Michael R Shirts

ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 55

Top Venues

Journal of chemical theory and computation

The journal of physical chemistry. B

Journal of chemical information and modeling

ACS chemical biology

University of Colorado Boulder

Stanford University (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Colorado Boulder Jan 01 2016

United States

Associate Professor :: Department of Chemical and Biological Engineering

Education History

Stanford University Aug 25 1999 - Jan 05 2005

United States

PHD :: Chemistry

Publications

Edgar Olehnovics, Yifei Michelle Liu, Nada Mehio, Ahmad Y Sheikh, Michael R Shirts, Matteo Salvalaglio
Assessing the Accuracy and Efficiency of Free Energy Differences Obtained from Reweighted Flow-Based Probabilistic Generative Models. Journal of chemical theory and computation 20 (14) (2024)
Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey R Wagner, Daniel J Cole, Michael K Gilson, Michael R Shirts, David L Mobley
The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. The journal of physical chemistry. B 128 (29) (2024)
Connor M Davel, Timotej Bernat, Jeffrey R Wagner, Michael R Shirts
Parameterization of General Organic Polymers within the Open Force Field Framework. Journal of chemical information and modeling (2024)
Connor M Davel, Timotej Bernat, Jeffrey R Wagner, Michael R Shirts
Parameterization of General Organic Polymers within the Open Force Field Framework. Journal of chemical information and modeling 64 (4) (2024)
Kenichiro Takaba, Anika J Friedman, Chapin E Cavender, Pavan Kumar Behara, Iván Pulido, Michael M Henry, Hugo I MacDermott-Opeskin, Christopher R Iacovella, Arnav M Nagle, Alexander Matthew Payne, Michael R Shirts, David L Mobley, John D Chodera, Yuanqing Wang
Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chemical science 15 (32) (2024)
Edgar Olehnovics, Yifei Michelle Liu, Nada Mehio, Ahmad Y Sheikh, Michael R Shirts, Matteo Salvalaglio
Assessing the Accuracy and Efficiency of Free Energy Differences Obtained from Reweighted Flow-Based Probabilistic Generative Models. Journal of chemical theory and computation 20 (14) (2024)
Connor M Davel, Timotej Bernat, Jeffrey R Wagner, Michael R Shirts
Parameterization of General Organic Polymers within the Open Force Field Framework. Journal of chemical information and modeling 64 (4) (2024)
Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey R Wagner, Daniel J Cole, Michael K Gilson, Michael R Shirts, David L Mobley
The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. The journal of physical chemistry. B (2024)
Edgar Olehnovics, Yifei Michelle Liu, Nada Mehio, Ahmad Y Sheikh, Michael R Shirts, Matteo Salvalaglio
Assessing the Accuracy and Efficiency of Free Energy Differences Obtained from Reweighted Flow-Based Probabilistic Generative Models. Journal of chemical theory and computation 20 (14) (2024)
Kenichiro Takaba, Anika J Friedman, Chapin E Cavender, Pavan Kumar Behara, Iván Pulido, Michael M Henry, Hugo I MacDermott-Opeskin, Christopher R Iacovella, Arnav M Nagle, Alexander Matthew Payne, Michael R Shirts, David L Mobley, John D Chodera, Yuanqing Wang
Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chemical science 15 (32) (2024)
Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey R Wagner, Daniel J Cole, Michael K Gilson, Michael R Shirts, David L Mobley
The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. The journal of physical chemistry. B 128 (29) (2024)
Connor M Davel, Timotej Bernat, Jeffrey R Wagner, Michael R Shirts
Parameterization of General Organic Polymers within the Open Force Field Framework. Journal of chemical information and modeling 64 (4) (2024)
Alison C Leonard, Anika J Friedman, Rachel Chayer, Brian M Petersen, Janty Woojuh, Zenan Xing, Sean R Cutler, Joel L Kaar, Michael R Shirts, Timothy A Whitehead
Rationalizing Diverse Binding Mechanisms to the Same Protein Fold: Insights for Ligand Recognition and Biosensor Design. ACS chemical biology 19 (8) (2024)
Connor M Davel, Timotej Bernat, Jeffrey R Wagner, Michael R Shirts
Parameterization of General Organic Polymers within the Open Force Field Framework. Journal of chemical information and modeling 64 (4) (2024)
Alison C Leonard, Anika J Friedman, Rachel Chayer, Brian M Petersen, Janty Woojuh, Zenan Xing, Sean R Cutler, Joel L Kaar, Michael R Shirts, Timothy A Whitehead
Rationalizing Diverse Binding Mechanisms to the Same Protein Fold: Insights for Ligand Recognition and Biosensor Design. ACS chemical biology (2024)
Wei-Tse Hsu, Michael R Shirts
Replica Exchange of Expanded Ensembles: A Generalized Ensemble Approach with Enhanced Flexibility and Parallelizability. Journal of chemical theory and computation (2024)
Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey R Wagner, Daniel J Cole, Michael K Gilson, Michael R Shirts, David L Mobley
The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. The journal of physical chemistry. B 128 (29) (2024)
Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey R Wagner, Daniel J Cole, Michael K Gilson, Michael R Shirts, David L Mobley
The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. The journal of physical chemistry. B 128 (29) (2024)
Alison C Leonard, Anika J Friedman, Rachel Chayer, Brian M Petersen, Janty Woojuh, Zenan Xing, Sean R Cutler, Joel L Kaar, Michael R Shirts, Timothy A Whitehead
Rationalizing Diverse Binding Mechanisms to the Same Protein Fold: Insights for Ligand Recognition and Biosensor Design. ACS chemical biology (2024)
Edgar Olehnovics, Yifei Michelle Liu, Nada Mehio, Ahmad Y Sheikh, Michael R Shirts, Matteo Salvalaglio
Assessing the Accuracy and Efficiency of Free Energy Differences Obtained from Reweighted Flow-Based Probabilistic Generative Models. Journal of chemical theory and computation (2024)
Alison C Leonard, Anika J Friedman, Rachel Chayer, Brian M Petersen, Janty Woojuh, Zenan Xing, Sean R Cutler, Joel L Kaar, Michael R Shirts, Timothy A Whitehead
Rationalizing Diverse Binding Mechanisms to the Same Protein Fold: Insights for Ligand Recognition and Biosensor Design. ACS chemical biology 19 (8) (2024)
Kenichiro Takaba, Anika J Friedman, Chapin E Cavender, Pavan Kumar Behara, Iván Pulido, Michael M Henry, Hugo I MacDermott-Opeskin, Christopher R Iacovella, Arnav M Nagle, Alexander Matthew Payne, Michael R Shirts, David L Mobley, John D Chodera, Yuanqing Wang
Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chemical science 15 (32) (2024)
Connor M Davel, Timotej Bernat, Jeffrey R Wagner, Michael R Shirts
Parameterization of General Organic Polymers within the Open Force Field Framework. Journal of chemical information and modeling 64 (4) (2024)
Kenichiro Takaba, Anika J Friedman, Chapin E Cavender, Pavan Kumar Behara, Iván Pulido, Michael M Henry, Hugo I MacDermott-Opeskin, Christopher R Iacovella, Arnav M Nagle, Alexander Matthew Payne, Michael R Shirts, David L Mobley, John D Chodera, Yuanqing Wang
Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chemical science 15 (32) (2024)
Wei-Tse Hsu, Michael R Shirts
Replica Exchange of Expanded Ensembles: A Generalized Ensemble Approach with Enhanced Flexibility and Parallelizability. Journal of chemical theory and computation 20 (14) (2024)
Anika J Friedman, Hannah M Padgette, Levi Kramer, Evan T Liechty, Gregory W Donovan, Jerome M Fox, Michael R Shirts
A biophysical rationale for the selective inhibition of PTP1B over TCPTP by nonpolar terpenoids. bioRxiv : the preprint server for biology (2023)
Dominique A Ramirez, Loren E Hough, Michael R Shirts
Coiled-coil domains are sufficient to drive liquid-liquid phase separation of proteins in molecular models. bioRxiv : the preprint server for biology (2023)
Simon Boothroyd, Pavan Kumar Behara, Owen C Madin, David F Hahn, Hyesu Jang, Vytautas Gapsys, Jeffrey R Wagner, Joshua T Horton, David L Dotson, Matthew W Thompson, Jessica Maat, Trevor Gokey, Lee-Ping Wang, Daniel J Cole, Michael K Gilson, John D Chodera, Christopher I Bayly, Michael R Shirts, David L Mobley
Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. Journal of chemical theory and computation (2023)
Wei-Tse Hsu, Valerio Piomponi, Pascal T Merz, Giovanni Bussi, Michael R Shirts
Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations. Journal of chemical theory and computation (2023)
Wei-Tse Hsu, Valerio Piomponi, Pascal T Merz, Giovanni Bussi, Michael R Shirts
Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations. Journal of chemical theory and computation (2023)
Anika J Friedman, Hannah M Padgette, Levi Kramer, Evan T Liechty, Gregory W Donovan, Jerome M Fox, Michael R Shirts
Biophysical Rationale for the Selective Inhibition of PTP1B over TCPTP by Nonpolar Terpenoids. The journal of physical chemistry. B (2023)
Anika J Friedman, Hannah M Padgette, Levi Kramer, Evan T Liechty, Gregory W Donovan, Jerome M Fox, Michael R Shirts
A biophysical rationale for the selective inhibition of PTP1B over TCPTP by nonpolar terpenoids. bioRxiv : the preprint server for biology (2023)
Wei-Tse Hsu, Dominique A Ramirez, Tarek Sammakia, Zhongping Tan, Michael R Shirts
Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation. Journal of computer-aided molecular design 36 (4) (2022)
Theodore L Fobe, Christopher C Walker, Garrett A Meek, Michael R Shirts
Folding Coarse-Grained Oligomer Models with PyRosetta. Journal of chemical theory and computation 18 (10) (2022)
Owen C Madin, Simon Boothroyd, Richard A Messerly, Josh Fass, John D Chodera, Michael R Shirts
Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models. Journal of chemical information and modeling 62 (4) (2022)
Simon Boothroyd, Lee-Ping Wang, David L Mobley, John D Chodera, Michael R Shirts
Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation. Journal of chemical theory and computation 18 (6) (2022)
Subin Sahu, Nathanael S Schwindt, Benjamin J Coscia, Michael R Shirts
Obtaining and Characterizing Stable Bicontinuous Cubic Morphologies and Their Nanochannels in Lyotropic Liquid Crystal Membranes. The journal of physical chemistry. B 126 (48) (2022)
Anika J Friedman, Evan T Liechty, Levi Kramer, Ankur Sarkar, Jerome M Fox, Michael R Shirts
Allosteric Inhibition of PTP1B by a Nonpolar Terpenoid. The journal of physical chemistry. B 126 (42) (2022)
Simon Boothroyd, Owen C Madin, David L Mobley, Lee-Ping Wang, John D Chodera, Michael R Shirts
Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. Journal of chemical theory and computation 18 (6) (2022)
Adam F Kleman, Deseree L Dufek, Theodore L Fobe, Darrell R McCaslin, Brian P Cary, Michael R Shirts, Samuel H Gellman
Potential Foldamers Based on an ortho-Terphenyl Amino Acid. Organic letters 23 (12) (2021)
Si Zhang, David F Hahn, Michael R Shirts, Vincent A Voelz
Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies. Journal of chemical theory and computation 17 (10) (2021)
Yudong Qiu, Daniel G A Smith, Simon Boothroyd, Hyesu Jang, David F Hahn, Jeffrey Wagner, Caitlin C Bannan, Trevor Gokey, Victoria T Lim, Chaya D Stern, Andrea Rizzi, Bryon Tjanaka, Gary John Tresadern, Xavier Lucas, Michael R Shirts, Michael K Gilson, John D Chodera, Christopher I Bayly, David L Mobley, Lee-Ping Wang
Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. Journal of chemical theory and computation 17 (10) (2021)
Christopher C Walker, Garrett A Meek, Theodore L Fobe, Michael R Shirts
Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure. Journal of chemical theory and computation 17 (10) (2021)
Andrea Rizzi, Travis Jensen, David R Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M Henriksen, Bert L de Groot, Zoe Cournia, Alex Dickson, Julien Michel, Michael K Gilson, Michael R Shirts, David L Mobley, John D Chodera
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. Journal of computer-aided molecular design 34 (5) (2020)
Benjamin J Coscia, Michael R Shirts
Capturing Subdiffusive Solute Dynamics and Predicting Selectivity in Nanoscale Pores with Time Series Modeling. Journal of chemical theory and computation 16 (9) (2020)
Nathan S Abraham, Michael R Shirts
Statistical Mechanical Approximations to More Efficiently Determine Polymorph Free Energy Differences for Small Organic Molecules. Journal of chemical theory and computation 16 (10) (2020)
Benjamin J Coscia, Christopher P Calderon, Michael R Shirts
Statistical Inference of Transport Mechanisms and Long Time Scale Behavior from Time Series of Solute Trajectories in Nanostructured Membranes. The journal of physical chemistry. B 124 (37) (2020)
Michael R Shirts, Andrew L Ferguson
Statistically Optimal Continuous Free Energy Surfaces from Biased Simulations and Multistate Reweighting. Journal of chemical theory and computation 16 (7) (2020)
Benjamin J Coscia, Michael R Shirts
Chemically Selective Transport in a Cross-Linked HII Phase Lyotropic Liquid Crystal Membrane. The journal of physical chemistry. B 123 (29) (2019)
Camila Zanette, Caitlin C Bannan, Christopher I Bayly, Josh Fass, Michael K Gilson, Michael R Shirts, John D Chodera, David L Mobley
Toward Learned Chemical Perception of Force Field Typing Rules. Journal of chemical theory and computation 15 (1) (2018)
Richard A Messerly, Michael R Shirts, Andrei F Kazakov
Uncertainty quantification confirms unreliable extrapolation toward high pressures for united-atom Mie λ-6 force field. The Journal of chemical physics 149 (11) (2018)
Nathan S Abraham, Michael R Shirts
Thermal Gradient Approach for the Quasi-harmonic Approximation and Its Application to Improved Treatment of Anisotropic Expansion. Journal of chemical theory and computation 14 (11) (2018)
Natalie P Schieber, Eric C Dybeck, Michael R Shirts
Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams. The Journal of chemical physics 148 (14) (2018)
Benjamin J Coscia, Joseph Yelk, Matthew A Glaser, Douglas L Gin, Xunda Feng, Michael R Shirts
Understanding the Nanoscale Structure of Inverted Hexagonal Phase Lyotropic Liquid Crystal Polymer Membranes. The journal of physical chemistry. B 123 (1) (2018)
David L Mobley, Caitlin C Bannan, Andrea Rizzi, Christopher I Bayly, John D Chodera, Victoria T Lim, Nathan M Lim, Kyle A Beauchamp, David R Slochower, Michael R Shirts, Michael K Gilson, Peter K Eastman
Escaping Atom Types in Force Fields Using Direct Chemical Perception. Journal of chemical theory and computation 14 (11) (2018)

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Publication Activity (10 Years)

Top Topics

Top Venues

Michael R Shirts