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



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
5R35GM118078-09

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 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
2016 Analysis and prediction of molecular interactions 1R35GM118078-01 25
Showing 10 of 55 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. 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. PMID: 38456842
     
  2. 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. PMID: 38253327; DOI: 10.1021/acs.jcim.3c01761;
     
  3. 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; DOI: 10.1101/2023.11.29.569310;
     
  4. 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. PMID: 37905971; DOI: 10.1002/prot.26609;
     
  5. 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; DOI: 10.1002/prot.26587;
     
  6. 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. PMID: 37663788; DOI: 10.3389/fbinf.2023.1207380;
     
  7. 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. PMID: 37188806; DOI: 10.1038/s41596-023-00826-7;
     
  8. 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. PMID: 36961978; DOI: 10.1021/jacs.2c09387;
     
  9. 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. PMID: 36961978; PMCID: PMC10240388; DOI: 10.1021/jacs.2c09387;
     
  10. 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; DOI: 10.1146/annurev-biophys-102622-084607;
     
Showing 10 of 263 results. Show More

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

Bar chart showing 262 publications over 42 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
202210
20237
20242


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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