Papers+Conferences

2014
Villar EA, Beglov D, Chennamadhavuni S, Porco JA, Kozakov D, Vajda S, Whitty A.  2014.  How proteins bind macrocycles. Nature Chemical Biology.  Download: PDF (1.17 MB)
Chowdhury R, Beglov D, Moghadasi M, Paschalidis IC, Vakili P, Vajda S, Bajaj C, Kozakov D.  2014.  Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations. Journal of Chemical Theory and Computation. :140926082652006. Download: PDF (2.01 MB)
Mottarella SE, Beglov D, Beglova N, Nugent MA, Kozakov D, Vajda S.  2014.  Docking Server for the Identification of Heparin Binding Sites on Proteins. Journal of Chemical Information and Modeling. 54(7):2068-2078. Download: PDF (3.97 MB)
2013
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)
Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond ASJ, Karaca E, Schmitz C, van Dijk M, Bonvin AMJJ, Eisenstein M et al..  2013.  Blind prediction of interfacial water positions in CAPRI. Proteins: Structure, Function, and Bioinformatics. 82(4):620-632. Download: PDF (554.23 KB)
Mirzaei H, Villar E, Mottarella S, Beglov D, Paschalidis IC, Vajda S, Kozakov D, Vakili P.  2013.  Flexible refinement of protein-ligand docking on manifolds. 2013 IEEE 52nd Annual Conference on Decision and Control (CDC)52nd IEEE Conference on Decision and Control. :1392-1397. Download: PDF (384.37 KB)
Moghadasi M, Kozakov D, Vakili P, Vajda S, Paschalidis IC.  2013.  A new distributed algorithm for side-chain positioning in the process of protein docking. 2013 IEEE 52nd Annual Conference on Decision and Control (CDC)52nd IEEE Conference on Decision and Control. :739-744. Download: PDF (334.84 KB)
2012
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. 8(11):4374-4380.
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)
Moghadasi M, Kozakov D, Mamonov AB, Vakili P, Vajda S, Paschalidis IC.  2012.  A message passing approach to Side Chain Positioning with applications in protein docking refinement. 2012 IEEE 51st Annual Conference on Decision and Control (CDC)2012 IEEE 51st IEEE Conference on Decision and Control (CDC). :2310-2315.
Mirzaei H, Kozakov D, Beglov D, Paschalidis IC, Vajda S, Vakili P.  2012.  A new approach to rigid body minimization with application to molecular docking. 2012 IEEE 51st Annual Conference on Decision and Control (CDC)2012 IEEE 51st IEEE Conference on Decision and Control (CDC). :2983-2988.
2011
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)
2010
2009
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)
2008
2007
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)
2006
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)
2005
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)
2004
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)
2003
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)
2002
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)
2001
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)
2000
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)
1999
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)
1998
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)
1997
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)
1996
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)
1995
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)
1994
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.
1993
1992
1991
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
1990
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)
1989
1988
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.
1985
Vajda S, Valko P, Turányi T.  1985.  Principal component analysis of kinetic models. International Journal of Chemical Kinetics. 17(1):55-81.
1984
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.
1982
1981
Vajda S.  1981.  Structural equivalence of linear systems and compartmental models. Mathematical Biosciences. 55(1-2):39-64.
1979
Vajda S.  1979.  Comments on "Structural identifiability in linear time-invariant systems. IEEE Transactions on Automatic Control. 24(3):495-496.