 2013 Mar 26; 7(3):2396-405. PMID: 23398051; DOI: 10.1021/nn305639z;

Mirzaei H, Villar E, Mottarella S, Beglov D, Paschalidis IC, Vajda S, Kozakov D, Vakili P. Flexible Refinement of Protein-Ligand Docking on Manifolds. Proc IEEE Conf Decis Control. 2013; 1392-1397.View Related Profiles.

Beglov, Dmitri
Paschalidis, Ioannis
Vajda, Sandor

PMID: 24830567; PMCID: PMC4019453; DOI: 10.1109/CDC.2013.6760077;

Moghadasi M, Kozakov D, Vakili P, Vajda S, Paschalidis IC. A New Distributed Algorithm for Side-Chain Positioning in the Process of Protein Docking* Proc IEEE Conf Decis Control. 2013; 739-744.View Related Profiles.

Paschalidis, Ioannis
Vajda, Sandor

PMID: 24844567; PMCID: PMC4024309; DOI: 10.1109/CDC.2013.6759970;

Mirzaei H, Kozakov D, Beglov D, Paschalidis IC, Vajda S, Vakili P. A New Approach to Rigid Body Minimization with Application to Molecular Docking. Proc IEEE Conf Decis Control. 2012 Dec; 2983-2988.View Related Profiles.

Beglov, Dmitri
Paschalidis, Ioannis
Vajda, Sandor

PMID: 24763338; PMCID: PMC3992991; DOI: 10.1109/CDC.2012.6426267;

Liu C, Lee S, Su D, Lee B, Lee S, Winans RE, Yin C, Vajda S, Pfefferle L, Haller GL. Controlling the particle size of ZrO2 nanoparticles in hydrothermally stable ZrO2/MWCNT composites. Langmuir. 2012 Dec 11; 28(49):17159-67. PMID: 23151155; DOI: 10.1021/la303545y;

Brenke R, Hall DR, Chuang GY, Comeau SR, Bohnuud T, Beglov D, Schueler-Furman O, Vajda S, Kozakov D. Application of asymmetric statistical potentials to antibody-protein docking. Bioinformatics. 2012 Oct 15; 28(20):2608-14.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 23053206; PMCID: PMC3467743; DOI: 10.1093/bioinformatics/bts493;

Mirzaei H, Beglov D, Paschalidis IC, Vajda S, Vakili P, Kozakov D. Rigid Body Energy Minimization on Manifolds for Molecular Docking. J Chem Theory Comput. 2012 Nov 13; 8(11):4374-4380.View Related Profiles.

Beglov, Dmitri
Paschalidis, Ioannis
Vajda, Sandor

PMID: 23382659; PMCID: PMC3561712; DOI: 10.1021/ct300272j;

Zerbe BS, Hall DR, Vajda S, Whitty A, Kozakov D. Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces. J Chem Inf Model. 2012 Aug 27; 52(8):2236-44.View Related Profiles.

Whitty, Adrian
Vajda, Sandor

PMID: 22770357; PMCID: PMC3623692; DOI: 10.1021/ci300175u;

Hingtgen S, Kasmieh R, Elbayly E, Nesterenko I, Figueiredo JL, Dash R, Sarkar D, Hall D, Kozakov D, Vajda S, Fisher PB, Shah K. A first-generation multi-functional cytokine for simultaneous optical tracking and tumor therapy. PLoS One. 2012; 7(7):e40234. PMID: 22808125; PMCID: PMC3394792; DOI: 10.1371/journal.pone.0040234;

Bohnuud T, Beglov D, Ngan CH, Zerbe B, Hall DR, Brenke R, Vajda S, Frank-Kamenetskii MD, Kozakov D. Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde. Nucleic Acids Res. 2012 Sep; 40(16):7644-52.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 22705795; PMCID: PMC3439909; DOI: 10.1093/nar/gks519;

Ngan CH, Bohnuud T, Mottarella SE, Beglov D, Villar EA, Hall DR, Kozakov D, Vajda S. FTMAP: extended protein mapping with user-selected probe molecules. Nucleic Acids Res. 2012 Jul; 40(Web Server issue):W271-5.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 22589414; PMCID: PMC3394268; DOI: 10.1093/nar/gks441;

Lee S, Di Vece M, Lee B, Seifert S, Winans RE, Vajda S. Oxidative dehydrogenation of cyclohexene on size selected subnanometer cobalt clusters: improved catalytic performance via evolution of cluster-assembled nanostructures. Phys Chem Chem Phys. 2012 Jul 14; 14(26):9336-42. PMID: 22419008; DOI: 10.1039/c2cp40162b;

Moghadasi M, Kozakov D, Mamonov AB, Vakili P, Vajda S, Paschalidis IC. A Message Passing Approach to Side Chain Positioning with Applications in Protein Docking Refinement. Proc IEEE Conf Decis Control. 2012; 2310-2315.View Related Profiles.

Paschalidis, Ioannis
Vajda, Sandor

PMID: 23515575; PMCID: PMC3600151; DOI: 10.1109/cdc.2012.6426600;

Hall DR, Kozakov D, Vajda S. Analysis of protein binding sites by computational solvent mapping. Methods Mol Biol. 2012; 819:13-27. PMID: 22183527; PMCID: PMC3526383; DOI: 10.1007/978-1-61779-465-0_2;

Hall DR, Ngan CH, Zerbe BS, Kozakov D, Vajda S. Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery. J Chem Inf Model. 2012 Jan 23; 52(1):199-209. PMID: 22145575; PMCID: PMC3264775; DOI: 10.1021/ci200468p;

Hall DH, Grove LE, Yueh C, Ngan CH, Kozakov D, Vajda S. Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme. J Am Chem Soc. 2011 Dec 28; 133(51):20668-71. PMID: 22092261; PMCID: PMC3244821; DOI: 10.1021/ja207914y;

Beglov D, Hall DR, Brenke R, Shapovalov MV, Dunbrack RL, Kozakov D, Vajda S. Minimal ensembles of side chain conformers for modeling protein-protein interactions. Proteins. 2012 Feb; 80(2):591-601.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 22105850; PMCID: PMC3297704; DOI: 10.1002/prot.23222;

Ngan CH, Hall DR, Zerbe B, Grove LE, Kozakov D, Vajda S. FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinformatics. 2012 Jan 15; 28(2):286-7. PMID: 22113084; PMCID: PMC3259439; DOI: 10.1093/bioinformatics/btr651;

Negreiros FR, Aprà E, Barcaro G, Sementa L, Vajda S, Fortunelli A. A first-principles theoretical approach to heterogeneous nanocatalysis. Nanoscale. 2012 Feb 21; 4(4):1208-19. PMID: 22057595; DOI: 10.1039/c1nr11051a;

Buhrman G, O'Connor C, Zerbe B, Kearney BM, Napoleon R, Kovrigina EA, Vajda S, Kozakov D, Kovrigin EL, Mattos C. Analysis of binding site hot spots on the surface of Ras GTPase. J Mol Biol. 2011 Nov 04; 413(4):773-89. PMID: 21945529; PMCID: PMC3247908; DOI: 10.1016/j.jmb.2011.09.011;

Kozakov D, Hall DR, Chuang GY, Cencic R, Brenke R, Grove LE, Beglov D, Pelletier J, Whitty A, Vajda S. Structural conservation of druggable hot spots in protein-protein interfaces. Proc Natl Acad Sci U S A. 2011 Aug 16; 108(33):13528-33.View Related Profiles.

Whitty, Adrian
Beglov, Dmitri
Vajda, Sandor

PMID: 21808046; PMCID: PMC3158149; DOI: 10.1073/pnas.1101835108;

Cencic R, Desforges M, Hall DR, Kozakov D, Du Y, Min J, Dingledine R, Fu H, Vajda S, Talbot PJ, Pelletier J. Blocking eIF4E-eIF4G interaction as a strategy to impair coronavirus replication. J Virol. 2011 Jul; 85(13):6381-9. PMID: 21507972; PMCID: PMC3126520; DOI: 10.1128/JVI.00078-11;

Yin F, Lee S, Abdela A, Vajda S, Palmer RE. Communication: Suppression of sintering of size-selected Pd clusters under realistic reaction conditions for catalysis. J Chem Phys. 2011 Apr 14; 134(14):141101. PMID: 21495735; DOI: 10.1063/1.3575195;

Callard GV, Tarrant AM, Novillo A, Yacci P, Ciaccia L, Vajda S, Chuang GY, Kozakov D, Greytak SR, Sawyer S, Hoover C, Cotter KA. Evolutionary origins of the estrogen signaling system: insights from amphioxus. J Steroid Biochem Mol Biol. 2011 Nov; 127(3-5):176-88. PMID: 21514383

Cencic R, Hall DR, Robert F, Du Y, Min J, Li L, Qui M, Lewis I, Kurtkaya S, Dingledine R, Fu H, Kozakov D, Vajda S, Pelletier J. Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F. Proc Natl Acad Sci U S A. 2011 Jan 18; 108(3):1046-51. PMID: 21191102; PMCID: PMC3024666; DOI: 10.1073/pnas.1011477108;

Doczi J, Turiák L, Vajda S, Mándi M, Töröcsik B, Gerencser AA, Kiss G, Konràd C, Adam-Vizi V, Chinopoulos C. Complex contribution of cyclophilin D to Ca2+-induced permeability transition in brain mitochondria, with relation to the bioenergetic state. J Biol Chem. 2011 Feb 25; 286(8):6345-53.View Related Profiles.

Turiak, Lilla
Vajda, Sandor

PMID: 21173147; PMCID: PMC3057831; DOI: 10.1074/jbc.M110.196600;

Kozakov D, Hall DR, Beglov D, Brenke R, Comeau SR, Shen Y, Li K, Zheng J, Vakili P, Paschalidis ICh, Vajda S. Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19. Proteins. 2010 Nov 15; 78(15):3124-30.View Related Profiles.

Beglov, Dmitri
Paschalidis, Ioannis
Vajda, Sandor

PMID: 20818657; PMCID: PMC3027207; DOI: 10.1002/prot.22835;

Chuang GY, Mehra-Chaudhary R, Ngan CH, Zerbe BS, Kozakov D, Vajda S, Beamer LJ. Domain motion and interdomain hot spots in a multidomain enzyme. Protein Sci. 2010 Sep; 19(9):1662-72. PMID: 20589904; PMCID: PMC2975130; DOI: 10.1002/pro.446;

Wyrzgol SA, Schäfer S, Lee S, Lee B, Di Vece M, Li X, Seifert S, Winans RE, Stutzmann M, Lercher JA, Vajda S. Combined TPRx, in situ GISAXS and GIXAS studies of model semiconductor-supported platinum catalysts in the hydrogenation of ethene. Phys Chem Chem Phys. 2010 Jun 07; 12(21):5585-95. PMID: 20424733; DOI: 10.1039/b926493k;

Lei Y, Mehmood F, Lee S, Greeley J, Lee B, Seifert S, Winans RE, Elam JW, Meyer RJ, Redfern PC, Teschner D, Schlögl R, Pellin MJ, Curtiss LA, Vajda S. Increased silver activity for direct propylene epoxidation via subnanometer size effects. Science. 2010 Apr 09; 328(5975):224-8. PMID: 20378815; DOI: 10.1126/science.1185200;

Kozakov D, Chuang GY, Beglov D, Vajda S. Where does amantadine bind to the influenza virus M2 proton channel? Trends Biochem Sci. 2010 Sep; 35(9):471-5.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 20382026; PMCID: PMC2919587; DOI: 10.1016/j.tibs.2010.03.006;

Chinopoulos C, Gerencser AA, Mandi M, Mathe K, Töröcsik B, Doczi J, Turiak L, Kiss G, Konràd C, Vajda S, Vereczki V, Oh RJ, Adam-Vizi V. Forward operation of adenine nucleotide translocase during F0F1-ATPase reversal: critical role of matrix substrate-level phosphorylation. FASEB J. 2010 Jul; 24(7):2405-16.View Related Profiles.

Turiak, Lilla
Vajda, Sandor

PMID: 20207940; PMCID: PMC2887268; DOI: 10.1096/fj.09-149898;

Ngan CH, Beglov D, Rudnitskaya AN, Kozakov D, Waxman DJ, Vajda S. The structural basis of pregnane X receptor binding promiscuity. Biochemistry. 2009 Dec 8; 48(48):11572-81.View Related Profiles.

Waxman, David
Beglov, Dmitri
Vajda, Sandor

PMID: 19856963; PMCID: PMC2789303; DOI: 10.1021/bi901578n;

Kim MH, Lee B, Lee S, Larson C, Baik JM, Yavuz CT, Seifert S, Vajda S, Winans RE, Moskovits M, Stucky GD, Wodtke AM. Growth of metal oxide nanowires from supercooled liquid nanodroplets. Nano Lett. 2009 Dec; 9(12):4138-46. PMID: 19780585; DOI: 10.1021/nl902357q;

Beglov D, Lee CJ, De Biasio A, Kozakov D, Brenke R, Vajda S, Beglova N. Structural insights into recognition of beta2-glycoprotein I by the lipoprotein receptors. Proteins. 2009 Dec; 77(4):940-9.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 19676115; PMCID: PMC2767435; DOI: 10.1002/prot.22519;

Chuang GY, Kozakov D, Brenke R, Beglov D, Guarnieri F, Vajda S. Binding hot spots and amantadine orientation in the influenza a virus M2 proton channel. Biophys J. 2009 Nov 18; 97(10):2846-53.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 19917240; PMCID: PMC2776279; DOI: 10.1016/j.bpj.2009.09.004;

Vajda S, Lee S, Sell K, Barke I, Kleibert A, von Oeynhausen V, Meiwes-Broer KH, Rodríguez AF, Elam JW, Pellin MM, Lee B, Seifert S, Winans RE. Combined temperature-programmed reaction and in situ x-ray scattering studies of size-selected silver clusters under realistic reaction conditions in the epoxidation of propene. J Chem Phys. 2009 Sep 28; 131(12):121104. PMID: 19791845; DOI: 10.1063/1.3237158;

Landon MR, Lieberman RL, Hoang QQ, Ju S, Caaveiro JM, Orwig SD, Kozakov D, Brenke R, Chuang GY, Beglov D, Vajda S, Petsko GA, Ringe D. Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. J Comput Aided Mol Des. 2009 Aug; 23(8):491-500. PMID: 19521672; PMCID: PMC2889209; DOI: 10.1007/s10822-009-9283-2;

Vajda S, Mándi M, Konràd C, Kiss G, Ambrus A, Adam-Vizi V, Chinopoulos C. A re-evaluation of the role of matrix acidification in uncoupler-induced Ca2+ release from mitochondria. FEBS J. 2009 May; 276(10):2713-24. PMID: 19459934; DOI: 10.1111/j.1742-4658.2009.06995.x;

Vajda S, Kozakov D. Convergence and combination of methods in protein-protein docking. Curr Opin Struct Biol. 2009 Apr; 19(2):164-70. PMID: 19327983; PMCID: PMC2763924; DOI: 10.1016/j.sbi.2009.02.008;

Chinopoulos C, Vajda S, Csanády L, Mándi M, Mathe K, Adam-Vizi V. A novel kinetic assay of mitochondrial ATP-ADP exchange rate mediated by the ANT. Biophys J. 2009 Mar 18; 96(6):2490-504. PMID: 19289073; PMCID: PMC2907717; DOI: 10.1016/j.bpj.2008.12.3915;

Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13; 17(2):151-9. PMID: 19217386; PMCID: PMC2739730

Vajda S, Pellin MJ, Greeley JP, Marshall CL, Curtiss LA, Ballentine GA, Elam JW, Catillon-Mucherie S, Redfern PC, Mehmood F, Zapol P. Subnanometre platinum clusters as highly active and selective catalysts for the oxidative dehydrogenation of propane. Nat Mater. 2009 Mar; 8(3):213-6. PMID: 19202544; DOI: 10.1038/nmat2384;

Brenke R, Kozakov D, Chuang GY, Beglov D, Hall D, Landon MR, Mattos C, Vajda S. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics. 2009 Mar 01; 25(5):621-7.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 19176554; PMCID: PMC2647826; DOI: 10.1093/bioinformatics/btp036;

Lee S, Molina LM, López MJ, Alonso JA, Hammer B, Lee B, Seifert S, Winans RE, Elam JW, Pellin MJ, Vajda S. Selective propene epoxidation on immobilized au(6-10) clusters: the effect of hydrogen and water on activity and selectivity. Angew Chem Int Ed Engl. 2009; 48(8):1467-71. PMID: 19152388; DOI: 10.1002/anie.200804154;

Beglov D, Brenke R, Chuang G-Y, Hall D, Landon M, Ngan CH, Shen Y, Thiel S, Zerbe B, Kozakov D, Vajda S. Nussinov R and Schreiber G (eds.) Computational Protein-Protein Interactions. Identification of druggable hot spots on proteins and in protein-protein interfaces. CRC Press. Boca Raton, FL. 2009; 253-280.

Shen Y, Paschalidis ICh, Vakili P, Vajda S. Protein docking by the underestimation of free energy funnels in the space of encounter complexes. PLoS Comput Biol. 2008 Oct; 4(10):e1000191.View Related Profiles.

Paschalidis, Ioannis
Vajda, Sandor

PMID: 18846200; PMCID: PMC2538569; DOI: 10.1371/journal.pcbi.1000191;

Kozakov D, Schueler-Furman O, Vajda S. Discrimination of near-native structures in protein-protein docking by testing the stability of local minima. Proteins. 2008 Aug 15; 72(3):993-1004. PMID: 18300245; PMCID: PMC2823634; DOI: 10.1002/prot.21997;

Chuang GY, Kozakov D, Brenke R, Comeau SR, Vajda S. DARS (Decoys As the Reference State) potentials for protein-protein docking. Biophys J. 2008 Nov 01; 95(9):4217-27. PMID: 18676649; PMCID: PMC2567923; DOI: 10.1529/biophysj.108.135814;

Ritchie DW, Kozakov D, Vajda S. Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinformatics. 2008 Sep 01; 24(17):1865-73. PMID: 18591193; PMCID: PMC2732220; DOI: 10.1093/bioinformatics/btn334;

Landon MR, Amaro RE, Baron R, Ngan CH, Ozonoff D, McCammon JA, Vajda S. Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des. 2008 Feb; 71(2):106-16.View Related Profiles.

Ozonoff, David
Vajda, Sandor

PMID: 18205727; PMCID: PMC2438278; DOI: 10.1111/j.1747-0285.2007.00614.x;

Vajda S, Bartha K, Wilhelm I, Krizbai IA, Adam-Vizi V. Identification of protease-activated receptor-4 (PAR-4) in puromycin-purified brain capillary endothelial cells cultured on Matrigel. Neurochem Int. 2008 May; 52(6):1234-9. PMID: 18294734; DOI: 10.1016/j.neuint.2008.01.003;

Comeau SR, Kozakov D, Brenke R, Shen Y, Beglov D, Vajda S. ClusPro: performance in CAPRI rounds 6-11 and the new server. Proteins. 2007 Dec 01; 69(4):781-5.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 17876812; DOI: 10.1002/prot.21795;

Shen Y, Brenke R, Kozakov D, Comeau SR, Beglov D, Vajda S. Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI. Proteins. 2007 Dec 01; 69(4):734-42.View Related Profiles.

Beglov, Dmitri
Vajda, Sandor

PMID: 17853451; DOI: 10.1002/prot.21754;

Vajda S, Baczkó I, Leprán I. Selective cardiac plasma-membrane K(ATP) channel inhibition is defibrillatory and improves survival during acute myocardial ischemia and reperfusion. Eur J Pharmacol. 2007 Dec 22; 577(1-3):115-23. PMID: 17904545; DOI: 10.1016/j.ejphar.2007.08.016;

Silberstein M, Damborsky J, Vajda S. Exploring the binding sites of the haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Biochemistry. 2007 Aug 14; 46(32):9239-49. PMID: 17645312

Paschalidis IC, Shen Y, Vakili P, Vajda S. SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking. IEEE Trans Automat Contr. 2007 Apr 01; 52(4):664-676.View Related Profiles.

Paschalidis, Ioannis
Vajda, Sandor

PMID: 19759849

Landon MR, Lancia DR, Yu J, Thiel SC, Vajda S. Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. J Med Chem. 2007 Mar 22; 50(6):1231-40. PMID: 17305325

Prasad JC, Goldstone JV, Camacho CJ, Vajda S, Stegeman JJ. Ensemble modeling of substrate binding to cytochromes P450: analysis of catalytic differences between CYP1A orthologs. Biochemistry. 2007 Mar 13; 46(10):2640-54. PMID: 17300179

Kozakov D, Brenke R, Comeau SR, Vajda S. PIPER: an FFT-based protein docking program with pairwise potentials. Proteins. 2006 Nov 01; 65(2):392-406. PMID: 16933295

Leprán I, Pollesello P, Vajda S, Varró A, Papp JG. Preconditioning effects of levosimendan in a rabbit cardiac ischemia-reperfusion model. J Cardiovasc Pharmacol. 2006 Oct; 48(4):148-52. PMID: 17086092; DOI: 10.1097/01.fjc.0000246151.39758.2a;

Aslan FM, Yu Y, Vajda S, Mohr SC, Cantor CR. Engineering a novel, stable dimeric streptavidin with lower isoelectric point. J Biotechnol. 2007 Feb 01; 128(2):213-25. PMID: 17000019

Clodfelter KH, Waxman DJ, Vajda S. Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450. Biochemistry. 2006 Aug 8; 45(31):9393-407.View Related Profiles.

Waxman, David
Vajda, Sandor

PMID: 16878974

Kaya T, Mohr SC, Waxman DJ, Vajda S. Computational screening of phthalate monoesters for binding to PPARgamma. Chem Res Toxicol. 2006 Aug; 19(8):999-1009.View Related Profiles.

Waxman, David
Vajda, Sandor

PMID: 16918238

Vajda S, Guarnieri F. Characterization of protein-ligand interaction sites using experimental and computational methods. Curr Opin Drug Discov Devel. 2006 May; 9(3):354-62. PMID: 16729732

Földes G, Vajda S, Lakó-Futó Z, Sármán B, Skoumal R, Ilves M, deChâtel R, Karádi I, Tóth M, Ruskoaho H, Leprán I. Distinct modulation of angiotensin II-induced early left ventricular hypertrophic gene programming by dietary fat type. J Lipid Res. 2006 Jun; 47(6):1219-26. PMID: 16569909; DOI: 10.1194/jlr.M500550-JLR200;

Silberstein M, Landon MR, Wang YE, Perl A, Vajda S. Computational methods for functional site identification suggest a substrate access channel in transaldolase. Genome Inform. 2006; 17(1):13-22. PMID: 17503352

Paschalidis ICh, Shen Y, Vakili P, Vajda S. Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. Conf Proc IEEE Eng Med Biol Soc. 2006; 2006:5330-3.View Related Profiles.

Paschalidis, Ioannis
Vajda, Sandor

PMID: 17946298; PMCID: PMC2446401; DOI: 10.1109/IEMBS.2006.260790;

Landon MR, Lancia DR, Clodfelter KH, Vajda S. Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns. J Mol Graph Model. 2006 May; 24(6):426-33. PMID: 16221553

Lee B, Seifert S, Riley SJ, Tikhonov G, Tomczyk NA, Vajda S, Winans RE. Anomalous grazing incidence small-angle x-ray scattering studies of platinum nanoparticles formed by cluster deposition. J Chem Phys. 2005 Aug 15; 123(7):074701. PMID: 16229604; DOI: 10.1063/1.1999627;

Vajda S. Classification of protein complexes based on docking difficulty. Proteins. 2005 Aug 01; 60(2):176-80. PMID: 15981248

Comeau SR, Vajda S, Camacho CJ. Performance of the first protein docking server ClusPro in CAPRI rounds 3-5. Proteins. 2005 Aug 01; 60(2):239-44. PMID: 15981265

Socaciu-Siebert LD, Hagen J, Le Roux J, Popolan D, Vaida M, Vajda S, Bernhardt TM, Wöste L. Ultrafast nuclear dynamics induced by photodetachment of Ag2- and Ag2O2-: oxygen desorption from a molecular silver surface. Phys Chem Chem Phys. 2005 Jul 21; 7(14):2706-9. PMID: 16189583; DOI: 10.1039/b506034f;

Kozakov D, Clodfelter KH, Vajda S, Camacho CJ. Optimal clustering for detecting near-native conformations in protein docking. Biophys J. 2005 Aug; 89(2):867-75. PMID: 15908573

Sheu SH, Kaya T, Waxman DJ, Vajda S. Exploring the binding site structure of the PPAR gamma ligand-binding domain by computational solvent mapping. Biochemistry. 2005 Feb 1; 44(4):1193-209.View Related Profiles.

Waxman, David
Vajda, Sandor

PMID: 15667213

Sheu SH, Lancia DR, Clodfelter KH, Landon MR, Vajda S. PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D206-11. PMID: 15608178

Grossman CE, Niland B, Stancato C, Verhoeven NM, Van Der Knaap MS, Jakobs C, Brown LM, Vajda S, Banki K, Perl A. Deletion of Ser-171 causes inactivation, proteasome-mediated degradation and complete deficiency of human transaldolase. Biochem J. 2004 Sep 01; 382(Pt 2):725-31. PMID: 15115436

Rajamani D, Thiel S, Vajda S, Camacho CJ. Anchor residues in protein-protein interactions. Proc Natl Acad Sci U S A. 2004 Aug 03; 101(31):11287-92. PMID: 15269345

Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res. 2004 Jul 01; 32(Web Server issue):W96-9. PMID: 15215358

Prasad JC, Vajda S, Camacho CJ. Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Res. 2004 Jul 01; 32(Web Server issue):W50-4. PMID: 15215349

Vajda S, Camacho CJ. Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol. 2004 Mar; 22(3):110-6. PMID: 15036860

Socaciu LD, Hagen J, Le Roux J, Popolan D, Bernhardt TM, Woste L, Vajda S. Strongly cluster size dependent reaction behavior of CO with O2 on free silver cluster anions. J Chem Phys. 2004 Feb 01; 120(5):2078-81. PMID: 15268345; DOI: 10.1063/1.1644103;

Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics. 2004 Jan 01; 20(1):45-50. PMID: 14693807

Murphy J, Gatchell DW, Prasad JC, Vajda S. Combination of scoring functions improves discrimination in protein-protein docking. Proteins. 2003 Dec 1; 53(4):840-54.View Related Profiles.

Murphy, Jaime
Vajda, Sandor

PMID: 14635126

Silberstein M, Dennis S, Brown L, Kortvelyesi T, Clodfelter K, Vajda S. Identification of substrate binding sites in enzymes by computational solvent mapping. J Mol Biol. 2003 Oct 03; 332(5):1095-113. PMID: 14499612

Prasad JC, Comeau SR, Vajda S, Camacho CJ. Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics. 2003 Sep 01; 19(13):1682-91. PMID: 12967965

Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins. 2003 Jul 01; 52(1):2-9. PMID: 12784359

Kortvelyesi T, Dennis S, Silberstein M, Brown L, Vajda S. Algorithms for computational solvent mapping of proteins. Proteins. 2003 May 15; 51(3):340-51. PMID: 12696046

Kortvelyesi T, Silberstein M, Dennis S, Vajda S. Improved mapping of protein binding sites. J Comput Aided Mol Des. 2003 Feb-Apr; 17(2-4):173-86. PMID: 13677484

Daniel C, Full J, González L, Lupulescu C, Manz J, Merli A, Vajda S, Wöste L. Deciphering the reaction dynamics underlying optimal control laser fields. Science. 2003 Jan 24; 299(5606):536-9. PMID: 12543966; DOI: 10.1126/science.1078517;

Prasad JC, Silberstein M, Camacho CJ, Vajda S. Benson G and Page R (eds.) Algorithms in Bioinformatics. Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment. Springer. Verlag. 2003; 389-401.

Vajda S, Lupulescu C, Merli A, Budzyn F, Wöste L, Hartmann M, Pittner J, Bonacic-Koutecký V. Observation and theoretical description of periodic geometric rearrangement in electronically excited nonstoichiometric sodium-fluoride clusters. Phys Rev Lett. 2002 Nov 18; 89(21):213404. PMID: 12443410; DOI: 10.1103/PhysRevLett.89.213404;

Vajda S, Vakser IA, Sternberg MJ, Janin J. Modeling of protein interactions in genomes. Proteins. 2002 Jun 01; 47(4):444-6. PMID: 12001222

Dennis S, Kortvelyesi T, Vajda S. Computational mapping identifies the binding sites of organic solvents on proteins. Proc Natl Acad Sci U S A. 2002 Apr 02; 99(7):4290-5. PMID: 11904374

Camacho CJ, Vajda S. Protein-protein association kinetics and protein docking. Curr Opin Struct Biol. 2002 Feb; 12(1):36-40. PMID: 11839487

Dennis S, Vajda S. Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins. J Comput Chem. 2002 Feb; 23(3):319-34. PMID: 11908495

Reznik GO, Vajda S, Cantor CR, Sano T. A streptavidin mutant useful for directed immobilization on solid surfaces. Bioconjug Chem. 2001 Nov-Dec; 12(6):1000-4. PMID: 11716692

Camacho CJ, Vajda S. Protein docking along smooth association pathways. Proc Natl Acad Sci U S A. 2001 Sep 11; 98(19):10636-41. PMID: 11517309

Kimura SR, Brower RC, Vajda S, Camacho CJ. Dynamical view of the positions of key side chains in protein-protein recognition. Biophys J. 2001 Feb; 80(2):635-42. PMID: 11159432

Camacho CJ, Vajda S. RR Raffa, (ed.) The Thermodynamics of the Drug-Receptor Interaction. Thermodynamic maps of receptor-ligand pairs reveal how some proteins bind. Wiley. New York. 2001; 581-592.

Gatchell DW, Dennis S, Vajda S. Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins. 2000 Dec 01; 41(4):518-34. PMID: 11056039

Camacho CJ, Gatchell DW, Kimura SR, Vajda S. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins. 2000 Aug 15; 40(3):525-37. PMID: 10861944

Camacho CJ, Kimura SR, DeLisi C, Vajda S. Kinetics of desolvation-mediated protein-protein binding. Biophys J. 2000 Mar; 78(3):1094-105. PMID: 10692300

Dennis S, Camacho CJ, Vajda S. Continuum electrostatic analysis of preferred solvation sites around proteins in solution. Proteins. 2000 Feb 01; 38(2):176-88. PMID: 10656264

Dennis S, Camacho CJ, Vajda S. Floudas CA and Pardalos C (eds.) Optimization in Computational Chemistry and Molecular Biology. Exploring potential solvation sites of proteins by multistart local minimization. Kluwer Academic. 2000; 243-261.

Esposito M, Venkatesh V, Otvos L, Weng Z, Vajda S, Banki K, Perl A. Human transaldolase and cross-reactive viral epitopes identified by autoantibodies of multiple sclerosis patients. J Immunol. 1999 Oct 01; 163(7):4027-32. PMID: 10491006

Camacho CJ, Weng Z, Vajda S, DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophys J. 1999 Mar; 76(3):1166-78. PMID: 10049302

Reznik GO, Vajda S, Sano T, Cantor CR. A streptavidin mutant with altered ligand-binding specificity. Proc Natl Acad Sci U S A. 1998 Nov 10; 95(23):13525-30. PMID: 9811833

Sano T, Vajda S, Cantor CR. Genetic engineering of streptavidin, a versatile affinity tag. J Chromatogr B Biomed Sci Appl. 1998 Sep 11; 715(1):85-91. PMID: 9792500

Janardhan A, Vajda S. Selecting near-native conformations in homology modeling: the role of molecular mechanics and solvation terms. Protein Sci. 1998 Aug; 7(8):1772-80. PMID: 10082374

Weng Z, Delisi C, Vajda S. Empirical free energy calculation: comparison to calorimetric data. Protein Sci. 1997 Sep; 6(9):1976-84. PMID: 9300497

Sano T, Vajda S, Smith CL, Cantor CR. Engineering subunit association of multisubunit proteins: a dimeric streptavidin. Proc Natl Acad Sci U S A. 1997 Jun 10; 94(12):6153-8. PMID: 9177186

Zhu Q, Vajda S, Smith TF. Beta-turn new classification and its some features in proteins. Chin Med Sci J. 1997 Jun; 12(2):84-91. PMID: 11324505

Vajda S, Sippl M, Novotny J. Empirical potentials and functions for protein folding and binding. Curr Opin Struct Biol. 1997 Apr; 7(2):222-8. PMID: 9094333

Sano T, Vajda S, Reznik GO, Smith CL, Cantor CR. Molecular engineering of streptavidin. Ann N Y Acad Sci. 1996 Oct 12; 799:383-90. PMID: 8958100

Luidens MK, Figge J, Breese K, Vajda S. Predicted and trifluoroethanol-induced alpha-helicity of polypeptides. Biopolymers. 1996 Sep; 39(3):367-76. PMID: 8756516

Reznik GO, Vajda S, Smith CL, Cantor CR, Sano T. Streptavidins with intersubunit crosslinks have enhanced stability. Nat Biotechnol. 1996 Aug; 14(8):1007-11. PMID: 9631041

Sezerman U, Vajda S, DeLisi C. Free energy mapping of class I MHC molecules and structural determination of bound peptides. Protein Sci. 1996 Jul; 5(7):1272-81. PMID: 8819160

King BL, Vajda S, DeLisi C. Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors. FEBS Lett. 1996 Apr 08; 384(1):87-91. PMID: 8797810

Weng Z, Vajda S, Delisi C. Prediction of protein complexes using empirical free energy functions. Protein Sci. 1996 Apr; 5(4):614-26. PMID: 8845751

Vajda S, Weng Z, DeLisi C. Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments. Protein Eng. 1995 Nov; 8(11):1081-92. PMID: 8819974

Rosenfeld R, Zheng Q, Vajda S, DeLisi C. Flexible docking of peptides to class I major-histocompatibility-complex receptors. Genet Anal. 1995 Mar; 12(1):1-21. PMID: 7648466

Rosenfeld R, Vajda S, DeLisi C. Flexible docking and design. Annu Rev Biophys Biomol Struct. 1995; 24:677-700. PMID: 7663131

Vajda S, Weng Z, Rosenfeld R, DeLisi C. Effect of conformational flexibility and solvation on receptor-ligand binding free energies. Biochemistry. 1994 Nov 29; 33(47):13977-88. PMID: 7947806

Godfrey KR, Chapman MJ, Vajda S. Identifiability and indistinguishability of nonlinear pharmacokinetic models. J Pharmacokinet Biopharm. 1994 Jun; 22(3):229-51. PMID: 7884651; DOI: 10.1007/BF02353330;

Vajda S, DeLisi C. Merz KM and LeGrand S (eds.) The Protein Folding Problem and Tertiary Structure Determination. An adaptive branch-and-bound minimization method based on dynamic programming. Birkhauser. Boston, MA. 1994; 409-432.

Chapman MJ, Godfrey KR, Vajda S. Indistinguishability for a class of nonlinear compartmental models. Math Biosci. 1994 Jan; 119(1):77-95. PMID: 8111137; DOI: 10.1016/0025-5564(94)90005-1;

Rosenfeld R, Zheng Q, Vajda S, DeLisi C. Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptors. J Mol Biol. 1993 Dec 05; 234(3):515-21. PMID: 8254656

Sezerman U, Vajda S, Cornette J, DeLisi C. Toward computational determination of peptide-receptor structure. Protein Sci. 1993 Nov; 2(11):1827-43. PMID: 7505681

Zheng Q, Rosenfeld R, Vajda S, DeLisi C. Determining protein loop conformation using scaling-relaxation techniques. Protein Sci. 1993 Aug; 2(8):1242-8. PMID: 8401209

Rao S, Zhu QL, Vajda S, Smith T. The local information content of the protein structural database. FEBS Lett. 1993 May 10; 322(2):143-6. PMID: 8482381

Figge J, Breese K, Vajda S, Zhu QL, Eisele L, Andersen TT, MacColl R, Friedrich T, Smith TF. The binding domain structure of retinoblastoma-binding proteins. Protein Sci. 1993 Feb; 2(2):155-64. PMID: 8382993

Vajda S. Conformational filtering in polypeptides and proteins. J Mol Biol. 1993 Jan 05; 229(1):125-45. PMID: 8421296

Vajda S, Jafri MS, Sezerman OU, DeLisi C. Necessary conditions for avoiding incorrect polypeptide folds in conformational search by energy minimization. Biopolymers. 1993 Jan; 33(1):173-92. PMID: 8427934

Jafri MS, Vajda S, Pasik P, Gillo B. A membrane model for cytosolic calcium oscillations. A study using Xenopus oocytes. Biophys J. 1992 Jul; 63(1):235-46. PMID: 1420870

Vajda S, Valko P. Pallai I and Veress G (eds.) In Studies in Computer-Aided Modeling, Design, and Operation. Modeling and regression. Elsevier. Amsterdam. 1992; 28-95.

Anzenbacher P, Hudecek J, Vajda S, Fidler V, Larroque C, Lange R. Nanosecond fluorescence of tryptophans in cytochrome P-450scc (CYP11A1): effect of substrate binding. Biochem Biophys Res Commun. 1991 Dec 31; 181(3):1493-9. PMID: 1764099; DOI: 10.1016/0006-291x(91)92108-v;

Eisenfeld J, Vajda S, Sugar I, DeLisi C. Constrained optimization and protein structure determination. Am J Physiol. 1991 Aug; 261(2 Pt 1):C376-86. PMID: 1872378

Vajda S, Delisi C. Determining minimum energy conformations of polypeptides by dynamic programming. Biopolymers. 1990 Dec; 29(14):1755-72. PMID: 2207285

Chappell MJ, Godfrey KR, Vajda S. Global identifiability of the parameters of nonlinear systems with specified inputs: a comparison of methods. Math Biosci. 1990 Nov; 102(1):41-73. PMID: 2134490; DOI: 10.1016/0025-5564(90)90055-4;

Vajda S, Kataoka R, DeLisi C, Margalit H, Berzofsky JA, Cornette JL. Molecular structure and vaccine design. Annu Rev Biophys Biophys Chem. 1990; 19:69-82. PMID: 1694668; DOI: 10.1146/annurev.bb.19.060190.000441;

Vajda S, Distefano JJ, Godfrey KR, Fagarasan J. Parameter space boundaries for unidentifiable compartmental models. Math Biosci. 1989 Nov; 97(1):27-60. PMID: 2520205; DOI: 10.1016/0025-5564(89)90042-4;

Anzenbacher P, Hudecek J, Vajda S, Fidler V. Nanosecond fluorometry of the single tryptophan in cytochrome P-450e (P450IIB2). Biochem Biophys Res Commun. 1989 Aug 15; 162(3):921-5. PMID: 2764945

Vajda S, Godfrey KR, Rabitz H. Similarity transformation approach to identifiability analysis of nonlinear compartmental models. Math Biosci. 1989 Apr; 93(2):217-48. PMID: 2520030; DOI: 10.1016/0025-5564(89)90024-2;

Valko P, Vajda S. Advanced Scientific Computing in BASIC with Applications in Chemistry, Biology and Pharmacology. Elsevier. Amsterdam. 1989.

Vajda S, Godfrey KR, Valko P. Numerical deconvolution using system identification methods. J Pharmacokinet Biopharm. 1988 Feb; 16(1):85-107. PMID: 3373420; DOI: 10.1007/BF01061863;

Vajda S. Walter E (ed.) Structural Identifiability of Parametric Models. Identifiability of polynomial systems. Pergamon Press. New York. 1987; 42-49.

Lönnroth T, Beausang CW, Fossan DB, Hildingsson L, Piel WF, Quader MA, Vajda S, Chapuran T, Warburton EK. Excited states in neutron-deficient 195Bi. Phys Rev C Nucl Phys. 1986 May; 33(5):1641-1648. PMID: 9953326; DOI: 10.1103/physrevc.33.1641;

Ballon D, Niv Y, Vajda S, Benczer-Koller N, Zamick L, Leander GA. Magnetic moments of the (3/2)1- and (5/2)1- states in 107,109Ag. Phys Rev C Nucl Phys. 1986 Apr; 33(4):1461-1470. PMID: 9953297; DOI: 10.1103/physrevc.33.1461;

Valko P, Vajda S. Solving Engineering and Science Problems on Personal Computers. Muszaki Konyvkiado. Budapest, Hungary. 1986.

Piel WF, Chowdhury P, Garg U, Quader MA, Stwertka PM, Vajda S, Fossan DB. Collective structures in the odd-Z transitional nuclei 115,117I and 121,123Sb. Phys Rev C Nucl Phys. 1985 Feb; 31(2):456-464. PMID: 9952541; DOI: 10.1103/physrevc.31.456;

Vajda S . Dynamics and Control of Chemical Processes. TII. Budapest, Hungary. 1984.

Vajda S, Várkonyi P. A computer program for the analysis of structural identifiability and equivalence of linear compartmental models. Comput Programs Biomed. 1982 Aug; 15(1):27-44. PMID: 7128122; DOI: 10.1016/0010-468x(82)90054-x;

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 267 publications over 42 distinct years, with a maximum of 17 publications in 2014 and 2019

Bar chart showing 267 publications over 42 distinct years, with a maximum of 17 publications in 2014 and 2019

Year	Publications
1982	1
1984	1
1985	1
1986	3
1987	1
1988	1
1989	4
1990	3
1991	2
1992	2
1993	7
1994	4
1995	3
1996	6
1997	4
1998	3
1999	2
2000	5
2001	4
2002	5
2003	8
2004	7
2005	8
2006	9
2007	7
2008	6
2009	14
2010	8
2011	10
2012	11
2013	11
2014	17
2015	14
2016	10
2017	4
2018	6
2019	17
2020	7
2021	7
2022	10
2023	7
2024	7