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Sandor Vajda

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Laurie E Grove; David R Hall; Dmitri Beglov; Sandor Vajda; Dima Kozakov
FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots.
Mary S Golden; Dima Kozakov; Marianna Sayeg; Stephen L Sazinsky; Sandor Vajda; Elizabeth A Villar; Dmitri Beglov; Shaun M Cote; Rosina M Georgiadis; Brandon S Zerbe; Adrian Whitty
Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface.
Ryan Brenke; Gwo-Yu Chuang; Stephen R Comeau; David R Hall; Dmitri Beglov; Tanggis Bohnuud; Ora Schueler-Furman; Sandor Vajda; Dima Kozakov
Application of asymmetric statistical potentials to antibody-protein docking.

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All Publications

2013: Laurie E Grove; David R Hall; Dmitri Beglov; Sandor Vajda; Dima Kozakov
FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots.
Bioinformatics (Oxford, England) 2013;29(9):1218-9.
2013: Mary S Golden; Dima Kozakov; Marianna Sayeg; Stephen L Sazinsky; Sandor Vajda; Elizabeth A Villar; Dmitri Beglov; Shaun M Cote; Rosina M Georgiadis; Brandon S Zerbe; Adrian Whitty
Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface.
Journal of the American Chemical Society 2013;135(16):6242-56.
2012: Ryan Brenke; Gwo-Yu Chuang; Stephen R Comeau; David R Hall; Dmitri Beglov; Tanggis Bohnuud; Ora Schueler-Furman; Sandor Vajda; Dima Kozakov
Application of asymmetric statistical potentials to antibody-protein docking.
Bioinformatics (Oxford, England) 2012;28(20):2608-14.
2012: Tanggis Bohnuud; Ryan Brenke; Maxim D Frank-Kamenetskii; David R Hall; Chi Ho Ngan; Sandor Vajda; Brandon Zerbe; Dmitri Beglov; Dima Kozakov
Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde.
Nucleic acids research 2012;40(16):7644-52.
2012: Brandon S Zerbe; David R Hall; Sandor Vajda; Adrian Whitty; Dima Kozakov
Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces.
Journal of chemical information and modeling 2012;52(8):2236-44.
2012: Chi Ho Ngan; Elizabeth A Villar; Dmitri Beglov; Tanggis Bohnuud; David R Hall; Dima Kozakov; Scott E Mottarella; Sandor Vajda
FTMAP: extended protein mapping with user-selected probe molecules.
Nucleic acids research 2012;40(Web Server issue):W271-5.
2012: David R Hall; Dima Kozakov; Chi Ho Ngan; Brandon S Zerbe; Sandor Vajda
Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery.
Journal of chemical information and modeling 2012;52(1):199-209.
2012: Chi-Ho Ngan; Laurie E Grove; David R Hall; Dima Kozakov; Brandon Zerbe; Sandor Vajda
FTSite: high accuracy detection of ligand binding sites on unbound protein structures.
Bioinformatics (Oxford, England) 2012;28(2):286-7.
2012: Shawn Hingtgen; Randa Kasmieh; Dima Kozakov; Irina Nesterenko; Devanand Sarkar; Rupesh Dash; Elizabeth Elbayly; Jose-Luiz Figueiredo; Paul B Fisher; David Hall; Sandor Vajda; Khalid Shah
A first-generation multi-functional cytokine for simultaneous optical tracking and tumor therapy.
PloS one 2012;7(7):e40234.
2011: Greg Buhrman; Bradley M Kearney; Evgenii L Kovrigin; Elizaveta A Kovrigina; Dima Kozakov; Raeanne Napoleon; Sandor Vajda; Brandon Zerbe; Casey O'Connor; Carla Mattos
Analysis of binding site hot spots on the surface of Ras GTPase.
Journal of molecular biology 2011;413(4):773-89.
2011: Gloria V Callard; G-Y Chuang; L Ciaccia; Sarah R Greytak; C Hoover; Dima Kozakov; Apolonia Novillo; S Sawyer; A M Tarrant; Sandor Vajda; P Yacci; K A Cotter
Evolutionary origins of the estrogen signaling system: insights from amphioxus.
The Journal of steroid biochemistry and molecular biology 2011;127(3-5):176-88.
2011: Dima Kozakov; Jerry Pelletier; Adrian Whitty; Dmitri Beglov; Ryan Brenke; Regina Cencic; Gwo-Yu Chuang; Laurie E Grove; David R Hall; Sandor Vajda
Structural conservation of druggable hot spots in protein-protein interfaces.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(33):13528-33.
2011: Regina Cencic; Marc Desforges; ray dingledine; Yuhong Du; Haian Fu; David R Hall; Dima Kozakov; Jaeki Min; Pierre J Talbot; Sandor Vajda; Jerry Pelletier
Blocking eIF4E-eIF4G interaction as a strategy to impair coronavirus replication.
Journal of virology 2011;85(13):6381-9.
2011: Regina Cencic; David R Hall; Francis Robert; Yuhong Du; Jaeki Min; Lian Li; Min Qui; Iestyn Lewis; Serdar Kurtkaya; ray dingledine; Haian Fu; Dima Kozakov; Sandor Vajda; Jerry Pelletier
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 2011;108(3):1046-51.
2010: Dima Kozakov; David R Hall; Dmitri Beglov; Ryan Brenke; Stephen R Comeau; Yang Shen; Keyong Li; Jiefu Zheng; Pirooz Vakili; Ioannis Ch Paschalidis; Sandor Vajda
Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19.
Proteins 2010;78(15):3124-30.
2010: Gwo-Yu Chuang; Ritcha Mehra-Chaudhary; Chi-Ho Ngan; Brandon S Zerbe; Dima Kozakov; Sandor Vajda; Lesa J Beamer
Domain motion and interdomain hot spots in a multidomain enzyme.
Protein science : a publication of the Protein Society 2010;19(9):1662-72.
2010: Dima Kozakov; Gwo-Yu Chuang; Dmitri Beglov; Sandor Vajda
Where does amantadine bind to the influenza virus M2 proton channel?
Trends in biochemical sciences 2010;35(9):471-5.
2009: Chi-Ho Ngan; Dmitri Beglov; Aleksandra N Rudnitskaya; Dima Kozakov; David J Waxman; Sandor Vajda
The structural basis of pregnane X receptor binding promiscuity.
Biochemistry 2009;48(48):11572-81.
2009: Dmitri Beglov; Chang-Jin Lee; Alfredo De Biasio; Dima Kozakov; Ryan Brenke; Sandor Vajda; Natalia Beglova
Structural insights into recognition of beta2-glycoprotein I by the lipoprotein receptors.
Proteins 2009;77(4):940-9.
2009: Gwo-Yu Chuang; Dima Kozakov; Ryan Brenke; Dmitri Beglov; Frank Guarnieri; Sandor Vajda
Binding hot spots and amantadine orientation in the influenza a virus M2 proton channel.
Biophysical journal 2009;97(10):2846-53.
2009: Melissa R Landon; Raquel L Lieberman; Susan D Orwig; Gregory A Petsko; Dmitry Beglov; Ryan Brenke; Jose M M Caaveiro; Gwo-Yu Chuang; Quyen Q Hoang; Shulin Ju; Dima Kozakov; Sandor Vajda; Dagmar Ringe
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 2009;23(8):491-500.
2009: Sandor Vajda; Dima Kozakov
Convergence and combination of methods in protein-protein docking.
Current opinion in structural biology 2009;19(2):164-70.
2009: Ryan Brenke; Dima Kozakov; Gwo-Yu Chuang; Dmitri Beglov; David Hall; Melissa R Landon; Carla Mattos; Sandor Vajda
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques.
Bioinformatics (Oxford, England) 2009;25(5):621-7.
2008: Gwo-Yu Chuang; Dima Kozakov; Ryan Brenke; Stephen R Comeau; Sandor Vajda
DARS (Decoys As the Reference State) potentials for protein-protein docking.
Biophysical journal 2008;95(9):4217-27.
2008: Yang Shen; Ioannis Ch Paschalidis; Pirooz Vakili; Sandor Vajda
Protein docking by the underestimation of free energy funnels in the space of encounter complexes.
PLoS computational biology 2008;4(10):e1000191.
2008: David W Ritchie; Dima Kozakov; Sandor Vajda
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions.
Bioinformatics (Oxford, England) 2008;24(17):1865-73.
2008: Dima Kozakov; Ora Schueler-Furman; Sandor Vajda
Discrimination of near-native structures in protein-protein docking by testing the stability of local minima.
Proteins 2008;72(3):993-1004.
2008: Melissa R Landon; Rommie E Amaro; Riccardo Baron; Chi Ho Ngan; David Ozonoff; J Andrew McCammon; Sandor Vajda
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 2008;71(2):106-16.
2007: Stephen R Comeau; Dima Kozakov; Ryan Brenke; Yang Shen; Dmitri Beglov; Sandor Vajda
ClusPro: performance in CAPRI rounds 6-11 and the new server.
Proteins 2007;69(4):781-5.
2007: Yang Shen; Ryan Brenke; Dima Kozakov; Stephen R Comeau; Dmitri Beglov; Sandor Vajda
Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI.
Proteins 2007;69(4):734-42.
2007: Michael Silberstein; Jiri Damborsky; Sandor Vajda
Exploring the binding sites of the haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10.
Biochemistry 2007;46(32):9239-49.
2007: Melissa R Landon; David R Lancia; Jessamin Yu; Spencer C Thiel; Sandor Vajda
Identification of hot spots within druggable binding regions by computational solvent mapping of proteins.
Journal of medicinal chemistry 2007;50(6):1231-40.
2007: Jahnavi C Prasad; Jared V Goldstone; Carlos J Camacho; Sandor Vajda; John J Stegeman
Ensemble modeling of substrate binding to cytochromes P450: analysis of catalytic differences between CYP1A orthologs.
Biochemistry 2007;46(10):2640-54.
2007: Filiz M Aslan; Yong Yu; Sandor Vajda; Scott C Mohr; Charles R Cantor
Engineering a novel, stable dimeric streptavidin with lower isoelectric point.
Journal of biotechnology 2007;128(2):213-25.
2006: Dima Kozakov; Ryan Brenke; Stephen R Comeau; Sandor Vajda
PIPER: an FFT-based protein docking program with pairwise potentials.
Proteins 2006;65(2):392-406.
2006: Karl H Clodfelter; David J Waxman; Sandor Vajda
Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450.
Biochemistry 2006;45(31):9393-407.
2006: Taner Kaya; Scott C Mohr; David J Waxman; Sandor Vajda
Computational screening of phthalate monoesters for binding to PPARgamma.
Chemical research in toxicology 2006;19(8):999-1009.
2006: Sandor Vajda; Frank Guarnieri
Characterization of protein-ligand interaction sites using experimental and computational methods.
Current opinion in drug discovery & development 2006;9(3):354-62.
2006: Melissa R Landon; David R Lancia; Karl H Clodfelter; Sandor Vajda
Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns.
Journal of molecular graphics & modelling 2006;24(6):426-33.
2006: Michael Silberstein; Melissa R Landon; Yaoyu E Wang; Andras Perl; Sandor Vajda
Computational methods for functional site identification suggest a substrate access channel in transaldolase.
Genome informatics. International Conference on Genome Informatics 2006;17(1):13-22.
2005: Stephen R Comeau; Sandor Vajda; Carlos J Camacho
Performance of the first protein docking server ClusPro in CAPRI rounds 3-5.
Proteins 2005;60(2):239-44.
2005: Sandor Vajda
Classification of protein complexes based on docking difficulty.
Proteins 2005;60(2):176-80.
2005: Dima Kozakov; Karl H Clodfelter; Sandor Vajda; Carlos J Camacho
Optimal clustering for detecting near-native conformations in protein docking.
Biophysical journal 2005;89(2):867-75.
2005: Shu-Hsien Sheu; Taner Kaya; David J Waxman; Sandor Vajda
Exploring the binding site structure of the PPAR gamma ligand-binding domain by computational solvent mapping.
Biochemistry 2005;44(4):1193-209.
2005: Shu-Hsien Sheu; David R Lancia; Karl H Clodfelter; Melissa R Landon; Sandor Vajda
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes.
Nucleic acids research 2005;33(Database issue):D206-11.
2004: Deepa Rajamani; Spencer Thiel; Sandor Vajda; Carlos J Camacho
Anchor residues in protein-protein interactions.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(31):11287-92.
2004: Stephen R Comeau; David W Gatchell; Sandor Vajda; Carlos J Camacho
ClusPro: a fully automated algorithm for protein-protein docking.
Nucleic acids research 2004;32(Web Server issue):W96-9.
2004: Jahnavi C Prasad; Sandor Vajda; Carlos J Camacho
Consensus alignment server for reliable comparative modeling with distant templates.
Nucleic acids research 2004;32(Web Server issue):W50-4.
2004: Sandor Vajda; Carlos J Camacho
Protein-protein docking: is the glass half-full or half-empty?
Trends in biotechnology 2004;22(3):110-6.
2004: Stephen R Comeau; David W Gatchell; Sandor Vajda; Carlos J Camacho
ClusPro: an automated docking and discrimination method for the prediction of protein complexes.
Bioinformatics (Oxford, England) 2004;20(1):45-50.
2003: John Murphy; David W Gatchell; Jahnavi C Prasad; Sandor Vajda
Combination of scoring functions improves discrimination in protein-protein docking.
Proteins 2003;53(4):840-54.
2003: Michael Silberstein; Sheldon Dennis; Lawrence Brown; Tamas Kortvelyesi; Karl H Clodfelter; Sandor Vajda
Identification of substrate binding sites in enzymes by computational solvent mapping.
Journal of molecular biology 2003;332(5):1095-113.
2003: Jahnavi C Prasad; Stephen R Comeau; Sandor Vajda; Carlos J Camacho
Consensus alignment for reliable framework prediction in homology modeling.
Bioinformatics (Oxford, England) 2003;19(13):1682-91.
2003: Joël Janin; Kim Henrick; John Moult; Lynn Ten Eyck; Michael J E Sternberg; Sandor Vajda; Ilva Vakser; Shoshana J Wodak
CAPRI: a Critical Assessment of PRedicted Interactions.
Proteins 2003;52(1):2-9.
2003: Tamas Kortvelyesi; Sheldon Dennis; Michael Silberstein; Lawrence Brown; Sandor Vajda
Algorithms for computational solvent mapping of proteins.
Proteins 2003;51(3):340-51.
2003: Tamas Kortvelyesi; Michael Silberstein; Sheldon Dennis; Sandor Vajda
Improved mapping of protein binding sites.
Journal of computer-aided molecular design 2003;17(2-4):173-86.
2002: Sandor Vajda; Ilva Vakser; Michael J E Sternberg; Joël Janin
Modeling of protein interactions in genomes.
Proteins 2002;47(4):444-6.
2002: Sheldon Dennis; Tamas Kortvelyesi; Sandor Vajda
Computational mapping identifies the binding sites of organic solvents on proteins.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(7):4290-5.
2002: Sheldon Dennis; Sandor Vajda
Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins.
Journal of computational chemistry 2002;23(3):319-34.
2002: Carlos J Camacho; Sandor Vajda
Protein-protein association kinetics and protein docking.
Current opinion in structural biology 2002;12(1):36-40.
2001: Gabriel O Reznik; Sandor Vajda; Charles R Cantor; T Sano
A streptavidin mutant useful for directed immobilization on solid surfaces.
Bioconjugate chemistry 2001;12(6):1000-4.
2001: Carlos J Camacho; Sandor Vajda
Protein docking along smooth association pathways.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(19):10636-41.
2001: S R Kimura; R C Brower; Sandor Vajda; Carlos J Camacho
Dynamical view of the positions of key side chains in protein-protein recognition.
Biophysical journal 2001;80(2):635-42.
2000: David W Gatchell; Sheldon Dennis; Sandor Vajda
Discrimination of near-native protein structures from misfolded models by empirical free energy functions.
Proteins 2000;41(4):518-34.
2000: Carlos J Camacho; David W Gatchell; S R Kimura; Sandor Vajda
Scoring docked conformations generated by rigid-body protein-protein docking.
Proteins 2000;40(3):525-37.
2000: Carlos J Camacho; S R Kimura; Charles DeLisi; Sandor Vajda
Kinetics of desolvation-mediated protein-protein binding.
Biophysical journal 2000;78(3):1094-105.
2000: Sheldon Dennis; Carlos J Camacho; Sandor Vajda
Continuum electrostatic analysis of preferred solvation sites around proteins in solution.
Proteins 2000;38(2):176-88.
1999: Carlos J Camacho; Z Weng; Sandor Vajda; Charles DeLisi
Free energy landscapes of encounter complexes in protein-protein association.
Biophysical journal 1999;76(3):1166-78.
1998: Gabriel O Reznik; Sandor Vajda; T Sano; Charles R Cantor
A streptavidin mutant with altered ligand-binding specificity.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(23):13525-30.
1998: T Sano; Sandor Vajda; Charles R Cantor
Genetic engineering of streptavidin, a versatile affinity tag.
Journal of chromatography. B, Biomedical sciences and applications 1998;715(1):85-91.
1998: A Janardhan; Sandor Vajda
Selecting near-native conformations in homology modeling: the role of molecular mechanics and solvation terms.
Protein science : a publication of the Protein Society 1998;7(8):1772-80.
1997: Zhiping Weng; Charles DeLisi; Sandor Vajda
Empirical free energy calculation: comparison to calorimetric data.
Protein science : a publication of the Protein Society 1997;6(9):1976-84.
1997: T Sano; Sandor Vajda; Cassandra Lynn Smith; Charles R Cantor
Engineering subunit association of multisubunit proteins: a dimeric streptavidin.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(12):6153-8.
1997: Sandor Vajda; M Sippl; J Novotny
Empirical potentials and functions for protein folding and binding.
Current opinion in structural biology 1997;7(2):222-8.
1996: T Sano; Sandor Vajda; G O Reznik; Cassandra Lynn Smith; Charles R Cantor
Molecular engineering of streptavidin.
Annals of the New York Academy of Sciences 1996;799():383-90.
1996: M K Luidens; James J Figge; K Breese; Sandor Vajda
Predicted and trifluoroethanol-induced alpha-helicity of polypeptides.
Biopolymers 1996;39(3):367-76.
1996: G O Reznik; Sandor Vajda; Cassandra Lynn Smith; Charles R Cantor; T Sano
Streptavidins with intersubunit crosslinks have enhanced stability.
Nature biotechnology 1996;14(8):1007-11.
1996: U Sezerman; Sandor Vajda; Charles DeLisi
Free energy mapping of class I MHC molecules and structural determination of bound peptides.
Protein science : a publication of the Protein Society 1996;5(7):1272-81.
1996: B L King; Sandor Vajda; Charles DeLisi
Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors.
FEBS letters 1996;384(1):87-91.
1996: Z Weng; Sandor Vajda; Charles DeLisi
Prediction of protein complexes using empirical free energy functions.
Protein science : a publication of the Protein Society 1996;5(4):614-26.
1995: Sandor Vajda; Z Weng; Charles DeLisi
Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments.
Protein engineering 1995;8(11):1081-92.
1995: R Rosenfeld; Q Zheng; Sandor Vajda; Charles DeLisi
Flexible docking of peptides to class I major-histocompatibility-complex receptors.
Genetic analysis : biomolecular engineering 1995;12(1):1-21.
1995: R Rosenfeld; Sandor Vajda; Charles DeLisi
Flexible docking and design.
Annual review of biophysics and biomolecular structure 1995;24():677-700.
1994: Sandor Vajda; Z Weng; R Rosenfeld; Charles DeLisi
Effect of conformational flexibility and solvation on receptor-ligand binding free energies.
Biochemistry 1994;33(47):13977-88.
1993: R Rosenfeld; Q Zheng; Sandor Vajda; Charles DeLisi
Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptors.
Journal of molecular biology 1993;234(3):515-21.
1993: U Sezerman; Sandor Vajda; J Cornette; Charles DeLisi
Toward computational determination of peptide-receptor structure.
Protein science : a publication of the Protein Society 1993;2(11):1827-43.
1993: Q Zheng; R Rosenfeld; Sandor Vajda; Charles DeLisi
Determining protein loop conformation using scaling-relaxation techniques.
Protein science : a publication of the Protein Society 1993;2(8):1242-8.
1993: S Rao; Q L Zhu; Sandor Vajda; T Smith
The local information content of the protein structural database.
FEBS letters 1993;322(2):143-6.
1993: James J Figge; K Breese; Sandor Vajda; Q L Zhu; Leslie Eisele; T T Andersen; R MacColl; T Friedrich; T F Smith
The binding domain structure of retinoblastoma-binding proteins.
Protein science : a publication of the Protein Society 1993;2(2):155-64.
1993: Sandor Vajda
Conformational filtering in polypeptides and proteins.
Journal of molecular biology 1993;229(1):125-45.
1993: Sandor Vajda; M Saleet Jafri; O U Sezerman; Charles DeLisi
Necessary conditions for avoiding incorrect polypeptide folds in conformational search by energy minimization.
Biopolymers 1993;33(1):173-92.
1992: M Saleet Jafri; Sandor Vajda; P Pasik; B Gillo
A membrane model for cytosolic calcium oscillations. A study using Xenopus oocytes.
Biophysical journal 1992;63(1):235-46.
1991: J Eisenfeld; Sandor Vajda; I Sugar; Charles DeLisi
Constrained optimization and protein structure determination.
The American journal of physiology 1991;261(2 Pt 1):C376-86.
1990: Sandor Vajda; Charles DeLisi
Determining minimum energy conformations of polypeptides by dynamic programming.
Biopolymers 1990;29(14):1755-72.
1990: Sandor Vajda; Ryoichi Kataoka; Charles DeLisi; Hanah Margalit; J A Berzofsky; J L Cornette
Molecular structure and vaccine design.
Annual review of biophysics and biophysical chemistry 1990;19():69-82.