Structural
BioinformaticsLab

Landon, MR, Lieberman RL, Hoang QQ, Ju S, Caaveiro JMM, Orwig SD, Kozakov D, Brenke R, Chuang G-Y, Beglov D et al..  2009.  Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. Journal of Computer-Aided Molecular Design. 23(8):491-500. Download: PDF (574.15 KB)

Vajda, S, Kozakov D.  2009.  Convergence and combination of methods in protein–protein docking. Current Opinion in Structural Biology. 19(2):164-170. Download: PDF (250.8 KB)

Schwede, T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV et al..  2009.  Outcome of a Workshop on Applications of Protein Models in Biomedical Research. Structure. 17(2):151-159. Download: PDF (248.58 KB)

Brenke, R, Kozakov D, Chuang G-Y, 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. Download: PDF (412.04 KB)

Beglov, D, Brenke R, Chuang G-Y, Hall D, Landon M, Ngan C H, Shen Y, Thiel S, Zerbe B, Kozakov D et al..  2009.  Identification of Druggable Hot Spots on Proteins and in Protein Protein Interfaces. Computational Protein-Protein Interactions.

Chuang, G-Y, Kozakov D, Brenke R, Comeau SR, Vajda S.  2008.  DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking. Biophysical Journal. 95(9):4217-4227. Download: PDF (317.38 KB)

Shen, Y, Paschalidis I C., Vakili P, Vajda S.  2008.  Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes. PLoS Computational Biology. 4(10):e1000191. Download: PDF (497.62 KB)

Kozakov, D, Schueler‐Furman O, Vajda S.  2008.  Discrimination of near‐native structures in protein–protein docking by testing the stability of local minima. Proteins: Structure, Function, and Bioinformatics. 72(3):993-1004. Download: PDF (328.1 KB)

Ritchie, DW, Kozakov D, Vajda S.  2008.  Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinformatics. 24(17):1865-1873. Download: PDF (328.1 KB)

Landon, MR, Amaro RE, Baron R, Ngan C H, Ozonoff D, McCammon AJ, Vajda S.  2008.  Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble. Chemical Biology & Drug Design. 71(2):106-116. Download: PDF (845.42 KB)

Comeau, SR, Kozakov D, Brenke R, Shen Y, Beglov D, Vajda S.  2007.  ClusPro: Performance in CAPRI rounds 6–11 and the new server. Proteins: Structure, Function, and Bioinformatics. 69(4):781-785. Download: PDF (213.15 KB)

Shen, Y, Brenke R, Kozakov D, Comeau SR, Beglov D, Vajda S.  2007.  Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI. Proteins: Structure, Function, and Bioinformatics. 69(4):734-742. Download: PDF (274.39 KB)

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. Download: PDF (428.17 KB)

Paschalidis, I C., Shen Y, Vakili P, Vajda S.  2007.  SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking. IEEE Transactions on Automatic Control. 52(4):664-676. Download: PDF (1.13 MB)

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 Orthologs. Biochemistry. 46(10):2640-2654. Download: PDF (1012 KB)

Landon, MR, David R. Lancia J., Yu J, Thiel SC, Vajda S.  2007.  Identification of Hot Spots within Druggable Binding Regions by Computational Solvent Mapping of Proteins. Journal of Medicinal Chemistry. 50(6):1231-1240. Download: PDF (822.44 KB)

Aslan, FM, Yu Y, Vajda S, Mohr SC, Cantor CR.  2007.  Engineering a novel, stable dimeric streptavidin with lower isoelectric point. Journal of Biotechnology. 128(2):213-225. Download: PDF (983.8 KB)

Kozakov, D, Brenke R, Comeau SR, Vajda S.  2006.  PIPER: An FFT-based protein docking program with pairwise potentials. Proteins: Structure, Function, and Bioinformatics. 65(2):392-406. Download: PDF (385.54 KB)

Kaya, T, Mohr SC, Waxman DJ, Vajda S.  2006.  Computational Screening of Phthalate Monoesters for Binding to PPARγ. Chemical Research in Toxicology. 19(8):999-1009. Download: PDF (904.06 KB)

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):9393-9407. Download: PDF (1.07 MB)

Landon, MR, David R. Lancia J., 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. Download: PDF (768.35 KB)

Vajda, S, Guarnieri F.  2006.  Characterization of protein-ligand interaction sites using experimental and computational methods. Current Opinion in Drug Discovery and Development. 9(3):363-369. Download: PDF (955.74 KB)

Paschalidis, I C., Shen Y, Vakili P, Vajda S.  2006.  Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. :5330-5333. Download: PDF (295.9 KB)

Silberstein, M, Landon MR, Wang YE, Perl A, Vajda S.  2006.  Computational methods for functional site identification suggest a substrate access channel in transaldolase. Genome Informatics. 17(1):13-22. Download: PDF (2.84 MB)

Vajda, S.  2006.  Classification of protein complexes based on the biophysics of association. ASBMB Annual Meeting.  Download: PPT (14.8 MB)

Vajda, S.  2006.  Computational Mapping of Proteins for Fragment Based Drug Design. Keystone Symposium on Structure Based Drug Discovery.  Download: PPT (3.01 MB)

Paschalidis, IC, Shen Y, Vakili P, Vajda S.  2006.  Protein Docking by Exploiting Multi-dimensional Energy Funnels. IEEE 2006 International Conference of EMBS.  Download: PDF (1.25 MB)ZIP (8.05 MB)

Landon, MR, Yu J, Thiel SC, David R. Lancia J., Vajda S.  2006.  Identification of "Hot Spots" in Druggable Binding Pockets by Computational Solvent Mapping of Proteins. 232nd National Meeting & Exposition of the American Chemical Society.  Download: PPT (8.62 MB)

Vajda, S.  2005.  Classification of protein complexes based on docking difficulty. Proteins: Structure, Function, and Bioinformatics. 60(2):176-180. Download: PDF (78.99 KB)

Kozakov, D, Clodfelter KH, Vajda S, Camacho CJ.  2005.  Optimal Clustering for Detecting Near-Native Conformations in Protein Docking. Biophysical Journal. 89(2):867-875. Download: PDF (326.16 KB)

Comeau, SR, Vajda S, Camacho CJ.  2005.  Performance of the first protein docking server ClusPro in CAPRI rounds 3-5. Proteins: Structure, Function, and Bioinformatics. 60(2):239-244. Download: PDF (245.43 KB)

Sheu, S-H, Kaya T, Waxman DJ, Vajda S.  2005.  Exploring the Binding Site Structure of the PPARγ Ligand-Binding Domain by Computational Solvent Mapping. Biochemistry. 44(4):1193-1209. Download: PDF (947.12 KB)

Kozakov, D, Clodfelter KH, Vajda S, Camacho CJ.  2005.  Optimal Clustering for Detecting Near-Native Conformation in Protein Docking. CAPRI Meeting.  Download: PPT (5.34 MB)

Sheu, S-H, David R. Lancia J., Clodfelter KH, Landon MR, Vajda S.  2004.  PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. Nucleic Acids Research. 33(Database):D206-D211. Download: PDF (673.78 KB)

Rajamani, D, Thiel SC, Vajda S, Camacho CJ.  2004.  Anchor residues in protein-protein interactions. Proceedings of the National Academy of Sciences. 101(31):11287-11292. Download: PDF (487.94 KB)

Comeau, SR, Gatchell DW, Vajda S, Camacho CJ.  2004.  ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Research. 32(Web Server):W96-W99. Download: PDF (249.72 KB)

Prasad, JC, Vajda S, Camacho CJ.  2004.  Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Research. 32(Web Server):W50-W54. Download: PDF (376.98 KB)

Vajda, S, Camacho CJ.  2004.  Protein–protein docking: is the glass half-full or half-empty? Trends in Biotechnology. 22(3):110-116. Download: PDF (166.17 KB)

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. Download: PDF (67.49 KB)

Murphy, J, Gatchell DW, Prasad JC, Vajda S.  2003.  Combination of scoring functions improves discrimination in protein-protein docking. Proteins: Structure, Function, and Genetics. 53(4):840-854. Download: PDF (1.65 MB)

Silberstein, M, Dennis S, Brown L, Kortvelyesi T, Clodfelter KH, Vajda S.  2003.  Identification of Substrate Binding Sites in Enzymes by Computational Solvent Mapping. Journal of Molecular Biology. 332(5):1095-1113. Download: PDF (1.9 MB)

Prasad, JC, Comeau SR, Vajda S, Camacho CJ.  2003.  Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics. 19(13):1682-1691. Download: PDF (269.21 KB)

Janin, J, Henrick K, Moult J, Eyck L T, Sternberg MJE, Vajda S, Vakser IA, Wodak SJ.  2003.  CAPRI: A Critical Assessment of PRedicted Interactions. Proteins: Structure, Function, and Genetics. 52(1):2-9. Download: PDF (199.51 KB)

Kortvelyesi, T, Silberstein M, Dennis S, Vajda S.  2003.  Improved mapping of protein binding sites. Journal of Computer-Aided Molecular Design. 17(2/4):173-186. Download: PDF (397.37 KB)

Kortvelyesi, T, Dennis S, Silberstein M, Brown L, Vajda S.  2003.  Algorithms for computational solvent mapping of proteins. Proteins: Structure, Function, and Genetics. 51(3):340-351. Download: PDF (220.47 KB)

Valkó, PP, Vajda S.  2002.  Inversion of Noise-Free Laplace Transforms: Towards a Standardized Set of Test Problems. Inverse Problems in Engineering. 10(5):467-483. Download: PDF (316.72 KB)

Vajda, S, Vakser IA, Sternberg MJE, Janin J.  2002.  Modeling of protein interactions in genomes. Proteins: Structure, Function, and Genetics. 47(4):444-446. Download: PDF (56.23 KB)

Dennis, S, Vajda S.  2002.  Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins. Journal of Computational Chemistry. 23(3):319-334. Download: PDF (1.58 MB)

Camacho, CJ, Vajda S.  2002.  Protein–protein association kinetics and protein docking. Current Opinion in Structural Biology. 12(1):36-40. Download: PDF (78.31 KB)

Dennis, S, Kortvelyesi T, Vajda S.  2002.  Computational mapping identifies the binding sites of organic solvents on proteins. Proceedings of the National Academy of Sciences. 99(7):4290-4295. Download: PDF (156.98 KB)

Kimura, S. R, Brower RC, Vajda S, Camacho CJ.  2001.  Dynamical View of the Positions of Key Side Chains in Protein-Protein Recognition. Biophysical Journal. 80(2):635-642. Download: PDF (809.61 KB)

Camacho, CJ, Vajda S.  2001.  Protein docking along smooth association pathways. Proceedings of the National Academy of Sciences. 98(19):10636-10641. Download: PDF (355.4 KB)

Camacho, CJ, Vajda S.  2001.  Thermodynamic maps of receptor-ligand pairs reveal how some proteins bind. Drug-Receptor Thermodynamics. :581-592.

Gatchell, DW, Dennis S, Vajda S.  2000.  Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins: Structure, Function, and Genetics. 41(4):518-534. Download: PDF (554.3 KB)

Camacho, CJ, Gatchell DW, Kimura S. R, Vajda S.  2000.  Scoring docked conformations generated by rigid-body protein-protein docking. Proteins: Structure, Function, and Genetics. 40(3):525-537. Download: PDF (291.33 KB)

Camacho, CJ, Kimura S. R, DeLisi C, Vajda S.  2000.  Kinetics of Desolvation-Mediated Protein–Protein Binding. Biophysical Journal. 78(3):1094-1105. Download: PDF (150.72 KB)

Dennis, S, Camacho CJ, Vajda S.  2000.  Continuum electrostatic analysis of preferred solvation sites around proteins in solution. Proteins: Structure, Function, and Genetics. 38(2):176-188. Download: PDF (232.57 KB)

Dennis, S, Camacho CJ, Vajda S.  2000.  Exploring potential solvation sites of proteins by multistart local minimization. Optimization in Computational Chemistry and Molecular Biology. :243-261. Download: PDF (289.95 KB)

Camacho, CJ, Weng Z, Vajda S, DeLisi C.  1999.  Free Energy Landscapes of Encounter Complexes in Protein-Protein Association. Biophysical Journal. 76(3):1166-1178. Download: PDF (497.62 KB)

Esposito, M, Venkatesh V, Otvos L, Weng Z, Vajda S, Banki K, Perl A.  1999.  Human Transaldolase and Cross-Reactive Viral Epitopes Identified by Autoantibodies of Multiple Sclerosis Patients. The Journal of Immunology. 163:4027-4032. Download: PDF (897.36 KB)

DeLisi, C, Vajda S.  1999.  Computational problems in cell biology. Computing in Science & Engineering. 1(3):26-32. Download: PDF (185.29 KB)

Janardhan, A, Vajda S.  1998.  Selecting near-native conformations in homology modeling: The role of molecular mechanics and solvation terms. Protein Science. 7(8):1772-1780. Download: PDF (924.87 KB)

Zhang, C, Brower RC, Kimura S. R, Weng Z, Vajda S, DeLisi C.  1998.  The waters of life. Journal of the Franklin Institute. 335(2):213-240. Download: PDF (1.59 MB)

Sano, T, Vajda S, Cantor CR.  1998.  Genetic engineering of streptavidin, a versatile affinity tag. Journal of Chromatography B: Biomedical Sciences and Applications. 715(1):85-91. Download: PDF (208.85 KB)

Reznik, GO, Vajda S, Sano T, Cantor CR.  1998.  A streptavidin mutant with altered ligand-binding specificity. Proceedings of the National Academy of Sciences. 95(23):13525-13530. Download: PDF (207.53 KB)

Vajda, S.  1998.  Conformational Analysis. Encyclopedia of Computational Chemistry.

Weng, Z, DeLisi C, Vajda S.  1997.  Empirical free energy calculation: Comparison to calorimetric data. Protein Science. 6(9):1976-1984. Download: PDF (975.1 KB)

Sano, T, Vajda S, Smith CL, Cantor CR.  1997.  Engineering subunit association of multisubunit proteins: A dimeric streptavidin. Proceedings of the National Academy of Sciences. 94(12):6153-6158. Download: PDF (325.92 KB)

Vajda, S, Sippl M, Novotny J.  1997.  Empirical potentials and functions for protein folding and binding. Current Opinion in Structural Biology. 7(2):222-228. Download: PDF (101.87 KB)

Reznik, GO, Vajda S, Smith CL, Cantor CR, Sano T.  1996.  Streptavidins with intersubunit crosslinks have enhanced stability. Nature Biotechnology. 14(8):1007-1011. Download: PDF (691.06 KB)

Sano, T, Vajda S, Reznik GO, Smith CL, Cantor CR.  1996.  Molecular Engineering of Streptavidin. Annals of the New York Academy of Sciences. 799(Enzyme Eng):383-390. Download: PDF (497.24 KB)

Luidens, M K, Figge J, Breese K, Vajda S.  1996.  Predicted and trifluoroethanol-induced α-helicity of polypeptides. Biopolymers. 39(3):367-376. Download: PDF (800.66 KB)

Sezerman, U, Vajda S, DeLisi C.  1996.  Free energy mapping of class I MHC molecules and structural determination of bound peptides. Protein Science. 5(7):1272-1281. Download: PDF (3.29 MB)

King, B, Vajda S, DeLisi C.  1996.  Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors. FEBS Letters. 384(1):87-91. Download: PDF (429.51 KB)

Gulukota, K, Vajda S, DeLisi C.  1996.  Peptide docking using dynamic programming. Journal of Computational Chemistry. 17(4):418-428. Download: PDF (996.56 KB)

Weng, Z, Vajda S, DeLisi C.  1996.  Prediction of protein complexes using empirical free energy functions. Protein Science. 5:614–626. Download: PDF (3.56 MB)

Rosenfeld, R, Vajda S, DeLisi C.  1995.  Flexible Docking and Design. Annual Review of Biophysics and Biomolecular Structure. 24(1):677-700. Download: PDF (601.67 KB)

Vajda, S, Weng Z, Rosenfeld R, DeLisi C.  1994.  Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies. Biochemistry. 33(47):13977-13988. Download: PDF (1.95 MB)

Vajda, S, Kataoka R, DeLisi C, Margalit H, Berzofsky JA, Cornette JL.  1990.  Molecular Structure and Vaccine Design. Annual Review of Biophysics and Biophysical Chemistry. 19(1):69-82. Download: PDF (461.74 KB)