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List of works by Thomas Simonson

A Hybrid Monte Carlo Scheme for Multibackbone Protein Design

scientific article published on 24 October 2016

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

scientific article published on 26 September 2017

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

A molecular mechanics model for imatinib and imatinib:kinase binding

scientific article published in May 2010

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

scientific article

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

scientific article published in March 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....

scientific article published on March 2010

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

scientific article published on 9 August 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

scientific article published on 03 September 2020

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

scientific article published in December 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

scientific article published on 27 July 2017

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

scientific article published on 20 May 2016

Computational Design of the Tiam1 PDZ Domain and Its Ligand Binding

scientific article published on 10 April 2017

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

scientific article published on 20 November 2017

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

scientific article published in April 2010

Computational protein design as a tool for fold recognition

scientific article

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

scientific article published on 11 May 2011

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

scientific article published in May 2008

Computational protein design: the Proteus software and selected applications

scientific article published on 26 August 2013

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

scientific article

Computational sidechain placement and protein mutagenesis with implicit solvent models.

scientific article

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

scientific article published in May 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"

scientific article published on 02 January 2019

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

scientific article

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

scientific article

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

scientific article

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

scientific article published in November 2001

Dielectric relaxation in proteins: the computational perspective

scientific article published on 29 April 2008

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

scientific article

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

scientific article published on 2 February 2017

Free energy simulations come of age: protein-ligand recognition

scientific article

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

scientific article published on 2 May 2011

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

scientific article published in February 2006

Full Protein Sequence Redesign with an MMGBSA Energy Function

scientific article published on 8 September 2017

Gaussian fluctuations and linear response in an electron transfer protein

scientific article

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

scientific article published on 9 October 2008

Hybrid MC/MD for protein design

scientific article published on 01 August 2020

Implicit solvent models

scientific article

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

scientific article published in Journal of Biological Chemistry

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

scientific article published in January 2008

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

scientific article published on 3 March 2010

Molecular mechanics models for tetracycline analogs

scientific article published in January 2009

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

scientific article published on 5 October 2013

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

scientific article

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

scientific article

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

scientific article published on 23 May 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

scientific article published on 01 January 1996

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

scientific article published in August 2010

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

scientific article published in May 2008

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

scientific article published on 27 November 2016

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

scientific article

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

scientific article

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

scientific article published in January 1999

Protein: Ligand Recognition: Simple Models for Electrostatic Effects ⬇️

scientific article published on January 1, 2013

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

Proteus and the Design of Ligand Binding Sites

scientific article published in January 2016

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 27 July 2007

Redesigning the stereospecificity of tyrosyl-tRNA synthetase

scientific article

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

scientific article published on 27 November 2003

Simple models for nonpolar solvation: Parameterization and testing

scientific article published on 7 August 2017

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

scientific article

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

scientific article published on 21 December 2014

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on September 15, 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?

scientific article published on 19 September 2013

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