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



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




Analysis and Prediction of Molecular Interactions
06/01/2021 - 03/31/2026 (PI)
NIH/National Institute of General Medical Sciences
5R35GM118078-07

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
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 3R35GM118078-03S1 25
2018 Analysis and prediction of molecular interactions 5R35GM118078-03 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
Showing 10 of 53 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. 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
     
  2. Wakefield AE, Kozakov D, Vajda S. Mapping the binding sites of challenging drug targets. Curr Opin Struct Biol. 2022 Aug; 75:102396. PMID: 35636004
     
  3. 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;
     
  4. 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
     
  5. 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
     
  6. 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;
     
  7. 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;
     
  8. 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;
     
  9. 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;
     
  10. 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;
     
Showing 10 of 248 results. Show More

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

Bar chart showing 248 publications over 40 distinct years, with a maximum of 17 publications in 2014 and 2019

YearPublications
19821
19841
19851
19863
19871
19881
19894
19903
19912
19922
19937
19944
19953
19966
19974
19983
19992
20005
20014
20025
20038
20047
20058
20069
20077
20086
200914
20108
201110
201211
201311
201417
201514
201610
20174
20186
201917
20207
20217
20225


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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