Sandor Vajda - RankMe

47 papers C 1Journal 36Unranked 10

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Impact of Protein Conformational Diversity on Structure-Based Prediction of Druggability. J. Chem. Inf. Model. Ayse A. Bekar-Cesaretli, Shray Vats, Adrian Whitty, Dima Kozakov, Diane Joseph-McCarthy, Sandor Vajda
2024	J	`jnl`	Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. J. Chem. Inf. Model. Ayse A. Bekar-Cesaretli, Omeir Khan, Thu Nguyen, Dima Kozakov, Diane Joseph-McCarthy, Sandor Vajda
2024	J	`jnl`	Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. J. Chem. Inf. Model. Omeir Khan, George Jones, Maria Lazou, Diane Joseph-McCarthy, Dima Kozakov, Dmitri Beglov, Sandor Vajda
2023	J	`jnl`	Improved prediction of MHC-peptide binding using protein language models. Frontiers Bioinform. Nasser Hashemi, Boran Hao, Mikhail Ignatov, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda, Dima Kozakov
2022	J	`jnl`	Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors. J. Chem. Inf. Model. Amanda E. Wakefield, Dávid Bajusz, Dima Kozakov, György M. Keserü, Sandor Vajda
2020	J	`jnl`	Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. J. Chem. Inf. Model. Amanda E. Wakefield, Christine Yueh, Dmitri Beglov, Marcelo Santos Castilho, Dima Kozakov, György M. Keserü, Adrian Whitty, Sandor Vajda
2016	J	`jnl`	Accounting for pairwise distance restraints in FFT-based protein-protein docking. Bioinform. Bing Xia, Sandor Vajda, Dima Kozakov
2016	J	`jnl`	Focused grid-based resampling for protein docking and mapping. J. Comput. Chem. Artem B. Mamonov, Mohammad Moghadasi, Hanieh Mirzaei, Shahrooz Zarbafian, Laurie E. Grove, Tanggis Bohnuud, Pirooz Vakili, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov
2015	J	`jnl`	Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro. J. Comput. Chem. Bing Xia, Artem B. Mamonov, Seppe Leysen, Karen N. Allen, Sergei V. Strelkov, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov
2015	J	`jnl`	The Impact of Side-Chain Packing on Protein Docking Refinement. J. Chem. Inf. Model. Mohammad Moghadasi, Hanieh Mirzaei, Artem B. Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis, Dima Kozakov
2014	—	`conf`	A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking. CDC Feng Nan, Mohammad Moghadasi, Pirooz Vakili, Sandor Vajda, Dima Kozakov, Ioannis Ch. Paschalidis
2014	J	`jnl`	Docking Server for the Identification of Heparin Binding Sites on Proteins. J. Chem. Inf. Model. Scott E. Mottarella, Dmitri Beglov, Natalia Beglova, Matthew A. Nugent, Dima Kozakov, Sandor Vajda
2014	J	`jnl`	Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces. PLoS Comput. Biol. Tanggis Bohnuud, Dima Kozakov, Sandor Vajda
2014	—	`conf`	Optimization on the space of rigid and flexible motions: An alternative manifold optimization approach. CDC Pirooz Vakili, Hanieh Mirzaei, Shahrooz Zarbafian, Ioannis Ch. Paschalidis, Dima Kozakov, Sandor Vajda
2013	—	`conf`	A new distributed algorithm for side-chain positioning in the process of protein docking. CDC Mohammad Moghadasi, Dima Kozakov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis
2013	J	`jnl`	FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. Bioinform. Laurie E. Grove, David R. Hall, Dmitri Beglov, Sandor Vajda, Dima Kozakov
2013	—	`conf`	Flexible refinement of protein-ligand docking on manifolds. CDC Hanieh Mirzaei, Elizabeth A. Villar, Scott E. Mottarella, Dmitri Beglov, Ioannis Ch. Paschalidis, Sandor Vajda, Dima Kozakov, Pirooz Vakili
2012	—	`conf`	A message passing approach to Side Chain Positioning with applications in protein docking refinement. CDC Mohammad Moghadasi, Dima Kozakov, Artem B. Mamonov, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis
2012	—	`conf`	A new approach to rigid body minimization with application to molecular docking. CDC Hanieh Mirzaei, Dima Kozakov, Dmitri Beglov, Ioannis Ch. Paschalidis, Sandor Vajda, Pirooz Vakili
2012	J	`jnl`	Application of asymmetric statistical potentials to antibody-protein docking. Bioinform. Ryan Brenke, David R. Hall, Gwo-Yu Chuang, Stephen R. Comeau, Tanggis Bohnuud, Dmitri Beglov, Ora Schueler-Furman, Sandor Vajda, Dima Kozakov
2012	J	`jnl`	FTMAP: extended protein mapping with user-selected probe molecules. Nucleic Acids Res. Chi-Ho Ngan, Tanggis Bohnuud, Scott E. Mottarella, Dmitri Beglov, Elizabeth A. Villar, David R. Hall, Dima Kozakov, Sandor Vajda
2012	J	`jnl`	FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinform. Chi-Ho Ngan, David R. Hall, Brandon S. Zerbe, Laurie E. Grove, Dima Kozakov, Sandor Vajda
2012	J	`jnl`	Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery. J. Chem. Inf. Model. David R. Hall, Chi-Ho Ngan, Brandon S. Zerbe, Dima Kozakov, Sandor Vajda
2012	J	`jnl`	Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces. J. Chem. Inf. Model. Brandon S. Zerbe, David R. Hall, Sandor Vajda, Adrian Whitty, Dima Kozakov
2009	J	`jnl`	Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. J. Comput. Aided Mol. Des. 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
2009	J	`jnl`	Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinform. Ryan Brenke, Dima Kozakov, Gwo-Yu Chuang, Dmitri Beglov, David R. Hall, Melissa R. Landon, Carla Mattos, Sandor Vajda
2008	J	`jnl`	Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinform. David W. Ritchie, Dima Kozakov, Sandor Vajda
2008	—	`conf`	Clustering versus Scoring for the Identification of Near-Native Poses in Protein-Ligand Docking. BIOCOMP Taner Kaya, Dima Kozakov, Sandor Vajda
2008	J	`jnl`	Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes. PLoS Comput. Biol. Yang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda
2007	—	`conf`	Optimizing noisy funnel-like functions on the euclidean group with applications to protein docking. CDC Yang Shen, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis
2007	J	`jnl`	SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking. IEEE Trans. Autom. Control. Ioannis Ch. Paschalidis, Yang Shen, Pirooz Vakili, Sandor Vajda
2006	—	`conf`	Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. EMBC Ioannis Ch. Paschalidis, Yang Shen, Pirooz Vakili, Sandor Vajda
2005	—	`conf`	A Semi-Definite programming-based Underestimation method for global optimization in molecular docking. CDC/ECC Ioannis Ch. Paschalidis, Yang Shen, Sandor Vajda, Pirooz Vakili
2005	J	`jnl`	PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. Nucleic Acids Res. Shu-Hsien Sheu, David R. Lancia Jr., Karl H. Clodfelter, Melissa R. Landon, Sandor Vajda
2004	J	`jnl`	ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res. Stephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho
2004	J	`jnl`	ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinform. Stephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho
2004	J	`jnl`	Consensus alignment server for reliable comparative modeling with distant templates. Nucleic Acids Res. Jahnavi C. Prasad, Sandor Vajda, Carlos J. Camacho
2003	J	`jnl`	Consensus alignment for reliable framework prediction in homology modeling. Bioinform. Jahnavi C. Prasad, Stephen R. Comeau, Sandor Vajda, Carlos J. Camacho
2003	C	`conf`	Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment. WABI Jahnavi C. Prasad, Michael Silberstein, Carlos J. Camacho, Sandor Vajda
2003	J	`jnl`	Improved mapping of protein binding sites. J. Comput. Aided Mol. Des. Tamas Kortvelyesi, Michael Silberstein, Sheldon Dennis, Sandor Vajda
2002	J	`jnl`	Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins. J. Comput. Chem. Sheldon Dennis, Sandor Vajda
1999	J	`jnl`	Computational problems in cell biology. Comput. Sci. Eng. Charles DeLisi, Sandor Vajda
1996	J	`jnl`	Peptide docking using dynamic programming. J. Comput. Chem. Kamalakar Gulukota, Sandor Vajda, Charles DeLisi
1994	J	`jnl`	Finite-State and Reduced-Parameter Representations of Protein Backbone Conformations. J. Comput. Chem. Ljubomir J. Buturovic, Temple F. Smith, Sandor Vajda
1993	J	`jnl`	Loop closure via bond scaling and relaxation. J. Comput. Chem. Qiang Zheng, Rakefet Rosenfeld, Sandor Vajda, Charles DeLisi
1987	J	`jnl`	Direct and indirect least squares methods in continuous-time parameter estimation. Autom. Sandor Vajda, P. Valkó, Keith R. Godfrey
1984	J	`jnl`	An extended ode solver for sensitivity calculations. Comput. Chem. P. Valkó, Sandor Vajda