Kozakov D, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Vajda S.  2013.  How good is automated protein docking? Proteins: Structure, Function, and Bioinformatics.  Download: PDF (207.49 KB)
Vajda S, Hall DR, Kozakov D.  2013.  Sampling and scoring: A marriage made in heaven. Proteins: Structure, Function, and Bioinformatics.  Download: PDF (212.68 KB)
Zerbe BS, Hall DR, Vajda S, Whitty A, Kozakov D.  2012.  Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces.. Journal of chemical information and modeling.  Download: PDF (3.75 MB)
Mirzaei H, Beglov D, Paschalidis IC, Vajda S, Vakili P, Kozakov D.  2012.  Rigid Body Energy Minimization on Manifolds for Molecular Docking. Journal of Chemical Theory and Computation. :120821123549006. Download: PDF (317.26 KB)
Ngan CH, Bohnuud T, Mottarella SE, Beglov D, Villar EA, Hall DR, Kozakov D, Vajda S.  2012.  FTMAP: extended protein mapping with user-selected probe molecules. Nucleic Acids Research. 40(W1):W271-W275. Download: PDF (1.33 MB)
Beglov D, Hall DR, Brenke R, Shapovalov MV, Dunbrack RL, Kozakov D, Vajda S.  2012.  Minimal ensembles of side chain conformers for modeling protein-protein interactions. Proteins: Structure, Function, and Bioinformatics. 80(2):591-601. Download: PDF (1.57 MB)
Hall DR, Ngan CH, Zerbe BS, Kozakov D, Vajda S.  2012.  Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery. Journal of Chemical Information and Modeling. 52(1):199-209. Download: PDF (1.92 MB)
Hall DR, Kozakov D, Vajda S.  2012.  Analysis of Protein Binding Sites by Computational Solvent Mapping. Methods in Molecular Biology. 819:13-27. Download: PDF (1.71 MB)
Hall DR, Grove LE, Yueh C, Ngan CH, Kozakov D, Vajda S.  2011.  Robust Identification of Binding Hot Spots Using Continuum Electrostatics: Application to Hen Egg-White Lysozyme. Journal of the American Chemical Society. 133(51):20668-20671. Download: PDF (3.55 MB)
Kozakov D, Hall DR, Chuang G-Y, Cencic R, Brenke R, Grove LE, Beglov D, Pelletier J, Whitty A, Vajda S.  2011.  Structural conservation of druggable hot spots in protein-protein interfaces. Proceedings of the National Academy of Sciences. 108(33):13528-13533. Download: PDF (7.25 MB)
Cencic R, Hall DR, Robert F, Du Y, Min J, Li L, Qui M, Lewis I, Kurtkaya S, Dingledine R et al..  2011.  Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F.. Proceedings of the National Academy of Sciences of the United States of America. 108(3):1046-51. Abstract  Download: PDF (2.42 MB)
Ngan CH, Beglov D, Rudnitskaya AN, Kozakov D, Waxman DJ, Vajda S.  2009.  The Structural Basis of Pregnane X Receptor Binding Promiscuity. Biochemistry. 48(48):11572-11581. Download: PDF (3.14 MB)
Beglov D, Lee C-J, De Biasio A, Kozakov D, Brenke R, Vajda S, Beglova N.  2009.  Structural insights into recognition of β2-glycoprotein I by the lipoprotein receptors. Proteins: Structure, Function, and Bioinformatics. 77(4):940-949. Download: PDF (419.27 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)
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)
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)
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)
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)
Landon MR, Yu J, Thiel SC, Lancia, Jr. DR, 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)
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)
Paschalidis IC, 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)
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)
Comeau SR, Camacho CJ.  2005.  Predicting oligomeric assemblies: N-mers a primer. Journal of Structural Biology. 150(3):233-244. Download: PDF (809.73 KB)
Sheu S-H, Lancia, Jr. DR, 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)
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)
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 LT, 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)
Camacho CJ, Gatchell DW.  2003.  Successful discrimination of protein interactions. Proteins: Structure, Function, and Genetics. 52(1):92-97. Download: PDF (147.76 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)
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)
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)
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)
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)
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)
Kimura SR, 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)
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 SR, 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 SR, 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)
DeLisi C, Vajda S.  1999.  Computational problems in cell biology. Computing in Science & Engineering. 1(3):26-32. Download: PDF (185.29 KB)
Zhang C, Brower RC, Kimura SR, 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)
Vajda S.  1998.  Conformational Analysis. Encyclopedia of Computational Chemistry.
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)
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)
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)
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)
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 MK, 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)
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)
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, Zheng Q, Vajda S, DeLisi C.  1995.  Flexible docking of peptides to class I major-histocompatibility-complex receptors. Genetic Analysis: Biomolecular Engineering. 12(1):1-21.
Vajda S, Weng Z, DeLisi C.  1995.  Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments. "Protein Engineering, Design and Selection". 8(11):1081-1092.
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)
Godfrey KR, Chapman MJ, Vajda S.  1994.  Identifiability and indistinguishability of nonlinear pharmacokinetic models. Journal of Pharmacokinetics and Biopharmaceutics. 22(3):229-251.
Vajda S, Rabitz H.  1994.  Identifiability and Distinguishability of General Reaction Systems. The Journal of Physical Chemistry. 98(20):5265-5271.
Eisenfeld J, Vajda S, Sugar I, DeLisi C.  1991.  Constrained optimization and protein structure determination.. The American journal of physiology. 261(2 Pt 1):C376-86. Abstract
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)
Vajda S, Godfrey KR, Valko P.  1988.  Numerical deconvolution using system identification methods. Journal of Pharmacokinetics and Biopharmaceutics. 16(1):85-107.
Vajda S, Rabitz H.  1988.  Identifiability and distinguishability of first-order reaction systems. The Journal of Physical Chemistry. 92(3):701-707.
Vajda S, Valko P, Turányi T.  1985.  Principal component analysis of kinetic models. International Journal of Chemical Kinetics. 17(1):55-81.
Vajda S.  1984.  Structural equivalence and exhaustive compartmental modeling. Mathematical Biosciences. 69(1):57-75.
Vajda S.  1984.  Analysis of unique structural identifiability via submodels. Mathematical Biosciences. 71(2):125-146.
Vajda S.  1981.  Structural equivalence of linear systems and compartmental models. Mathematical Biosciences. 55(1-2):39-64.
Vajda S.  1979.  Comments on "Structural identifiability in linear time-invariant systems. IEEE Transactions on Automatic Control. 24(3):495-496.