Lista de obras - Thomas Simonson - Dominio Público Uruguay

A Hybrid Monte Carlo Scheme for Multibackbone Protein Design

artículo científico publicado en 2016

A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain

artículo científico publicado en 2017

A large decoy set of protein-protein complexes produced by flexible docking

A molecular mechanics model for imatinib and imatinib:kinase binding

artículo científico publicado en 2010

A residue-pairwise generalized born scheme suitable for protein design calculations.

artículo científico publicado en 2005

Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations

artículo científico publicado en 2018

Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power

scientific article published on 09 January 2020

Adaptive landscape flattening in amino acid sequence space for the computational design of protein:peptide binding

Alchemical free energy simulations for biological complexes: powerful but temperamental....

artículo científico publicado en 2010

Ammonium scanning in an enzyme active site. The chiral specificity of aspartyl-tRNA synthetase

artículo científico publicado en 2007

An Overview of Electrostatic Free Energy Computations for Solutions and Proteins

Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens

artículo científico publicado en 2020

Binding of tetracyclines to elongation factor Tu, the Tet repressor, and the ribosome: a molecular dynamics simulation study

artículo científico publicado en 2008

Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg

scientific article published on 18 July 2018

Comparing pairwise-additive and many-body generalized Born models for acid/base calculations and protein design

artículo científico publicado en 2017

Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic

artículo científico publicado en 2016

Computational Design of the Tiam1 PDZ Domain and Its Ligand Binding

artículo científico publicado en 2017

Computational design of fully overlapping coding schemes for protein pairs and triplets

artículo científico publicado en 2017

Computational design of protein-ligand binding: modifying the specificity of asparaginyl-tRNA synthetase

artículo científico publicado en 2010

Computational protein design as a tool for fold recognition

artículo científico publicado en 2009

Computational protein design with a generalized Born solvent model: application to Asparaginyl-tRNA synthetase

artículo científico publicado en 2011

Computational protein design: software implementation, parameter optimization, and performance of a simple model

artículo científico publicado en 2008

Computational protein design: the Proteus software and selected applications

artículo científico publicado en 2013

Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition

artículo científico publicado en 2010

Computational sidechain placement and protein mutagenesis with implicit solvent models.

artículo científico publicado en 2007

Conformation of the Ras-binding domain of Raf studied by molecular dynamics and free energy simulations

artículo científico publicado en 1998

Conformational Selection by the aIF2 GTPase: A Molecular Dynamics Study of Functional Pathways

article

Conformational selection through electrostatics: Free energy simulations of gtp and gdp binding to archaeal initiation factor 2

article by Priyadarshi Satpati & Thomas Simonson published May 2012 in Proteins

Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg"

artículo científico publicado en 2019

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

artículo científico publicado en 1998

Cys(x)His(y)-Zn2+ interactions: possibilities and limitations of a simple pairwise force field

artículo científico publicado en 2005

Cys(x)His(y)-Zn2+ interactions: thiol vs. thiolate coordination

artículo científico publicado en 2002

Dielectric relaxation in an enzyme active site: molecular dynamics simulations interpreted with a macroscopic continuum model

artículo científico publicado en 2001

Dielectric relaxation in proteins: the computational perspective

artículo científico publicado en 2008

Electrostatic free energies in translational GTPases: Classic allostery and the rest

artículo científico publicado en 2014

Engineering an Mg2+ site to replace a structurally conserved arginine in the catalytic center of histidyl-tRNA synthetase by computer experiments

scientific article published on 01 August 1998

Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies

artículo científico publicado en 2017

Free energy simulations come of age: protein-ligand recognition

artículo científico publicado en 2002

Free energy simulations of a GTPase: GTP and GDP binding to archaeal initiation factor 2.

artículo científico publicado en 2011

Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase

artículo científico publicado en 2006

Full Protein Sequence Redesign with an MMGBSA Energy Function

artículo científico publicado en 2017

Gaussian fluctuations and linear response in an electron transfer protein

artículo científico publicado en 2002

Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations.

artículo científico publicado en 2008

Hybrid MC/MD for protein design

artículo científico publicado en 2020

Implicit solvent models

artículo científico publicado en 1999

Intramolecular dielectric screening in proteins.

scientific article published on April 1991

Molecular Dynamics Simulations Show That Bound Mg2+Contributes to Amino Acid and Aminoacyl Adenylate Binding Specificity in Aspartyl-tRNA Synthetase through Long Range Electrostatic Interactions

artículo científico publicado en 2006

Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site

artículo científico publicado en 2008

Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases

artículo científico publicado en 2010

Molecular mechanics models for tetracycline analogs

artículo científico publicado en 2009

Monte Carlo simulations of proteins at constant pH with generalized Born solvent, flexible sidechains, and an effective dielectric boundary

artículo científico publicado en 2013

Neutral evolution of protein-protein interactions: a computational study using simple models

artículo científico publicado en 2007

Neutral evolution of proteins: The superfunnel in sequence space and its relation to mutational robustness

Nonantibiotic properties of tetracyclines: structural basis for inhibition of secretory phospholipase A2

artículo científico publicado en 2010

Nucleotide recognition by the initiation factor aIF5B: Free energy simulations of a neoclassical GTPase

scholarly article by Thomas Simonson published in September 2012

Pairwise decomposition of an MMGBSA energy function for computational protein design

artículo científico publicado en 2014

Physics-Based Computational Protein Design: An Update

scientific article published on 10 November 2020

Polar fluctuations in proteins: molecular-dynamic studies of cytochrome c in aqueous solution

artículo científico publicado en 1996

Predicting the acid/base behavior of proteins: a constant-pH Monte Carlo approach with generalized born solvent

artículo científico publicado en 2010

Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations

artículo científico publicado en 2008

Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics

artículo científico publicado en 2016

Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculations

artículo científico publicado en 1995

Protein molecular dynamics with the generalized born/ACE solvent model

article

Protein p Ka's from Adaptive Landscape Flattening Instead of Constant-pH Simulations

scientific article published on 30 November 2018

Protein side chain conformation predictions with an MMGBSA energy function

artículo científico publicado en 2016

Protein-protein recognition: an experimental and computational study of the R89K mutation in Raf and its effect on Ras binding

artículo científico publicado en 1999

Protein: Ligand Recognition: Simple Models for Electrostatic Effects ⬇️

artículo científico publicado el 1 de enero de 2013

Protein:Ligand binding free energies: A stringent test for computational protein design

Proteus and the Design of Ligand Binding Sites

artículo científico publicado en 2016

Proton binding to proteins: a free-energy component analysis using a dielectric continuum model.

artículo científico publicado en 2005

Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.

artículo científico publicado en 2004

Protonation patterns in tetracycline:tet repressor recognition: simulations and experiments

artículo científico publicado en 2007

Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets

artículo científico publicado en 2007

Redesigning the stereospecificity of tyrosyl-tRNA synthetase

artículo científico publicado en 2015

Redox properties of cytochrome c: novel linear response and hybrid continuum-microscopic methodologies

scientific article published on 01 January 1997

Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum

artículo científico publicado en 2003

Simple models for nonpolar solvation: Parameterization and testing

artículo científico publicado en 2017

Simulating GTP:Mg and GDP:Mg with a simple force field: a structural and thermodynamic analysis

artículo científico publicado en 2012

Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations 1 1A. R. Fersht

Structure and thermodynamics of Mg:phosphate interactions in water: a simulation study

artículo científico publicado en 2014

Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.

artículo científico publicado en 2008

Tet repressor induction by tetracycline: a molecular dynamics, continuum electrostatics, and crystallographic study

artículo científico publicado en 2008

Tetracycline-tet repressor binding specificity: insights from experiments and simulations

artículo científico publicado en 2009

The << folding problem >>: can one predict the structure of proteins?

artículo científico publicado en 2005

The tetracycline: Mg2+ complex: A molecular mechanics force field

Theory and simulation: from protons to genomes

Thermodynamics of protein-peptide interactions in the ribonuclease-S system studied by molecular dynamics and free energy calculations

artículo científico publicado el 15 de septiembre de 1992

Variable Neighborhood Search with CostFunction Networks to Solve Large Computational Protein Design Problems

scientific article published on 14 November 2018

What Is the Dielectric Constant of a Protein When Its Backbone Is Fixed?

artículo científico publicado en 2013

Lista de obras de Thomas Simonson

A Hybrid Monte Carlo Scheme for Multibackbone Protein Design

A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain

A large decoy set of protein-protein complexes produced by flexible docking

A molecular mechanics model for imatinib and imatinib:kinase binding

A residue-pairwise generalized born scheme suitable for protein design calculations.

Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations

Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power

Adaptive landscape flattening in amino acid sequence space for the computational design of protein:peptide binding

Alchemical free energy simulations for biological complexes: powerful but temperamental....

Ammonium scanning in an enzyme active site. The chiral specificity of aspartyl-tRNA synthetase

An Overview of Electrostatic Free Energy Computations for Solutions and Proteins

Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens

Binding of tetracyclines to elongation factor Tu, the Tet repressor, and the ribosome: a molecular dynamics simulation study

Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg

Comparing pairwise-additive and many-body generalized Born models for acid/base calculations and protein design

Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic

Computational Design of the Tiam1 PDZ Domain and Its Ligand Binding

Computational design of fully overlapping coding schemes for protein pairs and triplets

Computational design of protein-ligand binding: modifying the specificity of asparaginyl-tRNA synthetase

Computational protein design as a tool for fold recognition

Computational protein design with a generalized Born solvent model: application to Asparaginyl-tRNA synthetase

Computational protein design: software implementation, parameter optimization, and performance of a simple model

Computational protein design: the Proteus software and selected applications

Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition

Computational sidechain placement and protein mutagenesis with implicit solvent models.

Conformation of the Ras-binding domain of Raf studied by molecular dynamics and free energy simulations

Conformational Selection by the aIF2 GTPase: A Molecular Dynamics Study of Functional Pathways

Conformational selection through electrostatics: Free energy simulations of gtp and gdp binding to archaeal initiation factor 2

Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg"

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

Cys(x)His(y)-Zn2+ interactions: possibilities and limitations of a simple pairwise force field

Cys(x)His(y)-Zn2+ interactions: thiol vs. thiolate coordination

Dielectric relaxation in an enzyme active site: molecular dynamics simulations interpreted with a macroscopic continuum model

Dielectric relaxation in proteins: the computational perspective

Electrostatic free energies in translational GTPases: Classic allostery and the rest

Engineering an Mg2+ site to replace a structurally conserved arginine in the catalytic center of histidyl-tRNA synthetase by computer experiments

Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies

Free energy simulations come of age: protein-ligand recognition

Free energy simulations of a GTPase: GTP and GDP binding to archaeal initiation factor 2.

Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase

Full Protein Sequence Redesign with an MMGBSA Energy Function

Gaussian fluctuations and linear response in an electron transfer protein

Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations.

Hybrid MC/MD for protein design

Implicit solvent models

Intramolecular dielectric screening in proteins.

Molecular Dynamics Simulations Show That Bound Mg2+Contributes to Amino Acid and Aminoacyl Adenylate Binding Specificity in Aspartyl-tRNA Synthetase through Long Range Electrostatic Interactions

Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site

Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases

Molecular mechanics models for tetracycline analogs

Monte Carlo simulations of proteins at constant pH with generalized Born solvent, flexible sidechains, and an effective dielectric boundary

Neutral evolution of protein-protein interactions: a computational study using simple models

Neutral evolution of proteins: The superfunnel in sequence space and its relation to mutational robustness

Nonantibiotic properties of tetracyclines: structural basis for inhibition of secretory phospholipase A2

Nucleotide recognition by the initiation factor aIF5B: Free energy simulations of a neoclassical GTPase

Pairwise decomposition of an MMGBSA energy function for computational protein design

Physics-Based Computational Protein Design: An Update

Polar fluctuations in proteins: molecular-dynamic studies of cytochrome c in aqueous solution

Predicting the acid/base behavior of proteins: a constant-pH Monte Carlo approach with generalized born solvent

Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations

Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics

Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculations

Protein molecular dynamics with the generalized born/ACE solvent model

Protein p Ka's from Adaptive Landscape Flattening Instead of Constant-pH Simulations

Protein side chain conformation predictions with an MMGBSA energy function

Protein-protein recognition: an experimental and computational study of the R89K mutation in Raf and its effect on Ras binding

Protein: Ligand Recognition: Simple Models for Electrostatic Effects ⬇️

Protein:Ligand binding free energies: A stringent test for computational protein design

Proteus and the Design of Ligand Binding Sites

Proton binding to proteins: a free-energy component analysis using a dielectric continuum model.

Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.

Protonation patterns in tetracycline:tet repressor recognition: simulations and experiments

Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets

Redesigning the stereospecificity of tyrosyl-tRNA synthetase

Redox properties of cytochrome c: novel linear response and hybrid continuum-microscopic methodologies

Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum

Simple models for nonpolar solvation: Parameterization and testing

Simulating GTP:Mg and GDP:Mg with a simple force field: a structural and thermodynamic analysis

Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations 1 1A. R. Fersht