An extended ode solver for sensitivity calculations. - P. Valkó; Sandor Vajda (Comput. Chem., 1984)

Direct and indirect least squares methods in continuous-time parameter estimation. - Sandor Vajda; P. Valkó; Keith R. Godfrey (Autom., 1987)

Loop closure via bond scaling and relaxation. - Qiang Zheng; Rakefet Rosenfeld; Sandor Vajda; Charles DeLisi (J. Comput. Chem., 1993)

Finite-State and Reduced-Parameter Representations of Protein Backbone Conformations. - Ljubomir J. Buturovic; Temple F. Smith; Sandor Vajda (J. Comput. Chem., 1994)

Peptide docking using dynamic programming. - Kamalakar Gulukota; Sandor Vajda; Charles DeLisi (J. Comput. Chem., 1996)

Computational problems in cell biology. - Charles DeLisi; Sandor Vajda (Comput. Sci. Eng., 1999)

Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins. - Sheldon Dennis; Sandor Vajda (J. Comput. Chem., 2002)

Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment. - Jahnavi C. Prasad; Michael Silberstein; Carlos J. Camacho; Sandor Vajda (WABI, 2003)

Consensus alignment for reliable framework prediction in homology modeling. - Jahnavi C. Prasad; Stephen R. Comeau; Sandor Vajda; Carlos J. Camacho (Bioinform., 2003)

Improved mapping of protein binding sites. - Tamas Kortvelyesi; Michael Silberstein; Sheldon Dennis; Sandor Vajda (J. Comput. Aided Mol. Des., 2003)

ClusPro: an automated docking and discrimination method for the prediction of protein complexes. - Stephen R. Comeau; David W. Gatchell; Sandor Vajda; Carlos J. Camacho (Bioinform., 2004)

ClusPro: a fully automated algorithm for protein-protein docking. - Stephen R. Comeau; David W. Gatchell; Sandor Vajda; Carlos J. Camacho (Nucleic Acids Res., 2004)

Consensus alignment server for reliable comparative modeling with distant templates. - Jahnavi C. Prasad; Sandor Vajda; Carlos J. Camacho (Nucleic Acids Res., 2004)

A Semi-Definite programming-based Underestimation method for global optimization in molecular docking. - Ioannis Ch. Paschalidis; Yang Shen 001; Sandor Vajda; Pirooz Vakili (CDC/ECC, 2005)

PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. - Shu-Hsien Sheu; David R. Lancia Jr.; Karl H. Clodfelter; Melissa R. Landon; Sandor Vajda (Nucleic Acids Res., 2005)

Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. - Ioannis Ch. Paschalidis; Yang Shen 001; Pirooz Vakili; Sandor Vajda (EMBC, 2006)

Optimizing noisy funnel-like functions on the euclidean group with applications to protein docking. - Yang Shen 001; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis (CDC, 2007)

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking. - Ioannis Ch. Paschalidis; Yang Shen 001; Pirooz Vakili; Sandor Vajda (IEEE Trans. Autom. Control., 2007)

Clustering versus Scoring for the Identification of Near-Native Poses in Protein-Ligand Docking. - Taner Kaya; Dima Kozakov; Sandor Vajda (BIOCOMP, 2008)

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. - David W. Ritchie; Dima Kozakov; Sandor Vajda (Bioinform., 2008)

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes. - Yang Shen 001; Ioannis Ch. Paschalidis; Pirooz Vakili; Sandor Vajda (PLoS Comput. Biol., 2008)

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. - Ryan Brenke; Dima Kozakov; Gwo-Yu Chuang; Dmitri Beglov; David R. Hall; Melissa R. Landon; Carla Mattos; Sandor Vajda (Bioinform., 2009)

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. - 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; et al. (J. Comput. Aided Mol. Des., 2009)

A new approach to rigid body minimization with application to molecular docking. - Hanieh Mirzaei; Dima Kozakov; Dmitri Beglov; Ioannis Ch. Paschalidis; Sandor Vajda; Pirooz Vakili (CDC, 2012)

A message passing approach to Side Chain Positioning with applications in protein docking refinement. - Mohammad Moghadasi; Dima Kozakov; Artem B. Mamonov; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis (CDC, 2012)

Application of asymmetric statistical potentials to antibody-protein docking. - Ryan Brenke; David R. Hall; Gwo-Yu Chuang; Stephen R. Comeau; Tanggis Bohnuud; Dmitri Beglov; Ora Schueler-Furman; Sandor Vajda; Dima Kozakov (Bioinform., 2012)

FTSite: high accuracy detection of ligand binding sites on unbound protein structures. - Chi-Ho Ngan; David R. Hall; Brandon S. Zerbe; Laurie E. Grove; Dima Kozakov; Sandor Vajda (Bioinform., 2012)

Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery. - David R. Hall; Chi-Ho Ngan; Brandon S. Zerbe; Dima Kozakov; Sandor Vajda (J. Chem. Inf. Model., 2012)

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces. - Brandon S. Zerbe; David R. Hall; Sandor Vajda; Adrian Whitty; Dima Kozakov (J. Chem. Inf. Model., 2012)

FTMAP: extended protein mapping with user-selected probe molecules. - Chi-Ho Ngan; Tanggis Bohnuud; Scott E. Mottarella; Dmitri Beglov; Elizabeth A. Villar; David R. Hall; Dima Kozakov; Sandor Vajda (Nucleic Acids Res., 2012)

Flexible refinement of protein-ligand docking on manifolds. - Hanieh Mirzaei; Elizabeth A. Villar; Scott E. Mottarella; Dmitri Beglov; Ioannis Ch. Paschalidis; Sandor Vajda; Dima Kozakov; Pirooz Vakili (CDC, 2013)

A new distributed algorithm for side-chain positioning in the process of protein docking. - Mohammad Moghadasi; Dima Kozakov; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis (CDC, 2013)

FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. - Laurie E. Grove; David R. Hall; Dmitri Beglov; Sandor Vajda; Dima Kozakov (Bioinform., 2013)

A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking. - Feng Nan; Mohammad Moghadasi; Pirooz Vakili; Sandor Vajda; Dima Kozakov; Ioannis Ch. Paschalidis (CDC, 2014)

Optimization on the space of rigid and flexible motions: An alternative manifold optimization approach. - Pirooz Vakili; Hanieh Mirzaei; Shahrooz Zarbafian; Ioannis Ch. Paschalidis; Dima Kozakov; Sandor Vajda (CDC, 2014)

Docking Server for the Identification of Heparin Binding Sites on Proteins. - Scott E. Mottarella; Dmitri Beglov; Natalia Beglova; Matthew A. Nugent; Dima Kozakov; Sandor Vajda (J. Chem. Inf. Model., 2014)

Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces. - Tanggis Bohnuud; Dima Kozakov; Sandor Vajda (PLoS Comput. Biol., 2014)

Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro. - Bing Xia; Artem B. Mamonov; Seppe Leysen; Karen N. Allen; Sergei V. Strelkov; Ioannis Ch. Paschalidis; Sandor Vajda; Dima Kozakov (J. Comput. Chem., 2015)

The Impact of Side-Chain Packing on Protein Docking Refinement. - Mohammad Moghadasi; Hanieh Mirzaei; Artem B. Mamonov; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis; Dima Kozakov (J. Chem. Inf. Model., 2015)

Accounting for pairwise distance restraints in FFT-based protein-protein docking. - Bing Xia; Sandor Vajda; Dima Kozakov (Bioinform., 2016)

Focused grid-based resampling for protein docking and mapping. - Artem B. Mamonov; Mohammad Moghadasi; Hanieh Mirzaei; Shahrooz Zarbafian; Laurie E. Grove; Tanggis Bohnuud; Pirooz Vakili; Ioannis Ch. Paschalidis; Sandor Vajda; Dima Kozakov (J. Comput. Chem., 2016)

Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. - Amanda E. Wakefield; Christine Yueh; Dmitri Beglov; Marcelo Santos Castilho; Dima Kozakov; György M. Keserü; Adrian Whitty; Sandor Vajda (J. Chem. Inf. Model., 2020)

Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors. - Amanda E. Wakefield; Dávid Bajusz; Dima Kozakov; György M. Keserü; Sandor Vajda (J. Chem. Inf. Model., 2022)

Improved prediction of MHC-peptide binding using protein language models. - Nasser Hashemi; Boran Hao; Mikhail Ignatov; Ioannis Ch. Paschalidis; Pirooz Vakili; Sandor Vajda; Dima Kozakov (Frontiers Bioinform., 2023)

Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. - Ayse A. Bekar-Cesaretli; Omeir Khan; Thu Nguyen; Dima Kozakov; Diane Joseph-McCarthy; Sandor Vajda (J. Chem. Inf. Model., 2024)

Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. - Omeir Khan; George Jones; Maria Lazou; Diane Joseph-McCarthy; Dima Kozakov; Dmitri Beglov; Sandor Vajda (J. Chem. Inf. Model., 2024)