Papers+Conferences

2013
Golden MS, Cote SM, Sayeg M, Zerbe BS, Villar EA, Beglov D, Sazinsky SL, Georgiadis RM, Vajda S, Kozakov D et al..  2013.  Comprehensive Experimental and Computational Analysis of Binding Energy Hot Spots at the NF-κB Essential Modulator (NEMO)/IKKβ Protein-Protein Interface. Journal of the American Chemical Society. :130318121200001. Download: PDF (3.15 MB)
Grove LE, Hall DR, Beglov D, Vajda S, Kozakov D.  2013.  FTFlex: Accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. Bioinformatics.  Download: PDF (321.96 KB)
2012
Hingtgen S, Kasmieh R, Elbayly E, Nesterenko I, Figueiredo J-L, Dash R, Sarkar D, Hall DR, Kozakov D, Vajda S et al..  2012.  A First-Generation Multi-Functional Cytokine for Simultaneous Optical Tracking and Tumor Therapy. PLoS ONE. 7(7):e40234. Download: PDF (1.67 MB)
Zerbe B, 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)
Brenke R, Hall DR, Chuang G-Y, Comeau SR, Bohnuud T, Beglov D, Schueler-Furman O, Vajda S, Kozakov D.  2012.  Application of asymmetric statistical potentials to antibody-protein docking. Bioinformatics. 28(20):2608-2614. Download: PDF (250.82 KB)
Bohnuud T, Beglov D, Ngan CH, Zerbe B, Hall DR, Brenke R, Vajda S, Frank-Kamenetskii MD, Kozakov D.  2012.  Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde. Nucleic Acids Research. 40(16):7644-7652. Download: PDF (3.83 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)
Ngan CH, Hall DR, Zerbe B, Grove LE, Kozakov D, Vajda S.  2012.  FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinformatics. 28(2):286-287. Download: PDF (268.3 KB)
Hall DR, Ngan CH, Zerbe B, 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)
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)
Buhrman G, O′Connor C, Zerbe B, Kearney BM, Napoleon R, Kovrigina EA, Vajda S, Kozakov D, Kovrigin EL, Mattos C.  2011.  Analysis of Binding Site Hot Spots on the Surface of Ras GTPase. Journal of Molecular Biology. 413(4):773-789.
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, Desforges M, Hall DR, Kozakov D, Du Y, Min J, Dingledine R, Fu H, Vajda S, Talbot PJ et al..  2011.  Blocking eIF4E-eIF4G Interaction as a Strategy To Impair Coronavirus Replication. Journal of Virology. 85(13):6381-6389. Download: PDF (2.21 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
Chuang G-Y, Mehra-Chaudhary R, Ngan CH, Zerbe B, Kozakov D, Vajda S, Beamer LJ.  2010.  Domain motion and inter-domain hot spots in a multi-domain enzyme. Protein Science.  Download: PDF (403.54 KB)
Kozakov D, Hall DR, Beglov D, Brenke R, Comeau SR, Shen Y, Li K, Zheng J, Vakili P, Paschalidis IC et al..  2010.  Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19. Proteins: Structure, Function, and Bioinformatics. 78(15):3124-3130. Download: PDF (297.68 KB)
Kozakov D, Chuang G-Y, Beglov D, Vajda S.  2010.  Where does amantadine bind to the influenza virus M2 proton channel? Trends in Biochemical Sciences.  Download: PDF (263.58 KB)
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)
Chuang G-Y, Kozakov D, Brenke R, Beglov D, Guarnieri F, Vajda S.  2009.  Binding Hot Spots and Amantadine Orientation in the Influenza A Virus M2 Proton Channel. Biophysical Journal. 97(10):2846-2853. Download: PDF (514.97 KB)
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 DR, 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)
2008
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 IC, 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 CH, 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)
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)
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 IC, 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, Lancia, Jr. DR, 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)
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)
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, Lancia, Jr. DR, 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)
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)
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)
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)
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)
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)
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)
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 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)
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)
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)
1998
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 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)
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)
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)
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, 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, Rabitz H.  1994.  Identifiability and Distinguishability of General Reaction Systems. The Journal of Physical Chemistry. 98(20):5265-5271.
Buturović LJ, Smith TF, Vajda S.  1994.  Finite-state and reduced-parameter representations of protein backbone conformations. Journal of Computational Chemistry. 15(3):300-312.
1993
Vajda S, Rabitz H.  1993.  Generalized parametric sensitivity: Application to a CSTR. Chemical Engineering Science. 48(13):2453-2461.
Rao S, Zhu Q-L, Vajda S, Smith T.  1993.  The local information content of the protein structural database. FEBS Letters. 322(2):143-146.
Rosenfeld R, Zheng Q, Vajda S, DeLisi C.  1993.  Computing the Structure of Bound Peptides. Journal of Molecular Biology. 234(3):515-521.
Sezerman U, Vajda S, Cornette J, DeLisi C.  1993.  Toward computational determination of peptide-receptor structure. Protein Science. 2(11):1827-1843.
Zheng Q, Rosenfeld R, Vajda S, DeLisi C.  1993.  Determining protein loop conformation using scaling-relaxation techniques. Protein Science. 2(8):1242-1248.
Zheng Q, Rosenfeld R, Vajda S, DeLisi C.  1993.  Loop closure via bond scaling and relaxation. Journal of Computational Chemistry. 14(5):556-565.
Figge J, Breese K, Vajda S, Zhu Q-L, Eisele L, Andersen TT, Maccoll R, Friedrich T, Smith TF.  1993.  The binding domain structure of retinoblastoma-binding proteins. Protein Science. 2(2):155-164.
1992
Jafri MS, Vajda S, Pasik P, Gillo B.  1992.  A membrane model for cytosolic calcium oscillations. A study using Xenopus oocytes. Biophysical Journal. 63(1):235-246.
Vajda S, Rabitz H.  1992.  Parametric sensitivity and self-similarity in thermal explosion theory. Chemical Engineering Science. 47(5):1063-1078.
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, DeLisi C.  1990.  Determining minimum energy conformations of polypeptides by dynamic programming. Biopolymers. 29(14):1755-1772.
Chappell MJ, Godfrey KR, Vajda S.  1990.  Global identifiability of the parameters of nonlinear systems with specified inputs: A comparison of methods. Mathematical Biosciences. 102(1):41-73.
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
Vajda S, Godfrey KR, Rabitz H.  1989.  Similarity transformation approach to identifiability analysis of nonlinear compartmental models. Mathematical Biosciences. 93(2):217-248.
Vajda S, Distefano JJ, Godfrey KR, Fagarasan J.  1989.  Parameter space boundaries for unidentifiable compartmental models. Mathematical Biosciences. 97(1):27-60.
Vajda S, Rabitz H, WALTER E, LECOURTIER Y.  1989.  QUALITATIVE AND QUANTITATIVE IDENTIFIABILITY ANALYSIS OF NONLINEAR CHEMICAL KINETIC MODELS. Chemical Engineering Communications. 83(1):191-219.
Turányi T, Bérces T, Vajda S.  1989.  Reaction rate analysis of complex kinetic systems. International Journal of Chemical Kinetics. 21(2):83-99.
Vajda S, Rabitz H.  1989.  State isomorphism approach to global identifiability of nonlinear systems. IEEE Transactions on Automatic Control. 34(2):220-223.
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
Vajda S.  1982.  Further comments on "On parameter and structural identifiability: Nonunique observability/reconstructibility for identifiable systems, other ambiguities, and new definitions". IEEE Transactions on Automatic Control. 27(5):1136-1137.
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.