List of works - Michael R. Shirts

A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods

scientific article

A Thermal Gradient Approach for the Quasi-Harmonic Approximation and its Application to Improved Treatment of Anisotropic Expansion

scientific article published on 26 October 2018

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

scientific article published on 19 October 2007

Alchemical free energy methods for drug discovery: progress and challenges

scientific article

An Introduction to Best Practices in Free Energy Calculations ⬇️

scientific article published on January 1, 2013

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database

scientific article published on 24 April 2017

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

scientific article

Best Practices for Alchemical Free Energy Calculations [Article v1.0]

scientific article published in 2020

Best practices in free energy calculations for drug design

scientific article

Capturing Entropic Contributions to Temperature-Mediated Polymorphic Transformations Through Molecular Modeling

Chemically Selective Transport in a Cross-Linked HII Phase Lyotropic Liquid Crystal Membrane

scientific article published on 11 July 2019

Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials

scientific article published on 23 March 2016

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

scientific article

Configurational mapping significantly increases the efficiency of solid-solid phase coexistence calculations via molecular dynamics: Determining the FCC-HCP coexistence line of Lennard-Jones particles

scientific article published on 01 April 2019

Configurational preferences of arylamide α-helix mimetics via alchemical free energy calculations of relative binding affinities

scientific article published on 27 August 2012

Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations

scientific article

Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

scientific article published in March 2015

Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field

scientific article published on 22 September 2021

Direct calculation of the binding free energies of FKBP ligands

scientific article published on August 2005

Distinct aggregation mechanisms of monoclonal antibody under thermal and freeze-thaw stresses revealed by hydrogen exchange

scientific article

Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures

scientific article

Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations

scientific article

Effects of a More Accurate Polarizable Hamiltonian on Polymorph Free Energies Computed Efficiently by Reweighting Point-Charge Potentials

scientific article

Effects of polymer graft properties on protein adsorption and transport in ion exchange chromatography: a multiscale modeling study

scientific article

Effects of protein properties on adsorption and transport in polymer-grafted ion exchangers: A multiscale modeling study

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods ⬇️

scientific article published on 02 October 2003

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

scientific article published on 27 July 2017

Escaping atom types in force fields using direct chemical perception

scientific article published on 30 October 2018

Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies

scientific article published on 13 September 2021

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

article

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

scientific article

Glycoside hydrolase processivity is directly related to oligosaccharide binding free energy

scientific article published on 05 December 2013

Identifying Differences and Similarities in Static and Dynamic Contact Angles between Nanoscale and Microscale Textured Surfaces Using Molecular Dynamics Simulations

scientific article

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

scientific article

Identifying low variance pathways for free energy calculations of molecular transformations in solution phase

scientific article

Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program: Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects

scientific article published in November 2007

Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties

scientific article published on 09 May 2022

Investigating the mutation resistance of nonnucleoside inhibitors of HIV-RT using multiple microsecond atomistic simulations

scientific article

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites

scientific article

Linear basis function approach to efficient alchemical free energy calculations. 2. Inserting and deleting particles with coulombic interactions

scientific article

Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable ⬇️

scientific article

Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes

scientific article published in March 2007

Multistate reweighting and configuration mapping together accelerate the efficiency of thermodynamic calculations as a function of molecular geometry by orders of magnitude

scientific article

Native-like mean structure in the unfolded ensemble of small proteins

scientific article published on October 2002

Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1

Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation

scientific article published on 04 May 2022

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

scientific article

Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase

scientific article

Overview of the SAMPL5 host-guest challenge: Are we doing better?

scientific article published on 22 September 2016

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics

scientific article

Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods

scientific article

Product binding varies dramatically between processive and nonprocessive cellulase enzymes

scientific article

Rapid Computation of Thermodynamic Properties over Multidimensional Nonbonded Parameter Spaces Using Adaptive Multistate Reweighting ⬇️

scientific article

Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing

scientific article published in November 2011

Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles

scientific article

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

scientific article

Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations

scientific article

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models

scientific article published in April 2005

Statistically optimal analysis of samples from multiple equilibrium states

scientific article published in September 2008

Testing for Physical Validity in Molecular Simulations

article published in 2018

Testing for physical validity in molecular simulations

scientific article published in PLoS ONE

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

scientific article published on 27 January 2020

The solvation interface is a determining factor in peptide conformational preferences

scientific article published on 05 December 2005

Thermodynamics of coupled protein adsorption and stability using hybrid Monte Carlo simulations

scientific article

Toward Learned Chemical Perception of Force Field Typing Rules

scientific article published on 24 December 2018

Uncertainty quantification confirms unreliable extrapolation toward high pressures for united-atom Mie λ-6 force field

scientific article published on 01 September 2018

Understanding the Nanoscale Structure of Inverted Hexagonal Phase Lyotropic Liquid Crystal Polymer Membranes

scientific article published on 24 December 2018

Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions

scientific article

Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

scientific article published on 08 September 2021

Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams

scientific article published in April 2018

Why We Need the Living Journal of Computational Molecular Science

scientific article published on 21 August 2017

physical_validation: A Python package to assess the physical validity of molecular simulation results

scientific article published on 06 January 2022

List of works by Michael R. Shirts

A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods

A Thermal Gradient Approach for the Quasi-Harmonic Approximation and its Application to Improved Treatment of Anisotropic Expansion

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

Alchemical free energy methods for drug discovery: progress and challenges

An Introduction to Best Practices in Free Energy Calculations ⬇️

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

Best Practices for Alchemical Free Energy Calculations [Article v1.0]

Best practices in free energy calculations for drug design

Capturing Entropic Contributions to Temperature-Mediated Polymorphic Transformations Through Molecular Modeling

Chemically Selective Transport in a Cross-Linked HII Phase Lyotropic Liquid Crystal Membrane

Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

Configurational mapping significantly increases the efficiency of solid-solid phase coexistence calculations via molecular dynamics: Determining the FCC-HCP coexistence line of Lennard-Jones particles

Configurational preferences of arylamide α-helix mimetics via alchemical free energy calculations of relative binding affinities

Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations

Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field

Direct calculation of the binding free energies of FKBP ligands

Distinct aggregation mechanisms of monoclonal antibody under thermal and freeze-thaw stresses revealed by hydrogen exchange

Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures

Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations

Effects of a More Accurate Polarizable Hamiltonian on Polymorph Free Energies Computed Efficiently by Reweighting Point-Charge Potentials

Effects of polymer graft properties on protein adsorption and transport in ion exchange chromatography: a multiscale modeling study

Effects of protein properties on adsorption and transport in polymer-grafted ion exchangers: A multiscale modeling study

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods ⬇️

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Escaping atom types in force fields using direct chemical perception

Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Glycoside hydrolase processivity is directly related to oligosaccharide binding free energy

Identifying Differences and Similarities in Static and Dynamic Contact Angles between Nanoscale and Microscale Textured Surfaces Using Molecular Dynamics Simulations

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

Identifying low variance pathways for free energy calculations of molecular transformations in solution phase

Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program: Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects

Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties

Investigating the mutation resistance of nonnucleoside inhibitors of HIV-RT using multiple microsecond atomistic simulations

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites

Linear basis function approach to efficient alchemical free energy calculations. 2. Inserting and deleting particles with coulombic interactions

Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable ⬇️

Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes

Multistate reweighting and configuration mapping together accelerate the efficiency of thermodynamic calculations as a function of molecular geometry by orders of magnitude

Native-like mean structure in the unfolded ensemble of small proteins

Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1

Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase

Overview of the SAMPL5 host-guest challenge: Are we doing better?

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics

Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods

Product binding varies dramatically between processive and nonprocessive cellulase enzymes

Rapid Computation of Thermodynamic Properties over Multidimensional Nonbonded Parameter Spaces Using Adaptive Multistate Reweighting ⬇️

Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing

Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models

Statistically optimal analysis of samples from multiple equilibrium states

Testing for Physical Validity in Molecular Simulations

Testing for Physical Validity in Molecular Simulations

Testing for Physical Validity in Molecular Simulations

Testing for physical validity in molecular simulations

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

The solvation interface is a determining factor in peptide conformational preferences

Thermodynamics of coupled protein adsorption and stability using hybrid Monte Carlo simulations

Toward Learned Chemical Perception of Force Field Typing Rules

Toward Learned Chemical Perception of Force Field Typing Rules

Toward Learned Chemical Perception of Force Field Typing Rules

Toward Learned Chemical Perception of Force Field Typing Rules

Toward Learned Chemical Perception of Force Field Typing Rules

Uncertainty quantification confirms unreliable extrapolation toward high pressures for united-atom Mie λ-6 force field

Understanding the Nanoscale Structure of Inverted Hexagonal Phase Lyotropic Liquid Crystal Polymer Membranes

Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions

Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams

Why We Need the Living Journal of Computational Molecular Science

physical_validation: A Python package to assess the physical validity of molecular simulation results