Sandor Vajda

发表

ClusPro: Performance in CAPRI rounds 6–11 and the new server

Stephen R Comeau, Dima Kozakov, Ryan Brenke, 2007, Proteins.

ClusPro LigTBM: Automated Template-Based Small Molecule Docking.

Andrey Alekseenko, Dima Kozakov, Sandor Vajda, 2019, Journal of molecular biology.

Clustering versus Scoring for the Identification of Near-Native Poses in Protein-Ligand Docking

Dima Kozakov, Sandor Vajda, Taner Kaya, 2008, BIOCOMP.

Modeling of protein interactions in genomes

Sandor Vajda, Michael J E Sternberg, Ilya A Vakser, 2002, Proteins.

Template‐based modeling by ClusPro in CASP13 and the potential for using co‐evolutionary information in docking

Andrey Alekseenko, Dima Kozakov, Dmitri Beglov, 2019, Proteins.

PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes

Sandor Vajda, Shu-Hsien Sheu, David R. Lancia, 2005, Nucleic Acids Res..

Accounting for pairwise distance restraints in FFT-based protein-protein docking

Bing Xia, Dima Kozakov, Sandor Vajda, 2016, Bioinform..

Optimizing noisy funnel-like functions on the euclidean group with applications to protein docking

Ioannis Ch. Paschalidis, Yang Shen, Sandor Vajda, 2007, 2007 46th IEEE Conference on Decision and Control.

Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment

Daisuke Kihara, Keehyoung Joo, Daisuke Kuroda, 2016, Proteins.

ClusPro: a fully automated algorithm for protein-protein docking

Sandor Vajda, Carlos J. Camacho, Stephen R. Comeau, 2004, Nucleic Acids Res..

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes

Ioannis Ch. Paschalidis, Yang Shen, Sandor Vajda, 2008, PLoS Comput. Biol..

Performance and Its Limits in Rigid Body Protein-Protein Docking.

Dima Kozakov, Sandor Vajda, Kathryn A Porter, 2020, Structure.

Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment

Sandor Vajda, Michael Silberstein, Carlos J. Camacho, 2003, WABI.

The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2015, Nature Protocols.

Classification of protein complexes based on docking difficulty

Sandor Vajda, S. Vajda, 2005, Proteins.

The ClusPro web server for protein–protein docking

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2017, Nature Protocols.

What method to use for protein-protein docking?

Dima Kozakov, Sandor Vajda, Kathryn A Porter, 2019, Current opinion in structural biology.

Outcome of a workshop on applications of protein models in biomedical research.

Roland L Dunbrack, Roland L. Dunbrack, Andrej Sali, 2009, Structure.

Optimization on the space of rigid and flexible motions: An alternative manifold optimization approach

Ioannis Ch. Paschalidis, Dima Kozakov, Sandor Vajda, 2014, 53rd IEEE Conference on Decision and Control.

Mapping global protein contacts

Sandor Vajda, Andrew Emili, 2019, Science.

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2009, J. Comput. Aided Mol. Des..

How good is automated protein docking?

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2013, Proteins.

Focused grid‐based resampling for protein docking and mapping

Ioannis Ch. Paschalidis, Mohammad Moghadasi, Dima Kozakov, 2016, J. Comput. Chem..

Peptide docking using dynamic programming

Charles DeLisi, Sandor Vajda, Kamalakar Gulukota, 1996 .

Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19

Stephen R Comeau, Dima Kozakov, Ryan Brenke, 2010, Proteins.

Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins

Sandor Vajda, Sheldon Dennis, 2002, J. Comput. Chem..

Author response for "ClusPro in rounds 38‐45 of CAPRI: Toward combining template‐based methods with free docking"

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2019 .

An Adaptive Branch-and-Bound Minimization Method Based on Dynamic Programming

Charles DeLisi, Sandor Vajda, C. DeLisi, 1994 .

Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces

Dima Kozakov, Sandor Vajda, Tanggis Bohnuud, 2014, PLoS Comput. Biol..

The Impact of Side-Chain Packing on Protein Docking Refinement

Ioannis Ch. Paschalidis, Mohammad Moghadasi, Dima Kozakov, 2015, J. Chem. Inf. Model..

Consensus alignment for reliable framework prediction in homology modeling

Sandor Vajda, Carlos J. Camacho, Stephen R. Comeau, 2003, Bioinform..

Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI

Stephen R Comeau, Dima Kozakov, Ryan Brenke, 2007, Proteins.

A new distributed algorithm for side-chain positioning in the process of protein docking

Ioannis Ch. Paschalidis, Mohammad Moghadasi, Dima Kozakov, 2013, 52nd IEEE Conference on Decision and Control.

Direct and indirect least squares methods in continuous-time parameter estimation

Keith R. Godfrey, Sandor Vajda, P. Valkó, 1987, Autom..

A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking

Ioannis Ch. Paschalidis, Mohammad Moghadasi, Dima Kozakov, 2014, 53rd IEEE Conference on Decision and Control.

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Elodie Laine, Alessandra Carbone, Adam Liwo, 2019, Proteins.

Performance of the first protein docking server ClusPro in CAPRI rounds 3–5

Stephen R Comeau, Sandor Vajda, Carlos J Camacho, 2005, Proteins.

ClusPro: an automated docking and discrimination method for the prediction of protein complexes

Sandor Vajda, Carlos J. Camacho, Stephen R. Comeau, 2004, Bioinform..

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking

Ioannis Ch. Paschalidis, Yang Shen, Sandor Vajda, 2007, IEEE Transactions on Automatic Control.

A new approach to rigid body minimization with application to molecular docking

Ioannis Ch. Paschalidis, Dima Kozakov, Dmitri Beglov, 2012, 2012 IEEE 51st IEEE Conference on Decision and Control (CDC).

Consensus alignment server for reliable comparative modeling with distant templates

Sandor Vajda, Carlos J. Camacho, Jahnavi C. Prasad, 2004, Nucleic Acids Res..

Peptide docking using dynamic programming

Charles DeLisi, Sandor Vajda, Kamalakar Gulukota, 1996, J. Comput. Chem..

A benchmark testing ground for integrating homology modeling and protein docking

Zhiping Weng, Alexandre M J J Bonvin, Dima Kozakov, 2017, Proteins.

Accounting for observed small angle X‐ray scattering profile in the protein–protein docking server cluspro

Bing Xia, Ioannis Ch. Paschalidis, Dima Kozakov, 2015, J. Comput. Chem..

An extended ode solver for sensitivity calculations

Sandor Vajda, P. Valkó, S. Vajda, 1984, Comput. Chem..

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces

Dima Kozakov, Sandor Vajda, David R. Hall, 2012, J. Chem. Inf. Model..

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2009, Bioinform..

Computational problems in cell biology

Charles DeLisi, Sandor Vajda, C. DeLisi, 1999, Comput. Sci. Eng..

Improved mapping of protein binding sites

Sandor Vajda, Sheldon Dennis, Michael Silberstein, 2003, J. Comput. Aided Mol. Des..

Computational Methods to Support Fragment‐based Drug Discovery

Dima Kozakov, Sandor Vajda, Laurie E. Grove, 2016 .

FTSite: high accuracy detection of ligand binding sites on unbound protein structures

Dima Kozakov, Sandor Vajda, David R. Hall, 2012, Bioinform..

Loop closure via bond scaling and relaxation

Qiang Zheng, Charles DeLisi, Sandor Vajda, 1993, J. Comput. Chem..

Convergence and combination of methods in protein-protein docking.

Dima Kozakov, Sandor Vajda, S. Vajda, 2009, Current opinion in structural biology.

A message passing approach to Side Chain Positioning with applications in protein docking refinement

Ioannis Ch. Paschalidis, Mohammad Moghadasi, Dima Kozakov, 2012, 2012 IEEE 51st IEEE Conference on Decision and Control (CDC).

CAPRI: A Critical Assessment of PRedicted Interactions

Sandor Vajda, Michael J E Sternberg, Joël Janin, 2003, Proteins.

New additions to the ClusPro server motivated by CAPRI

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2017, Proteins.

Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery

Dima Kozakov, Sandor Vajda, David R. Hall, 2012, J. Chem. Inf. Model..

ClusPro in rounds 38 to 45 of CAPRI: Toward combining template‐based methods with free docking

Andrey Alekseenko, Dima Kozakov, Dmitri Beglov, 2020, Proteins.

FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2013, Bioinform..

FTMAP: extended protein mapping with user-selected probe molecules

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2012, Nucleic Acids Res..

Docking Server for the Identification of Heparin Binding Sites on Proteins

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2014, J. Chem. Inf. Model..

Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes

Mohammad Moghadasi, Dima Kozakov, Sandor Vajda, 2018, Scientific Reports.

Application of asymmetric statistical potentials to antibody-protein docking

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2012, Bioinform..

Sampling and scoring: A marriage made in heaven

Dima Kozakov, Sandor Vajda, David R. Hall, 2013, Proteins.

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions

David W. Ritchie, Dima Kozakov, Sandor Vajda, 2008, Bioinform..

Flexible refinement of protein-ligand docking on manifolds

Ioannis Ch. Paschalidis, Dima Kozakov, Dmitri Beglov, 2013, 52nd IEEE Conference on Decision and Control.

Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations

Ioannis Ch. Paschalidis, Mohammad Moghadasi, Dima Kozakov, 2014, Journal of chemical theory and computation.

Ligand deconstruction: Why some fragment binding positions are conserved and others are not

Dima Kozakov, Sandor Vajda, David R Hall, 2015, Proceedings of the National Academy of Sciences.

Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble

David Ozonoff, Sandor Vajda, Rommie E Amaro, 2008, Chemical biology & drug design.

Encounter complexes and dimensionality reduction in protein–protein association

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2014, eLife.

Discrimination of near‐native structures in protein–protein docking by testing the stability of local minima

Dima Kozakov, Sandor Vajda, Ora Schueler-Furman, 2008, Proteins.

Where does amantadine bind to the influenza virus M2 proton channel?

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2010, Trends in biochemical sciences.

Exploring the binding site structure of the PPAR gamma ligand-binding domain by computational solvent mapping.

Sandor Vajda, Taner Kaya, S. Sheu, 2005, Biochemistry.

Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds

Dima Kozakov, Sandor Vajda, Yaroslav Kholodov, 2016, Proceedings of the National Academy of Sciences.

Ensemble modeling of substrate binding to cytochromes P450: analysis of catalytic differences between CYP1A orthologs.

Sandor Vajda, Carlos J Camacho, Jahnavi C. Prasad, 2007, Biochemistry.

Energy Minimization on Manifolds for Docking Flexible Molecules.

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2015, Journal of chemical theory and computation.

Rigid Body Energy Minimization on Manifolds for Molecular Docking.

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2012, Journal of chemical theory and computation.

Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels

Ioannis Ch. Paschalidis, Sandor Vajda, Pirooz Vakili, 2006, 2006 International Conference of the IEEE Engineering in Medicine and Biology Society.

DARS (Decoys As the Reference State) potentials for protein-protein docking.

Stephen R Comeau, Dima Kozakov, Ryan Brenke, 2008, Biophysical journal.

Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2012, Nucleic acids research.

Computational mapping identifies the binding sites of organic solvents on proteins

Sandor Vajda, Sheldon Dennis, Tamas Kortvelyesi, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Characterization of protein-ligand interaction sites using experimental and computational methods.

Sandor Vajda, Frank Guarnieri, S. Vajda, 2006, Current opinion in drug discovery & development.

Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery.

Dima Kozakov, Sandor Vajda, David R Hall, 2015, Trends in pharmacological sciences.

Robust Identification of Binding Hot Spots Using Continuum Electrostatics: Application to Hen Egg-White Lysozyme

Dima Kozakov, Sandor Vajda, Christine Yueh, 2011, Journal of the American Chemical Society.

Analysis of binding site hot spots on the surface of Ras GTPase.

Dima Kozakov, Sandor Vajda, Carla Mattos, 2011, Journal of molecular biology.

The structural basis of pregnane X receptor binding promiscuity.

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2009, Biochemistry.

Why Some Targets Benefit from beyond Rule of Five Drugs.

Sandor Vajda, Adrian Whitty, György M Keserű, 2019, Journal of medicinal chemistry.

Optimal clustering for detecting near-native conformations in protein docking.

Dima Kozakov, Sandor Vajda, Karl H. Clodfelter, 2005, Biophysical journal.

Combination of scoring functions improves discrimination in protein–protein docking

Sandor Vajda, Jahnavi C. Prasad, S. Vajda, 2003, Proteins.

New Frontiers in Druggability.

Dima Kozakov, Sandor Vajda, David R Hall, 2015, Journal of medicinal chemistry.

ClusPro-DC: Dimer Classification by the Cluspro Server for Protein-Protein Docking.

Dima Kozakov, Sandor Vajda, Dzmitry Padhorny, 2017, Journal of molecular biology.

Identification of hot spots within druggable binding regions by computational solvent mapping of proteins.

Sandor Vajda, David R Lancia, S. Vajda, 2007, Journal of medicinal chemistry.

Algorithms for computational solvent mapping of proteins

Sandor Vajda, Sheldon Dennis, Michael Silberstein, 2003, Proteins.

How Proteins Bind Macrocycles

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2014, Nature chemical biology.

Identifiability and indistinguishability of nonlinear pharmacokinetic models

Keith R. Godfrey, Sandor Vajda, Michael J. Chapman, 1994, Journal of Pharmacokinetics and Biopharmaceutics.

Protein-protein association kinetics and protein docking.

Sandor Vajda, Carlos J Camacho, S. Vajda, 2002, Current Opinion in Structural Biology.

Exploring the structural origins of cryptic sites on proteins

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2018, Proceedings of the National Academy of Sciences.

Binding hot spots and amantadine orientation in the influenza a virus M2 proton channel.

Dima Kozakov, Ryan Brenke, Dmitri Beglov, 2009, Biophysical journal.

Blind prediction of interfacial water positions in CAPRI

Kengo Kinoshita, Haruki Nakamura, Xiaoqin Zou, 2014, Proteins.

Computational screening of phthalate monoesters for binding to PPARgamma.

Sandor Vajda, Taner Kaya, Scott C Mohr, 2006, Chemical research in toxicology.

46 Encounter complexes and dimensionality reduction in protein-protein association

Dima Kozakov, Sandor Vajda, Pirooz Vakili, 2015, Journal of biomolecular structure & dynamics.

Computational methods for functional site identification suggest a substrate access channel in transaldolase.

Sandor Vajda, Michael Silberstein, M. Silberstein, 2006, Genome informatics. International Conference on Genome Informatics.

Analysis of protein binding sites by computational solvent mapping.

Dima Kozakov, Sandor Vajda, David R Hall, 2012, Methods in molecular biology.

Minimal ensembles of side chain conformers for modeling protein–protein interactions

Roland L Dunbrack, Roland L. Dunbrack, Dima Kozakov, 2012, Proteins.