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Person Details: Sandor Vajda

Superfund Research Program

Sandor Vajda

Boston University
Department of Biomedical Engineering
44 Cummington Street
Boston, Massachusetts 02215
Phone: 617-353-4757
Fax: 617-353-6766


Research Briefs




  • Parks A, 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. 2014. In silico identification of an aryl hydrocarbon receptor antagonist with biological activity in vitro and in vivo. Mol Pharmacol 86(5):593-608. doi:10.1124/mol.114.093369 PMID:25159092 PMCID:PMC4201140
  • Pillai HK, Fang M, Beglov D, Kozakov D, Vajda S, Stapleton HM, Webster TF, Schlezinger JJ. 2014. Ligand binding and activation of PPARγ by Firemaster® 550: effects on adipogenesis and osteogenesis in vitro. Environ Health Perspect 122(11):1225-1232. doi:10.1289/ehp.1408111 PMID:25062436 PMCID:PMC4216168


  • Callard GV, Tarrant AM, Novillo-Villajos A, Yacci P, Ciaccia L, Vajda S, Chuang G, Kozakov D, Greytak SR, Sawyer SJ, Hoover CA, Cotter KA. 2011. Evolutionary origins of the estrogen signaling system: Insights from amphioxus. Psychiatr Pol 127:176-188. doi:10.1016/j.jsbmb.2011.03.022 PMID:21514383 PMCID:PMC3179578


  • Beglov D, Brenke R, Chuang G, Hall D, Landon MR, Ngan CM, Shen Y, Thiel S, Zerbe B, Kozakov D, Vajda S. 2009. Identification of druggable hot spots on proteins and in protein-protein interfaces. In: Computational Protein-Protein Interactions.
  • Brenke R, Kozakov D, Chuang G, Beglov D, Hall D, Landon MR, Mattos C, Vajda S. 2009. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics 25(5):621-627. doi:10.1093/bioinformatics/btp036 PMID:19176554 PMCID:PMC2647826


  • Prasad JC, Goldstone JV, Camacho CJ, Vajda S, Stegeman JJ. 2007. Ensemble modeling of substrate binding to cytochromes P450: Analysis of catalytic differences between CYP1A orthologues. Biochemistry 46(10):2640-2654. PMID:17300179
  • Silberstein M, Damborsky J, Vajda S. 2007. Exploring the binding sites of the haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Biochemistry 46(32):9239-9249. doi:10.1021/bi700336y PMID:17645312
  • Vajda S. 2007. Mapping of Proteins for the Binding of Functional Groups from Xenobiotics. (non-peer reviewed)


  • Clodfelter KH, Waxman DJ, Vajda S. 2006. Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450. Biochemistry 45(31):9393-407. PMID:16878974
  • Kaya T, Mohr SC, Waxman DJ, Vajda S. 2006. Computational screening of phthalate monoesters for binding to PPARgamma. Chem Res Toxicol 19(8):999-1009. doi:10.1021/tx050301s PMID:16918238
  • Landon MR, Lancia DR, Clodfelter KH, Vajda S. 2006. Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns. Journal of Molecular Graphics and Modelling 24(6):426-433. PMID:16221553


  • Sheu S, Kaya T, Waxman DJ, Vajda S. 2005. Exploring the binding site structure of the PPAR gamma ligand-binding domain by computational solvent mapping. Biochemistry 44(4):1193-1209. doi:10.1021/bi048032c PMID:15667213
  • Sheu S, Lancia DR, Clodfelter KH, Landon MR, Vajda S. 2005. PRECISE: a database of predicted and consensus interaction sites in enzymes. Nucleic Acids Res 33(Databaseissue):D206-D211. doi:10.1093/nar/gki091 PMID:15608178 PMCID:PMC540045


  • Comeau SR, Gatchell DW, Vajda S, Camacho CJ. 2004. ClusPro: A fully automated algorithm for protein-protein docking. Nucleic Acids Res 32:W96-W99. PMID:15215358
  • Comeau SR, Gatchell DW, Vajda S, Camacho CJ. 2004. ClusPro: An automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 20(1):45-50. PMID:14693807
  • Prasad JC, Vajda S, Camacho CJ. 2004. Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Res 32:W50-W54. PMID:15215349


  • Kortvelyesi T, Dennis S, Silberstein S, Brown L, Vajda S. 2003. Algorithms for computational solvent mapping of proteins. Proteins: Structure, Function, and Genetics 51(3):340-351. PMID:12696046
  • Kortvelyesi T, Silberstein M, Dennis S, Vajda S. 2003. Improved mapping of protein binding sites. J Comput Aided Mol Des 17(2-4):173-186. PMID:13677484
  • Prasad JC, Comeau SR, Vajda S, Camacho CJ. 2003. Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics 19(13):1682-1691. PMID:12967965
  • Prasad JC, Silberstein M, Camacho CJ, Vajda S. 2003. Homology modeling of proteins using multiple models and consensus sequence alignment. Lecture Notes in Bioinformatics 2812:389-401.
  • Prasad JC, Vajda S, Goldstone JV, Camacho CJ, Stegeman JJ. 2003. Differences in Substrate Binding Between Mammalian and Fish Cytochrome P450 1As Predicted by Comparative Modeling and Flexible Docking. In: Presented at the International Society for the study of Xenobiotics, October. Providence, RI.
  • Silberstein M, Dennis S, Brown L, Kortvelyesi T, Clodfelter KH, Vajda S. 2003. Identification of substrate binding sites in enzymes by computational solvent mapping. J Mol Biol 332(5):1095-1113. doi:10.1016/j.jmb.2003.08.019 PMID:14499612


  • Dennis S, Kortvelyesi T, Vajda S. 2002. Computational mapping identifies the binding sites of organic solvents on proteins. Proc Natl Acad Sci U S A 99(7):4290-4295. PMID:11904374
  • Dennis S, Kortvelyesi T, Vajda S. 2002. Computational solvent mapping for the analysis of enzyme active sites. Abstr Pap Am Chem Soc 224:221-COMPPart1.
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