Sandor Vajda

Orcid: 0000-0003-1540-8220

According to our database1, Sandor Vajda authored at least 46 papers between 1984 and 2024.

Collaborative distances:
  • Dijkstra number2 of five.
  • Erdős number3 of four.

Timeline

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Bibliography

2024
Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites.
J. Chem. Inf. Model., 2024

Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2.
J. Chem. Inf. Model., 2024

2023
Improved prediction of MHC-peptide binding using protein language models.
Frontiers Bioinform., May, 2023

2022
Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors.
J. Chem. Inf. Model., 2022

2020
Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery.
J. Chem. Inf. Model., 2020

2016
Focused grid-based resampling for protein docking and mapping.
J. Comput. Chem., 2016

Accounting for pairwise distance restraints in FFT-based protein-protein docking.
Bioinform., 2016

2015
The Impact of Side-Chain Packing on Protein Docking Refinement.
J. Chem. Inf. Model., 2015

Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro.
J. Comput. Chem., 2015

2014
Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces.
PLoS Comput. Biol., 2014

Docking Server for the Identification of Heparin Binding Sites on Proteins.
J. Chem. Inf. Model., 2014

Optimization on the space of rigid and flexible motions: An alternative manifold optimization approach.
Proceedings of the 53rd IEEE Conference on Decision and Control, 2014

A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking.
Proceedings of the 53rd IEEE Conference on Decision and Control, 2014

2013
FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots.
Bioinform., 2013

A new distributed algorithm for side-chain positioning in the process of protein docking.
Proceedings of the 52nd IEEE Conference on Decision and Control, 2013

Flexible refinement of protein-ligand docking on manifolds.
Proceedings of the 52nd IEEE Conference on Decision and Control, 2013

2012
FTMAP: extended protein mapping with user-selected probe molecules.
Nucleic Acids Res., 2012

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces.
J. Chem. Inf. Model., 2012

Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery.
J. Chem. Inf. Model., 2012

FTSite: high accuracy detection of ligand binding sites on unbound protein structures.
Bioinform., 2012

Application of asymmetric statistical potentials to antibody-protein docking.
Bioinform., 2012

A message passing approach to Side Chain Positioning with applications in protein docking refinement.
Proceedings of the 51th IEEE Conference on Decision and Control, 2012

A new approach to rigid body minimization with application to molecular docking.
Proceedings of the 51th IEEE Conference on Decision and Control, 2012

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

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques.
Bioinform., 2009

2008
Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes.
PLoS Comput. Biol., 2008

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions.
Bioinform., 2008

Clustering versus Scoring for the Identification of Near-Native Poses in Protein-Ligand Docking.
Proceedings of the International Conference on Bioinformatics & Computational Biology, 2008

2007
SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking.
IEEE Trans. Autom. Control., 2007

Optimizing noisy funnel-like functions on the euclidean group with applications to protein docking.
Proceedings of the 46th IEEE Conference on Decision and Control, 2007

2006
Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels.
Proceedings of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, 2006

2005
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes.
Nucleic Acids Res., 2005

A Semi-Definite programming-based Underestimation method for global optimization in molecular docking.
Proceedings of the 44th IEEE IEEE Conference on Decision and Control and 8th European Control Conference Control, 2005

2004
Consensus alignment server for reliable comparative modeling with distant templates.
Nucleic Acids Res., 2004

ClusPro: a fully automated algorithm for protein-protein docking.
Nucleic Acids Res., 2004

ClusPro: an automated docking and discrimination method for the prediction of protein complexes.
Bioinform., 2004

2003
Improved mapping of protein binding sites.
J. Comput. Aided Mol. Des., 2003

Consensus alignment for reliable framework prediction in homology modeling.
Bioinform., 2003

Homology Modeling of Proteins Using Multiple Models and Consensus Sequence Alignment.
Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

2002
Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins.
J. Comput. Chem., 2002

1999
Computational problems in cell biology.
Comput. Sci. Eng., 1999

1996
Peptide docking using dynamic programming.
J. Comput. Chem., 1996

1994
Finite-State and Reduced-Parameter Representations of Protein Backbone Conformations.
J. Comput. Chem., 1994

1993
Loop closure via bond scaling and relaxation.
J. Comput. Chem., 1993

1987
Direct and indirect least squares methods in continuous-time parameter estimation.
Autom., 1987

1984
An extended ode solver for sensitivity calculations.
Comput. Chem., 1984


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