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Person Details

Superfund Basic Research Program

Sandor Vajda

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

Projects

• Boston University: Bioinformatics and Molecular Modeling (2000-2010)

Research Briefs

• 112 - Using Computational Approaches to Investigate Ligand-Receptor Interactions

Publications

2007

• Prasad, Jahnavi C., Jared V. Goldstone, Carlos J. Camacho, Sandor Vajda, and John J. Stegeman. 2007. Ensemble modeling of substrate binding to cytochromes P450: Analysis of catalytic differences between CYP1A orthologues. Biochemistry. (http://pubs.acs.org/journals/bichaw/index.htm l) 46(10):2640-2654.
• Silberstein, Michael, Jiri Damborsky, and Sandor Vajda. 2007. Exploring the binding sites of the haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Biochemistry. (http://pubs.acs.org/journals/bichaw/index.htm l) 46(32):9239-49.

2006

• Clodfelter, Karl H., David J. Waxman, and Sandor Vajda. 2006. Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450. Biochemistry. (http://pubs.acs.org/journals/bichaw/index.htm l) 45(31):9393-407.
• Kaya, Taner, S.C. Mohr, David J. Waxman, and Sandor Vajda. 2006. Computational screening of phthalate monoesters for binding to PPARgamma. Chemical Research in Toxicology. (http://pubs.acs.org/journals/crtoec/index.htm l) 19(8):999-1009.
• Landon, Melissa R., David R. Lancia, Karl H. Clodfelter, and Sandor Vajda. 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.

2005

• Sheu, Shu-Hsien, Taner Kaya, David J. Waxman, and Sandor Vajda. 2005. Exploring the binding site structure of the PPAR gamma ligand-binding domain by computational solvent mapping. Biochemistry. (http://pubs.acs.org/journals/bichaw/index.htm l) 44(4):1193-1209.
• Sheu, Shu-Hsien, David R. Lancia, Karl H. Clodfelter, Melissa R. Landon, and Sandor Vajda. 2005. PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. Nucleic Acids Research. (http://www3.oup.co.uk/nar/contents/) 33:D206-D211.

2004

• Comeau, Stephen R., David W. Gatchell, Sandor Vajda, and Carlos J. Camacho. 2004. ClusPro: An automated docking and discrimination method for the prediction of protein complexes. Bioinformatics. (http://bioinformatics.oupjournals.org/) 20(1):45-50.
• Prasad, Jahnavi C., Sandor Vajda, and Carlos J. Camacho. 2004. Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Research. (http://www3.oup.co.uk/nar/contents/) 32:W50-W54.
• Sheu, Shu-Hsien, Taner Kaya, David J. Waxman, and Sandor Vajda. 2004. Exploring the Binding Site Structure of the PPARg Ligand-Binding Domain by Computational Solvent Mapping. Biochemistry. (http://pubs.acs.org/journals/bichaw/index.htm l) 44:1193-1209.

2003

• Kortvelyesi, Tamas, Sheldon Dennis, S. Silberstein, Lawerence Brown, and Sandor Vajda. 2003. Algorithms for computational solvent mapping of proteins. Proteins. 51(3):340-351.
• Prasad, Jahnavi C., Stephen R. Comeau, Sandor Vajda, and Carlos J. Camacho. 2003. Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics. (http://bioinformatics.oupjournals.org/) 19(13):1682-1691.
• Prasad, Jahnavi C., Michael Silberstein, Carlos J. Camacho, and Sandor Vajda. 2003. Homology modeling of proteins using multiple models and consensus sequence alignment. Lecture Notes in Bioinformatics. (http://www.springeronline.com/sgw/cda/frontpa ge/0,11855,4-164-2-73658-0,00.html) 2812:389-401.
• Prasad, Jahnavi C., Sandor Vajda, and Carlos J. Camacho. 2003. Identification of substrate binding sites in enzymes by computational solvent mapping. Drug Metabolism Reviews. 35:331Suppl.2.
• Prasad, Jahnavi C., Sandor Vajda, Jared V. Goldstone, Carlos J. Camacho, and John J. Stegeman. 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.
• Prasad, Jahnavi C., Sandor Vajda, Jared V. Goldstone, Carlos J. Camacho, and John J. Stegeman. 2003. Identification of substrate binding sites in enzymes by computational solvent mapping. Drug Metabolism Reviews. 35:331Suppl.2.
• Silberstein, Michael, Sheldon Dennis, Lawerence Brown, Tamas Kortvelyesi, Karl H. Clodfelter, and Sandor Vajda. 2003. Identification of substrate binding sites in enzymes by computational solvent mapping. Journal of Molecular Biology. 332(5):1095-1113.

2002

• Dennis, Sheldon, Tamas Kortvelyesi, and Sandor Vajda. 2002. Computational mapping identifies the binding sites of organic solvents on proteins. Proceedings of the National Academy of Sciences of the United States of America (PNAS). (http://www.pnas.org/) 99(7):4290-4295.
• Dennis, Sheldon, Tamas Kortvelyesi, and Sandor Vajda. 2002. Computational solvent mapping for the analysis of enzyme active sites. Abstracts of Papers - American Chemical Society. (http://www.cas.org/) 224:221-COMPPart1.

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Last Reviewed: 19 May 2008