Research Articles
new Landon MR, Amaro R, Baron R, Ngan C, Ozonoff D, McCammon A, Vajda S. Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble. Chem Biol Drug Des. 2008 Jan 17 PDF
new Comeau SR, Kozakov D, Brenke R, Shen Y, Beglov D, Vajda S. ClusPro: Performance in CAPRI rounds 6-11 and the new server. Proteins. 2007 Sep 17 PDF
new Shen Y, Brenke R, Comeau SR, Beglov D, Vajda S. Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI. Proteins. 2007 Sep 17 PDF
new Silberstein M. , Damborsky J , Vajda S. Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Biochemistry. 2007 Jul 24 PDF
JC Prasad, JV Goldstone,CJ Camacho, Vajda S and JJ Stegeman. Ensemble Modelling of Substrate Binding to Cytochrome P450: Analysis of Vatalitic Differences between CYP1A Orthologs Biochemistry, 2007 Feb 15 . PDF
Landon MR, Lancia DR Jr, Jessamin Yu, Spencer C Thiel and Vajda S. Identification of Hot Spots within Druggable Binding Regions by Computational Solvent Mapping of Proteins J Med Chem, 2007 Feb 12 . PDF
Filiz M. Aslan, Yong Yu, Vajda S, Scott C. Mohr, Charles R. Cantor. Engineering a novel, stable dimeric streptavidin with lower isoelectric point Journal of Biotechnology, 128(2007)213-225; PDF
IC Paschalidis, Yang Shen, Pirooz Vakili , Vajda S . SDU: A Semi-Definite programming based Underestimation method for stochastic global optimizationin protein docking IEEE Transaction of Automatic Control, Vol 52, No.5 May (2007); PDF
IC Paschalidis, Shen Y,Vajda S, Vakili P. Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels.Conf Proc IEEE Eng Med Biol Soc 2006 (1):5330-5333 PDF
Silberstein M. , Landon MR, Wang Y, Perl A, Vajda S. Computational methods for functional site identification suggest a substrate access channel in transaldolase.Genome Inform.2006 ;17 (1):13-22 PDF
Kozakov D, Brenke R, Comeau SR, Vajda S. PIPER: An FFT-based protein docking program with pairwise potentials Proteins. 2006 Aug 24; PDF
Kaya T, Mohr SC, Waxman DJ, Vajda S. Computational screening of phthalate monoesters for binding to PPARgammaChem Res Toxicol, 2006 Aug;19(8):999-1009. PDF
Clodfelter KH, Waxman DJ, Vajda S. Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450 Biochemistry, 2006 Aug 8;45(31):9393-407. PDF
Vajda S, Guarnieri F. Characterization of protein-ligand interaction sites using experimental and computational methods. Curr Opin Drug Discov Devel, 2006 May;9(3):354-62. PDF
Landon MR, Lancia DR Jr, Clodfelter KH, Vajda S. Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns J Mol Graph Model, 2006 May 24(6):426-33. PDF
Vajda S. Classification of protein complexes based on docking difficulty. Proteins, 2005 Aug 1;60(2):176-80. PDF
Kozakov D, Clodfelter K.H, Vajda S, Camacho CJ. Optimal Clustering for Detecting Near-Native Conformation in Protein Docking. Biophysical Journal, 2005 Aug ;867-875:. PDF
Comeau SR, Vajda S, Camacho CJ. Performance of the first protein docking server ClusPro in CAPRI rounds 3-5. Proteins, 2005 Aug 1;60(2):239-44. PDF
Vajda S. Classification of protein complexes based on docking difficulty Proteins, 2005 Aug 1;60(2):176-80 PDF
Comeau SR, Camacho CJ. Predicting oligomeric assemblies: N-mers as a primer. J. Struct. Biol., 2005 Jun 150(3):233-44 PDF
Shu-Hsien Sheu, Taner Kaya, David J. Waxman, and Sandor Vajda. Exploring the Binding Site Structure of PPARγ Ligand-Binding Domain by Computational Solvent Mapping Biochemistry, 2005, 44, 1193-1209. PDF
Shu-Hsien Sheu, David R. Lancia Jr, Karl Clodefelter, Melissa R. Landon and Sandor Vajda. PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. Nucleic Acids Research, 2005 Jan 1; Vol 33 Database Issue:D206-11. PDF
Rajamani D, Thiel S, Vajda S, Camacho CJ. Anchor residues in protein-protein interactions. Proc. Natl. Acad. Sci. USA. 2004 Aug 3;101(31):11287-92. PDF
Stephen R. Comeau, David W. Gatchell, Sandor Vajda and Carlos J. Camacho. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Research Vol. 32, Web Server issue . PDF
J.C. Prasad, Camacho C. J., Vajda S. Consensus alignment server for reliable comparative modeling with distant templates Nucleic Acids Research Vol. 32, Web Server issue . PDF
Camacho C, and Vajda S. Protein protein docking: is the glass half-full or half-empty? TRENDS in Biotechnology. 2004 Mar;22(3):110-6. PDF
Stephen R. Comeau, David W. Gatchell, Sandor Vajda and Carlos J. Camacho. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. BIOINFORMATICS Vol. 20 no. 1 2004, pages 45-50. PDF
J.C. Prasad, S.R. Comeau, S. Vajda and C.J. Camacho. Consensus alignment for reliable framework prediction in homology modeling. BIOINFORMATICS Vol. 19 no. 13 2003, pages 1682-1691. PDF
Michael Silberstein, Sheldon Dennis, Lawrence Brown, Tamas Kortvelyesi Karl Clodfelter and Sandor Vajda. Identification of Substrate Binding Sites in Enzymes by Computational Solvent Mapping. J. Mol. Biol., 332, 1095-113, 2003. PDF
Peter P. Valko, and Sandor Vajda. Inversion of Noise-free Laplace Transforms: Towards a Standardized Set of Test Problems. Inverse Problems in Engineering Volume 10, Number 5, Year 2002, pp. 467 - 483. PDF
Janin J, Henrick K, Moult J, Eyck L, Sternberg M, Vajda S, Vakser I, and Wodak S. CAPRI: A critical assessment of predicted interactions. Proteins, 52:2-9, 2003. PDF
Murphy J, Gatchell D, Prasad J, and Vajda S. Combination of scoring functions improves discrimination in protein-protein docking. Proteins, 3 :840-854, 2003., PDF
Kortvelyesi T, Silberstein M, Dennis S, and Vajda S. Improved mapping of protein binding sites. Journal of Computer-Aided Molecular Design, 17: 173-186, 2003. PDF
Kortvelyesi T, Dennis S, Silberstein M, Brown III L, and Vajda S. Algorithms for computational solvent mapping of proteins. Proteins, 51: 340-351, 2003. PDF
Camacho C, and Gatchell D. Successful discrimination of protein interactions. Proteins, 52:92-97, 2003. PDF
Camacho C, and Vajda S. Protein-protein association kinetics and protein docking. Curr Opin Struct Biol. 12(1):36-40, 2002. PDF
Dennis S, Kortvelyesi T, and Vajda S. Computational mapping identifies the binding sites of organic solvents on proteins. Proc. Natl. Acad. Sci. USA. 99(7): 4290-4295, 2002. PDF
Dennis S, and Vajda S. Semi-global simplex optimization and its application to determining the preferred solvation sites of proteins. J. Comp. Chem. 23(3): 319-334, 2002. PDF
Camacho C, and Vajda S. Protein docking along smooth association pathways. Proc. Natl. Acad. Sci. USA. 98: 10636-10641, 2001. PDF
Kimura R, Brower R, Vajda S, and Camacho C. Dynamical view of the positions of key side chains in protein-protein recognition. Biophys. J., 80: 635-642, 2001. PDF
Dennis S, Camacho CJ, and Vajda S. Continuum electrostatic analysis of preferred solvation sites around proteins in solution. Proteins, 38: 176-188, 2000. PDF
Camacho C, Kimura SR, DeLisi C, and Vajda S. Kinetics of desolvation-mediated protein-protein binding. Biophys. J., 78: 1094-1105, 2000. PDF
Camacho C, Gatchell D, Kimura R, and Vajda S. Scoring docked conformations generated by rigid body protein-protein docking. Proteins, 40: 525-537, 2000. PDF
Gatchell D, Dennis S, and Vajda S. Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins, 41: 518-534, 2000. PDF
Camacho CJ, Weng Z, Vajda S, and DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophys. J., 76: 1166-1178, 1999. PDF
Esposito M, Venkatesh V, Otvos L, Weng Z, Vajda S, Banki K, and Perl A. Human transaldolase and cross-reactive viral epitopes identified by autoantibodies of multiple sclerosis patients. J. Immunol., 163: 4027-4032, 1999. PDF
Janardhan A, and Vajda S. Selecting near-native conformations in homology modeling: The role of molecular mechanics and solvation terms. Prot. Sci., 7: 1772-1780, 1998. HTML
Sano T, Vajda S, and Cantor C. Genetic engineering of streptavidin, a versatile affinity tag. J Chromatogr. B Biomed. Sci. Appl., 715: 85-91, 1998. PDF
Reznik GO, Vajda S, Sano T, and Cantor CR. A streptavidin mutant with altered ligand-binding specificity. Proc. Natl. Acad. Sci., 95: 13525-13530, 1998. PDF
Weng Z, DeLisi C, and Vajda S. Empirical free energy calculation: Comparison to calorimetric data. Prot. Sci., 9: 1976-1984, 1997. HTML
Sano T, Vajda S, Smith CL, and Cantor CR. Engineering subunit association of multisubunit proteins: A dimeric streptavidin. Proc. Natl. Acad. Sci., 94: 6153-6158, 1997. PDF
*Gukukota, K., Vajda, S. and DeLisi, C. Peptide docking using dynamic programming. J. Comput Chem., 17(4): 418-428, 1996.
King BL, Vajda S, and DeLisi C. Empirical free energy as a target function in docking and design: Application to HIV-1 protease inhibitors. FEBS Letters, 384: 87-91, 1996. PDF
Weng Z, Vajda S, and DeLisi C. The prediction of protein complexes using empirical free energy functions. Protein Sci., 5: 614-626, 1996. HTML
Sezerman U, Vajda S, and DeLisi C. Free energy mapping of class I MHC molecules and structural determination of bound peptides. Protein Sci., 5: 1272-1281, 1996. HTML
*Luidens MK, Figge J, Breese K, and Vajda S. Predicted and trifluorethanol-induced helicity of polypeptides. Biopolymers, 39 (3): 367-376, 1996.
*Sano T, Vajda S, Resnick G, Smith C, and Cantor C. Molecular engineering of streptavidin. Annals New York Acad. Sci., 799: 383-390, 1996.
*Reznik G,Vajda S, Smith C, Cantor C, and Sano T. Streptavidins with intersubunit crosslinks have enhanced stability. Nature Biotech., 14 (8): 1007-1011, 1996.
*Vajda S, Weng Z, Rosenfeld R, and DeLisi C. The effect of conformational flexibility and solvation on receptor-ligand binding free energies. Biochemistry, 33: 13977-13987, 1994.
Review Articles
Vajda S, Vakser IA, Sternberg MJE, and Janin J. Modeling of Protein Interactions in Genomes. Proteins: Structure, Function, and Genetics, 47: 444-446, 2002. PDF
*DeLisi, C. and Vajda, S. Computational problems in cell biology. Comp. Sci Engineering, 1 (3): 26-32, 1999.
Zhang, C., Kimura, S.R., Weng, Z.P., Vajda, S., Brower, R. and DeLisi, C. The waters of life. J. Franklin Inst. Eng. Appl. Math., 335B: 213-240, 1998. PDF
*Vajda, S. Conformational Analysis, In: The Encyclopedia of Computational Chemistry, Paul v. Rague Schleyer, Norman L. Allinger, Tim Clark, Johann Gasteiger, Peter A. Kollman, Henry F. Schaefer, and Peter R. Schreiner (Eds.), John Wiley & Sons Ltd., Chichester 1998.
Vajda, S., Sippl, M. and Novotny, J. Empirical potentials and functions for protein folding and binding. Curr. Op. Struct. Biol., 7: 222-228, 1997. PDF
*Rosenfeld, R., Vajda, S. and DeLisi, C. Flexible docking and design. Ann.Rev. Biophys. Biomol. Struct., 24: 677-700, 1995.
*Vajda, S., Kataoka, R., DeLisi, C., Margalit, H., Berzofsky, J. A. and Cornette, J. Molecular structure and vaccine design, Annu. Rev. Biophys. Biomol. Struct., 19: 69-82, 1990.
Book Chapters
Dennis, S., Camacho, C.J. and Vajda, S. Exploring potential solvation sites of proteins by multistart local minimization. In Optimization in Computational Chemistry and Molecular Biology, Floudas C. A. and Pardalos, C., Eds. Kluwer Academic, 2000, pp 243-261. PDF
Camacho, C.J. and Vajda, S. Thermodynamic maps of receptor-ligand pairs reveal how some proteins bind. In The Thermodynamics of the Drug-Receptor Interaction, R.R. Raffa, Ed., Wiley, NY, pp. 581-592, Wiley, NY, 2001