Sandor Vajda

Publication Activity (10 Years)

Years Active: 1984-2024
Publications (10 Years): 7

Top Topics

Mass Spectrometry

Top Venues

J. Chem. Inf. Model.

J. Comput. Chem.

Publications

Ayse A. Bekar-Cesaretli, Omeir Khan, Thu Nguyen, Dima Kozakov, Diane Joseph-Mccarthy, Sandor Vajda
Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. J. Chem. Inf. Model. 64 (3) (2024)
Omeir Khan, George Jones, Maria Lazou, Diane Joseph-McCarthy, Dima Kozakov, Dmitri Beglov, Sandor Vajda
Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. J. Chem. Inf. Model. 64 (6) (2024)
Nasser Hashemi, Boran Hao, Mikhail Ignatov, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda, Dima Kozakov
Improved prediction of MHC-peptide binding using protein language models. Frontiers Bioinform. 3 (2023)
Amanda E. Wakefield, Dávid Bajusz, Dima Kozakov, György M. Keserü, Sandor Vajda
Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors. J. Chem. Inf. Model. 62 (20) (2022)
Amanda E. Wakefield, Christine Yueh, Dmitri Beglov, Marcelo Santos Castilho, Dima Kozakov, György M. Keserü, Adrian Whitty, Sandor Vajda
Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. J. Chem. Inf. Model. 60 (12) (2020)
Artem B. Mamonov, Mohammad Moghadasi, Hanieh Mirzaei, Shahrooz Zarbafian, Laurie E. Grove, Tanggis Bohnuud, Pirooz Vakili, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov
Focused grid-based resampling for protein docking and mapping. J. Comput. Chem. 37 (11) (2016)
Bing Xia, Sandor Vajda, Dima Kozakov
Accounting for pairwise distance restraints in FFT-based protein-protein docking. Bioinform. 32 (21) (2016)
Bing Xia, Artem B. Mamonov, Seppe Leysen, Karen N. Allen, Sergei V. Strelkov, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov
Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro. J. Comput. Chem. 36 (20) (2015)
Mohammad Moghadasi, Hanieh Mirzaei, Artem B. Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis, Dima Kozakov
The Impact of Side-Chain Packing on Protein Docking Refinement. J. Chem. Inf. Model. 55 (4) (2015)
Tanggis Bohnuud, Dima Kozakov, Sandor Vajda
Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces. PLoS Comput. Biol. 10 (10) (2014)
Feng Nan, Mohammad Moghadasi, Pirooz Vakili, Sandor Vajda, Dima Kozakov, Ioannis Ch. Paschalidis
A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking. CDC (2014)
Scott E. Mottarella, Dmitri Beglov, Natalia Beglova, Matthew A. Nugent, Dima Kozakov, Sandor Vajda
Docking Server for the Identification of Heparin Binding Sites on Proteins. J. Chem. Inf. Model. 54 (7) (2014)
Pirooz Vakili, Hanieh Mirzaei, Shahrooz Zarbafian, Ioannis Ch. Paschalidis, Dima Kozakov, Sandor Vajda
Optimization on the space of rigid and flexible motions: An alternative manifold optimization approach. CDC (2014)
Mohammad Moghadasi, Dima Kozakov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis
A new distributed algorithm for side-chain positioning in the process of protein docking. CDC (2013)
Hanieh Mirzaei, Elizabeth A. Villar, Scott E. Mottarella, Dmitri Beglov, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov, Pirooz Vakili
Flexible refinement of protein-ligand docking on manifolds. CDC (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. Bioinform. 29 (9) (2013)
Chi-Ho Ngan, Tanggis Bohnuud, Scott E. Mottarella, Dmitri Beglov, Elizabeth A. Villar, David R. Hall, Dima Kozakov, Sandor Vajda
FTMAP: extended protein mapping with user-selected probe molecules. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Hanieh Mirzaei, Dima Kozakov, Dmitri Beglov, Ioannis Ch. Paschalidis, Sandor Vajda, Pirooz Vakili
A new approach to rigid body minimization with application to molecular docking. CDC (2012)
Ryan Brenke, David R. Hall, Gwo-Yu Chuang, Stephen R. Comeau, Tanggis Bohnuud, Dmitri Beglov, Ora Schueler-Furman, Sandor Vajda, Dima Kozakov
Application of asymmetric statistical potentials to antibody-protein docking. Bioinform. 28 (20) (2012)
Mohammad Moghadasi, Dima Kozakov, Artem B. Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis
A message passing approach to Side Chain Positioning with applications in protein docking refinement. CDC (2012)
David R. Hall, Chi-Ho Ngan, Brandon S. Zerbe, Dima Kozakov, Sandor Vajda
Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery. J. Chem. Inf. Model. 52 (1) (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. J. Chem. Inf. Model. 52 (8) (2012)
Chi-Ho Ngan, David R. Hall, Brandon S. Zerbe, Laurie E. Grove, Dima Kozakov, Sandor Vajda
FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinform. 28 (2) (2012)
Melissa R. Landon, Raquel L. Lieberman, Quyen Q. Hoang, Shulin Ju, Jose M. M. Caaveiro, Susan D. Orwig, Dima Kozakov, Ryan Brenke, Gwo-Yu Chuang, Dmitri Beglov, Sandor Vajda, Gregory A. Petsko, Dagmar Ringe
Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. J. Comput. Aided Mol. Des. 23 (8) (2009)
Ryan Brenke, Dima Kozakov, Gwo-Yu Chuang, Dmitri Beglov, David R. Hall, Melissa R. Landon, Carla Mattos, Sandor Vajda
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinform. 25 (5) (2009)
Taner Kaya, Dima Kozakov, Sandor Vajda
Clustering versus Scoring for the Identification of Near-Native Poses in Protein-Ligand Docking. BIOCOMP (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 Comput. Biol. 4 (10) (2008)
David W. Ritchie, Dima Kozakov, Sandor Vajda
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinform. 24 (17) (2008)
Ioannis Ch. Paschalidis, Yang Shen, Pirooz Vakili, Sandor Vajda
SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking. IEEE Trans. Autom. Control. 52 (4) (2007)
Yang Shen, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis
Optimizing noisy funnel-like functions on the euclidean group with applications to protein docking. CDC (2007)
Ioannis Ch. Paschalidis, Yang Shen, Pirooz Vakili, Sandor Vajda
Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. EMBC (2006)
Shu-Hsien Sheu, David R. Lancia Jr., Karl H. Clodfelter, Melissa R. Landon, Sandor Vajda
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. Nucleic Acids Res. 33 (Database-Issue) (2005)
Ioannis Ch. Paschalidis, Yang Shen, Sandor Vajda, Pirooz Vakili
A Semi-Definite programming-based Underestimation method for global optimization in molecular docking. CDC/ECC (2005)
Stephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho
ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Jahnavi C. Prasad, Sandor Vajda, Carlos J. Camacho
Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Res. 32 (Web-Server-Issue) (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. Bioinform. 20 (1) (2004)
Jahnavi C. Prasad, Michael Silberstein, Carlos J. Camacho, Sandor Vajda
Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment. WABI (2003)
Tamas Kortvelyesi, Michael Silberstein, Sheldon Dennis, Sandor Vajda
Improved mapping of protein binding sites. J. Comput. Aided Mol. Des. 17 (2-4) (2003)
Jahnavi C. Prasad, Stephen R. Comeau, Sandor Vajda, Carlos J. Camacho
Consensus alignment for reliable framework prediction in homology modeling. Bioinform. 19 (13) (2003)
Sheldon Dennis, Sandor Vajda
Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins. J. Comput. Chem. 23 (3) (2002)
Charles DeLisi, Sandor Vajda
Computational problems in cell biology. Comput. Sci. Eng. 1 (3) (1999)
Kamalakar Gulukota, Sandor Vajda, Charles DeLisi
Peptide docking using dynamic programming. J. Comput. Chem. 17 (4) (1996)
Ljubomir J. Buturovic, Temple F. Smith, Sandor Vajda
Finite-State and Reduced-Parameter Representations of Protein Backbone Conformations. J. Comput. Chem. 15 (3) (1994)
Qiang Zheng, Rakefet Rosenfeld, Sandor Vajda, Charles DeLisi
Loop closure via bond scaling and relaxation. J. Comput. Chem. 14 (5) (1993)
Sandor Vajda, P. Valkó, Keith R. Godfrey
Direct and indirect least squares methods in continuous-time parameter estimation. Autom. 23 (6) (1987)
P. Valkó, Sandor Vajda
An extended ode solver for sensitivity calculations. Comput. Chem. 8 (4) (1984)