Sandor Vajda, PhD
Professor
Boston University College of Engineering
Dept of Biomedical Engineering

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




Professor
Boston University College of Arts and Sciences
Chemistry




Analysis and Prediction of Molecular Interactions
06/01/2021 - 03/31/2026 (PI)
NIH/National Institute of General Medical Sciences
2R35GM118078-06

Optimization and Learning Strategies for Protein Docking
09/20/2019 - 08/31/2022 (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
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
2016 Analysis and prediction of molecular interactions 1R35GM118078-01 25
2016 A multistage approach to protein-protein docking 4R01GM061867-15 70
2015 Computational mapping of proteins for the binding of ligands 2R01GM064700-13 60
2015 A multistage approach to protein-protein docking 5R01GM061867-14 70
Showing 10 of 52 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

  1. 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
     
  2. 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; DOI: 10.1002/prot.26222;
     
  3. 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; DOI: 10.1002/prot.26209;
     
  4. 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; DOI: 10.1038/s41467-021-23443-y;
     
  5. 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; DOI: 10.1016/j.csbj.2021.04.048;
     
  6. 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. PMID: 33995918; DOI: 10.1016/j.csbj.2021.04.028;
     
  7. Vajda S, Porter KA, Kozakov D. Progress toward improved understanding of antibody maturation. Curr Opin Struct Biol. 2021 04; 67:226-231. PMID: 33610066; DOI: 10.1016/j.sbi.2020.11.008;
     
  8. 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. PMID: 33291870; DOI: 10.1021/acs.jcim.0c00877;
     
  9. 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; DOI: 10.1016/j.str.2020.06.006;
     
  10. 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. PMID: 32142178; DOI: 10.1002/prot.25887;
     
Showing 10 of 168 results. Show More

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

Bar chart showing 168 publications over 33 distinct years, with a maximum of 12 publications in 2019

YearPublications
19901
19911
19921
19937
19941
19953
19966
19973
19983
19992
20004
20013
20024
20036
20046
20056
20067
20076
20085
20097
20104
20118
20129
20138
201411
20159
20168
20172
20183
201912
20205
20216
20221


2016 National Institute of Health: R35 MIRA grant
2014 The American Institute for Medical and Biological Engineering: Elected Fellow
1986 SERC (UK) Postdoctoral Fellowship
1985 CNRS (France) Scholarship
1980 Eotvos Lorand University, Budapest, Hungary: Distinguished Diploma in Applied Mathematics
1975 College for Chemical Industry, Veszprem, Hungary: Technical Doctorate in Chemical Engineering, Summa Cum Laude
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44 Cummington St
Boston MA 02215
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