Sandor Vajda - researchr alias

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2024

Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2Ayse A. Bekar-Cesaretli, Omeir Khan, Thu Nguyen, Dima Kozakov, Diane Joseph-McCarthy, Sandor Vajda. jcisd, 64(3):960-973, 2024. [doi]

2022

Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled ReceptorsAmanda E. Wakefield, Dávid Bajusz, Dima Kozakov, György M. Keserü, Sandor Vajda. jcisd, 62(20):4937-4954, 2022. [doi]

2020

Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand DiscoveryAmanda E. Wakefield, Christine Yueh, Dmitri Beglov, Marcelo Santos Castilho, Dima Kozakov, György M. Keserü, Adrian Whitty, Sandor Vajda. jcisd, 60(12):6612-6623, 2020. [doi]

2016

Focused grid-based resampling for protein docking and mappingArtem B. Mamonov, Mohammad Moghadasi, Hanieh Mirzaei, Shahrooz Zarbafian, Laurie E. Grove, Tanggis Bohnuud, Pirooz Vakili, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov. jcc, 37(11):961-970, 2016. [doi]

Accounting for pairwise distance restraints in FFT-based protein-protein dockingBing Xia, Sandor Vajda, Dima Kozakov. bioinformatics, 32(21):3342-3344, 2016. [doi]

2015

2014

Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein InterfacesTanggis Bohnuud, Dima Kozakov, Sandor Vajda. ploscb, 10(10), 2014. [doi]

Docking Server for the Identification of Heparin Binding Sites on ProteinsScott E. Mottarella, Dmitri Beglov, Natalia Beglova, Matthew A. Nugent, Dima Kozakov, Sandor Vajda. jcisd, 54(7):2068-2078, 2014. [doi]

A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein dockingFeng Nan, Mohammad Moghadasi, Pirooz Vakili, Sandor Vajda, Dima Kozakov, Ioannis Ch. Paschalidis. cdc 2014: 4623-4628 [doi]

Optimization on the space of rigid and flexible motions: An alternative manifold optimization approachPirooz Vakili, Hanieh Mirzaei, Shahrooz Zarbafian, Ioannis Ch. Paschalidis, Dima Kozakov, Sandor Vajda. cdc 2014: 5825-5830 [doi]

2013

2012

Application of asymmetric statistical potentials to antibody-protein dockingRyan Brenke, David R. Hall, Gwo-Yu Chuang, Stephen R. Comeau, Tanggis Bohnuud, Dmitri Beglov, Ora Schueler-Furman, Sandor Vajda, Dima Kozakov. bioinformatics, 28(20):2608-2614, 2012. [doi]

Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug DiscoveryDavid R. Hall, Chi-Ho Ngan, Brandon Zerbe, Dima Kozakov, Sandor Vajda. jcisd, 52(1):199-209, 2012. [doi]

A new approach to rigid body minimization with application to molecular dockingHanieh Mirzaei, Dima Kozakov, Dmitri Beglov, Ioannis Ch. Paschalidis, Sandor Vajda, Pirooz Vakili. cdc 2012: 2983-2988 [doi]

A message passing approach to Side Chain Positioning with applications in protein docking refinementMohammad Moghadasi, Dima Kozakov, Artem B. Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis. cdc 2012: 2310-2315 [doi]

FTSite: high accuracy detection of ligand binding sites on unbound protein structuresChi-Ho Ngan, David R. Hall, Brandon Zerbe, Laurie E. Grove, Dima Kozakov, Sandor Vajda. bioinformatics, 28(2):286-287, 2012. [doi]

FTMAP: extended protein mapping with user-selected probe moleculesChi-Ho Ngan, Tanggis Bohnuud, Scott E. Mottarella, Dmitri Beglov, Elizabeth A. Villar, David R. Hall, Dima Kozakov, Sandor Vajda. nar, 40(Web-Server-Issue):271-275, 2012. [doi]

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein InterfacesBrandon S. Zerbe, David R. Hall, Sandor Vajda, Adrian Whitty, Dima Kozakov. jcisd, 52(8):2236-2244, 2012. [doi]

2009

2008

Clustering versus Scoring for the Identification of Near-Native Poses in Protein-Ligand DockingTaner Kaya, Dima Kozakov, Sandor Vajda. psb 2008: 1028-1032

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functionsDavid W. Ritchie, Dima Kozakov, Sandor Vajda. bioinformatics, 24(17):1865-1873, 2008. [doi]

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter ComplexesYang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda. ploscb, 4(10), 2008. [doi]

2007

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein DockingIoannis Ch. Paschalidis, Yang Shen, Pirooz Vakili, Sandor Vajda. tac, 52(4):664-676, 2007. [doi]

Optimizing noisy funnel-like functions on the euclidean group with applications to protein dockingYang Shen, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis. cdc 2007: 4545-4550 [doi]

2006

Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnelsIoannis Ch. Paschalidis, Yang Shen, Pirooz Vakili, Sandor Vajda. embc 2006: 5330-5333 [doi]

2005

A Semi-Definite programming-based Underestimation method for global optimization in molecular dockingIoannis Ch. Paschalidis, Yang Shen, Sandor Vajda, Pirooz Vakili. cdc 2005: 3675-3680 [doi]

PRECISE: a Database of Predicted and Consensus Interaction Sites in EnzymesShu-Hsien Sheu, David R. Lancia Jr., Karl H. Clodfelter, Melissa R. Landon, Sandor Vajda. nar, 33(Database-Issue):206-211, 2005. [doi]

2004

ClusPro: an automated docking and discrimination method for the prediction of protein complexesStephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho. bioinformatics, 20(1):45-50, 2004.

ClusPro: a fully automated algorithm for protein-protein dockingStephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho. nar, 32(Web-Server-Issue):96-99, 2004.

Consensus alignment server for reliable comparative modeling with distant templatesJahnavi C. Prasad, Sandor Vajda, Carlos J. Camacho. nar, 32(Web-Server-Issue):50-54, 2004.

2003

Improved mapping of protein binding sitesTamas Kortvelyesi, Michael Silberstein, Sheldon Dennis, Sandor Vajda. jcamd, 17(2-4):173-186, 2003.

Consensus alignment for reliable framework prediction in homology modelingJahnavi C. Prasad, Stephen R. Comeau, Sandor Vajda, Carlos J. Camacho. bioinformatics, 19(13):1682-1691, 2003.

Homology Modeling of Proteins Using Multiple Models and Consensus Sequence AlignmentJahnavi C. Prasad, Michael Silberstein, Carlos J. Camacho, Sandor Vajda. wabi 2003: 389-401 [doi]

2002

Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteinsSheldon Dennis, Sandor Vajda. jcc, 23(3):319-334, 2002. [doi]

1999

Computational problems in cell biologyCharles DeLisi, Sandor Vajda. cse, 1(3):26-32, 1999. [doi]

1996

Peptide docking using dynamic programmingKamalakar Gulukota, Sandor Vajda, Charles DeLisi. jcc, 17(4):418-428, 1996. [doi]

1994

Finite-State and Reduced-Parameter Representations of Protein Backbone ConformationsLjubomir J. Buturovic, Temple F. Smith, Sandor Vajda. jcc, 15(3):300-312, 1994.

1993

Loop closure via bond scaling and relaxationQiang Zheng, Rakefet Rosenfeld, Sandor Vajda, Charles DeLisi. jcc, 14(5):556-565, 1993. [doi]

1987

Direct and indirect least squares methods in continuous-time parameter estimationSandor Vajda, P. Valko, K. R. Godfrey. automatica, 23(6):707-718, 1987. [doi]

1984

An extended ode solver for sensitivity calculationsP. Valko, Sandor Vajda. CANDC, 8(4):255-271, 1984. [doi]

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