Lista de obras - Sandor Vajda - Dominio Público Uruguay

A New Approach to Rigid Body Minimization with Application to Molecular Docking

artículo científico publicado en 2012

A Streptavidin Mutant Useful for Directed Immobilization on Solid Surfaces ⬇️

artículo científico publicado el 1 de noviembre de 2001

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

artículo científico publicado en 2014

A benchmark testing ground for integrating homology modeling and protein docking

artículo científico publicado en 2016

A membrane model for cytosolic calcium oscillations. A study using Xenopus oocytes

artículo científico publicado en 1992

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

Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro

artículo científico publicado en 2015

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

artículo científico publicado en 2016

Algorithms for computational solvent mapping of proteins ⬇️

artículo científico publicado el 15 de mayo de 2003

Analysis of protein binding sites by computational solvent mapping

artículo científico publicado en 2012

Analysis of tractable allosteric sites in G protein-coupled receptors

artículo científico publicado en 2019

Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery

scientific article published on 08 December 2020

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

artículo científico publicado en 2009

CAPRI: a Critical Assessment of PRedicted Interactions

artículo científico publicado en 2003

Classification of protein complexes based on docking difficulty

artículo científico publicado en 2005

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

scientific article published on 06 March 2020

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

artículo científico publicado en 2016

ClusPro: performance in CAPRI rounds 6-11 and the new server

artículo científico publicado en 2007

Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns.

artículo científico publicado en 2005

Combination of scoring functions improves discrimination in protein-protein docking

artículo científico publicado en 2003

Computational Screening of Phthalate Monoesters for Binding to PPARγ

artículo científico publicado en 2006

Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identify the Functional Catalytic Core

artículo científico publicado en 2015

Convergence and combination of methods in protein-protein docking

scientific article published on 25 March 2009

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

artículo científico publicado en 2008

Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1

scientific article published on 06 February 2019

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

artículo científico publicado en 2008

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

artículo científico publicado en 2007

Dynamical view of the positions of key side chains in protein-protein recognition

artículo científico publicado en 2001

Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies

article

Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors

artículo científico publicado en 1996

Empirical free energy calculation: comparison to calorimetric data

artículo científico publicado en 1997

Empirical potentials and functions for protein folding and binding.

artículo científico publicado en 1997

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

artículo científico publicado en 2007

Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces

artículo científico publicado en 2014

Exploring the binding sites of the haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10.

artículo científico publicado en 2007

Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments

artículo científico publicado en 1995

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

artículo científico publicado en 2013

Finite-state and reduced-parameter representations of protein backbone conformations

Flexible Refinement of Protein-Ligand Docking on Manifolds

artículo científico publicado en 2013

Flexible docking of peptides to class I major-histocompatibility-complex receptors ⬇️

artículo científico publicado el 1 de marzo de 1995

Focused grid-based resampling for protein docking and mapping

artículo científico publicado en 2016

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

artículo científico publicado en 2009

Fragments and hot spots in drug discovery.

artículo científico publicado en 2015

Free energy landscapes of encounter complexes in protein-protein association

artículo científico publicado en 1999

Genetic engineering of streptavidin, a versatile affinity tag ⬇️

artículo científico publicado el 11 de septiembre de 1998

Identification of substrate binding sites in enzymes by computational solvent mapping.

artículo científico publicado en 2003

Indistinguishability for a class of nonlinear compartmental models

artículo científico publicado en 1994

Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2)

scientific article published on 02 January 2020

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases

scientific article published on 05 July 2019

Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery

artículo científico publicado en 2015

Loop closure via bond scaling and relaxation

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

artículo científico publicado en 2011

Modeling of protein interactions in genomes

artículo científico publicado en 2002

New Frontiers in Druggability

artículo científico publicado en 2015

New additions to the ClusPro server motivated by CAPRI.

artículo científico publicado en 2016

Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.

artículo científico publicado en 2008

Numerical deconvolution using system identification methods

scientific article published on 01 February 1988

Optimal clustering for detecting near-native conformations in protein docking

artículo científico publicado en 2005

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

artículo científico publicado en 2014

Parameter space boundaries for unidentifiable compartmental models

scientific article published on 01 November 1989

Parametric sensitivity and self-similarity in thermal explosion theory

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

artículo científico publicado en 2005

Predicted and trifluoroethanol-induced α-helicity of polypeptides

artículo científico publicado en 1998

Prediction of protein complexes using empirical free energy functions

artículo científico publicado en 1996

Protein docking by the underestimation of free energy funnels in the space of encounter complexes

artículo científico publicado en 2008

Protein-protein association kinetics and protein docking.

artículo científico publicado en 2002

Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds. ⬇️

artículo científico publicado en 2016

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

artículo científico publicado en 2006

Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs

artículo científico publicado en 2016

Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme

artículo científico publicado en 2011

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

scientific article published on April 2007

Sampling and scoring: a marriage made in heaven

artículo científico publicado en 2013

Scoring docked conformations generated by rigid-body protein-protein docking

artículo científico publicado en 2000

Stimulators of translation identified during a small molecule screening campaign

artículo científico publicado en 2014

Streptavidins with intersubunit crosslinks have enhanced stability ⬇️

artículo científico publicado el 1 de agosto de 1996

Structural insights into recognition of beta2-glycoprotein I by the lipoprotein receptors.

artículo científico publicado en 2009

The ClusPro web server for protein-protein docking

artículo científico publicado en 2017

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

artículo científico publicado en 2015

The binding domain structure of retinoblastoma-binding proteins

artículo científico publicado en 1993

The local information content of the protein structural database

artículo científico publicado en 1993

Toward computational determination of peptide-receptor structure.

artículo científico publicado en 1993

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

artículo científico publicado en 2010

Why Some Targets Benefit from beyond Rule of Five Drugs

artículo científico publicado en 2019

Lista de obras de Sandor Vajda

A New Approach to Rigid Body Minimization with Application to Molecular Docking

A Streptavidin Mutant Useful for Directed Immobilization on Solid Surfaces ⬇️

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

A benchmark testing ground for integrating homology modeling and protein docking

A membrane model for cytosolic calcium oscillations. A study using Xenopus oocytes

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

Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro

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

Algorithms for computational solvent mapping of proteins ⬇️

Analysis of protein binding sites by computational solvent mapping

Analysis of tractable allosteric sites in G protein-coupled receptors

Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery

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

CAPRI: a Critical Assessment of PRedicted Interactions

Classification of protein complexes based on docking difficulty

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

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

ClusPro: performance in CAPRI rounds 6-11 and the new server

Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns.

Combination of scoring functions improves discrimination in protein-protein docking

Computational Screening of Phthalate Monoesters for Binding to PPARγ

Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identify the Functional Catalytic Core

Convergence and combination of methods in protein-protein docking

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

Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1

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

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

Dynamical view of the positions of key side chains in protein-protein recognition

Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies

Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors

Empirical free energy calculation: comparison to calorimetric data

Empirical potentials and functions for protein folding and binding.

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

Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces

Exploring the binding sites of the haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10.

Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments

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

Finite-state and reduced-parameter representations of protein backbone conformations

Flexible Refinement of Protein-Ligand Docking on Manifolds

Flexible docking of peptides to class I major-histocompatibility-complex receptors ⬇️

Focused grid-based resampling for protein docking and mapping

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

Fragments and hot spots in drug discovery.

Free energy landscapes of encounter complexes in protein-protein association

Genetic engineering of streptavidin, a versatile affinity tag ⬇️

Identification of substrate binding sites in enzymes by computational solvent mapping.

Indistinguishability for a class of nonlinear compartmental models

Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2)

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases

Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery

Loop closure via bond scaling and relaxation

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

Modeling of protein interactions in genomes

New Frontiers in Druggability

New additions to the ClusPro server motivated by CAPRI.

Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.

Numerical deconvolution using system identification methods

Optimal clustering for detecting near-native conformations in protein docking

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

Parameter space boundaries for unidentifiable compartmental models

Parametric sensitivity and self-similarity in thermal explosion theory

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

Predicted and trifluoroethanol-induced α-helicity of polypeptides

Prediction of protein complexes using empirical free energy functions

Protein docking by the underestimation of free energy funnels in the space of encounter complexes

Protein-protein association kinetics and protein docking.

Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds. ⬇️

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

Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs

Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme

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

Sampling and scoring: a marriage made in heaven

Scoring docked conformations generated by rigid-body protein-protein docking

Stimulators of translation identified during a small molecule screening campaign

Streptavidins with intersubunit crosslinks have enhanced stability ⬇️

Structural insights into recognition of beta2-glycoprotein I by the lipoprotein receptors.

The ClusPro web server for protein-protein docking

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

The binding domain structure of retinoblastoma-binding proteins