Michael R. Shirts

Also affiliated with University of Colorado System

Biochemistry, Genetics and Molecular BiologyComputer ScienceChemistryMaterials Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 46 papers. Top paper: “GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit”.

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

Bioinformatics(2013)10.1093/bioinformatics/btt055

N/A

1.3DataRank · unranked

7514 citations

Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov +7 more

Programmable de novo designed coiled coil-mediated phase separation in mammalian cells

Nature Communications(2023)10.1038/s41467-023-43742-w

N/A

1.1DataRank · unranked

48 citations

Dominique Ramirez, Loren E. Hough, Michael R. Shirts, Sara Vidmar, Kristina Eleršič +3 more

Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field

ChemRxiv(2022)10.26434/chemrxiv-2022-n2z1c

N/A

0.345DataRank · unranked

9 citations

Pavan Kumar Behara, Owen Madin, David F. Hahn, Hyesu Jang, Vytautas Gapsys +14 more

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

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.1c00513

N/A

0DataRank · unranked

21 citations

David F. Hahn, Michael R. Shirts, Vincent A. Voelz, Si Zhang

Potential Foldamers Based on an ortho-Terphenyl Amino Acid

Organic Letters(2021)10.1021/acs.orglett.1c01592

N/A

0DataRank · unranked

4 citations

Deseree L. Dufek, Theodore L. Fobe, Darrell R. McCaslin, Brian P. Cary, Michael R. Shirts +2 more

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

(2021)10.33774/chemrxiv-2021-l070l-v3

N/A

0DataRank · unranked

18 citations

Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan +13 more

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

(2021)10.33774/chemrxiv-2021-l070l-v4

N/A

0DataRank · unranked

6 citations

Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan +13 more

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

ChemRxiv(2021)10.26434/chemrxiv.14665662.v1

N/A

0DataRank · unranked

5 citations

David F. Hahn, Michael R. Shirts, Vincent A. Voelz, Si Zhang

Improving force field accuracy by training against condensed phase mixture properties

ChemRxiv(2021)10.26434/chemrxiv-2021-gsgr4-v2

N/A

0DataRank · unranked

3 citations

Owen Madin, David L. Mobley, Lee‐Ping Wang, John D. Chodera, Michael R. Shirts +1 more

Improving force field accuracy by training against condensed phase mixture properties

ChemRxiv(2021)10.26434/chemrxiv-2021-gsgr4

N/A

0DataRank · unranked

2 citations

Owen Madin, David L. Mobley, Lee‐Ping Wang, John D. Chodera, Michael R. Shirts +1 more

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

ChemRxiv(2021)10.26434/chemrxiv-2021-l070l-v4

N/A

0DataRank · unranked

1 citations

Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan +13 more

Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation

(2021)10.33774/chemrxiv-2021-l2zd5-v2

N/A

0DataRank · unranked

0 citations

Dominique Ramirez, Tarek Sammakia, Zhongping Tan, Michael R. Shirts, Wei-Tse Hsu

Identifying signatures of proteolyticstability and monomeric propensity inO-glycosylated insulin using molecularsimulation

ChemRxiv(2021)10.26434/chemrxiv-2021-l2zd5-v2

N/A

0DataRank · unranked

0 citations

Dominique Ramirez, Tarek Sammakia, Zhongping Tan, Michael R. Shirts, Wei-Tse Hsu

Identifying signatures of proteolyticstability and monomeric propensity inO-glycosylated insulin using molecularsimulation

ChemRxiv(2021)10.26434/chemrxiv-2021-l2zd5

N/A

0DataRank · unranked

0 citations

Dominique Ramirez, Tarek Sammakia, Zhongping Tan, Michael R. Shirts, Wei-Tse Hsu

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

ChemRxiv(2021)10.26434/chemrxiv-2021-l070l-v3

N/A

0DataRank · unranked

0 citations

Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan +13 more

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

ChemRxiv(2021)10.26434/chemrxiv.14665662

N/A

0DataRank · unranked

0 citations

David F. Hahn, Michael R. Shirts, Vincent A. Voelz, Si Zhang

Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation

(2021)10.33774/chemrxiv-2021-l2zd5

N/A

0DataRank · unranked

0 citations

Dominique Ramirez, Tarek Sammakia, Zhongping Tan, Michael R. Shirts, Wei-Tse Hsu

Allosteric Inhibition of PTP1B by a Nonpolar Terpenoid

The Journal of Physical Chemistry B(2022)10.1021/acs.jpcb.2c05423

N/A

0DataRank · unranked

19 citations

Evan T. Liechty, Levi Kramer, Ankur Sarkar, Jerome M. Fox, Michael R. Shirts +1 more

Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation

Journal of Computer-Aided Molecular Design(2022)10.1007/s10822-022-00453-6

N/A

0DataRank · unranked

5 citations

Dominique Ramirez, Tarek Sammakia, Zhongping Tan, Michael R. Shirts, Wei-Tse Hsu

Improving force field accuracy by training against condensed phase mixture properties

ChemRxiv(2022)10.26434/chemrxiv-2021-gsgr4-v3

N/A

0DataRank · unranked

7 citations

Owen Madin, David L. Mobley, Lee‐Ping Wang, John D. Chodera, Michael R. Shirts +1 more

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

The Journal of Open Source Software(2022)10.21105/joss.03981

N/A

0DataRank · unranked

1 citations

Wei-Tse Hsu, Matt Thompson, Simon Boothroyd, Chris Walker, Michael R. Shirts +1 more

Allosteric Inhibition of PTP1B by a Nonpolar Terpenoid

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.18.492571

N/A

0DataRank · unranked

1 citations

Evan T. Liechty, Levi Kramer, Ankur Sarkar, Jerome M. Fox, Michael R. Shirts +1 more

Using physical property surrogate models to perform multi-fidelity global optimization of force field parameters

ChemRxiv(2022)10.26434/chemrxiv-2022-7bmzv

N/A

0DataRank · unranked

1 citations

Michael R. Shirts, Owen Madin

Using physical property surrogate models to perform multi-fidelity global optimization of force field parameters

ChemRxiv(2022)10.26434/chemrxiv-2022-7bmzv-v2

N/A

0DataRank · unranked

1 citations

Michael R. Shirts, Owen Madin

Identifying signatures of proteolyticstability and monomeric propensity inO-glycosylated insulin using molecularsimulation

ChemRxiv(2022)10.26434/chemrxiv-2021-l2zd5-v3

N/A

0DataRank · unranked

0 citations

Dominique Ramirez, Tarek Sammakia, Zhongping Tan, Michael R. Shirts, Wei-Tse Hsu

Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00039

N/A

0DataRank · unranked

193 citations

Pavan Kumar Behara, Owen Madin, David F. Hahn, Hyesu Jang, Vytautas Gapsys +14 more

Using physical property surrogate models to perform accelerated multi-fidelity optimization of force field parameters

Digital Discovery(2023)10.1039/d2dd00138a

N/A

0DataRank · unranked

14 citations

Michael R. Shirts, Owen Madin

Biophysical Rationale for the Selective Inhibition of PTP1B over TCPTP by Nonpolar Terpenoids

The Journal of Physical Chemistry B(2023)10.1021/acs.jpcb.3c03791

N/A

0DataRank · unranked

6 citations

Hannah M. Padgette, Levi Kramer, Evan T. Liechty, Gregory W. Donovan, Jerome M. Fox +2 more

Analysis of neutral mutational drift in an allosteric enzyme

Protein Science(2023)10.1002/pro.4719

N/A

0DataRank · unranked

3 citations

Andrew Hren, Levi Kramer, Gregory T. Donovan, Anika J. Friedman, Michael R. Shirts +2 more

Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field

ChemRxiv(2023)10.26434/chemrxiv-2022-n2z1c-v2

N/A

0DataRank · unranked

21 citations

Pavan Kumar Behara, Owen Madin, David F. Hahn, Hyesu Jang, Vytautas Gapsys +14 more

Coiled-coil domains are sufficient to drive liquid-liquid phase separation of proteins in molecular models

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.31.543124

N/A

0DataRank · unranked

12 citations

Loren E. Hough, Michael R. Shirts, Dominique Ramirez

Parameterization of general organic polymers within the Open Force Field framework

ChemRxiv(2023)10.26434/chemrxiv-2023-f2zxd-v2

N/A

0DataRank · unranked

1 citations

Timotej Bernat, Jeffrey Wagner, Michael R. Shirts, Connor Davel

A biophysical rationale for the selective inhibition of PTP1B over TCPTP by nonpolar terpenoids

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.17.537234

N/A

0DataRank · unranked

0 citations

Hannah M. Padgette, Levi Kramer, Evan T. Liechty, Gregory W. Donovan, Jerome M. Fox +2 more

Parameterization of general organic polymers within the Open Force Field framework

ChemRxiv(2023)10.26434/chemrxiv-2023-f2zxd

N/A

0DataRank · unranked

0 citations

Timotej Bernat, Jeffrey Wagner, Michael R. Shirts, Connor Davel

Coiled-coil domains are sufficient to drive liquid-liquid phase separation in protein models

Biophysical Journal(2024)10.1016/j.bpj.2024.02.007

N/A

0DataRank · unranked

45 citations

Loren E. Hough, Michael R. Shirts, Dominique Ramirez

Machine-learned molecular mechanics force fields from large-scale quantum chemical data

Chemical Science(2024)10.1039/d4sc00690a

N/A

0DataRank · unranked

40 citations

Anika J. Friedman, Chapin E. Cavender, Pavan Kumar Behara, Iván Pulido, Michael M. Henry +9 more

alchemlyb: the simple alchemistry library

The Journal of Open Source Software(2024)10.21105/joss.06934

N/A

0DataRank · unranked

32 citations

David Dotson, Irfan Alibay, Bryce K. Allen, Mohammad Soroush Barhaghi, Jérôme Hénin +13 more

Parameterization of General Organic Polymers within the Open Force Field Framework

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.3c01691

N/A

0DataRank · unranked

9 citations

Timotej Bernat, Jeffrey Wagner, Michael R. Shirts, Connor Davel

Rationalizing diverse binding mechanisms to the same protein fold: insights for ligand recognition and biosensor design

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.25.586677

N/A

0DataRank · unranked

1 citations

Anika J. Friedman, Rachel Chayer, Brian M. Petersen, Joel L. Kaar, Michael R. Shirts +2 more

Force Switching and Potential Shifting Lead to Significant Cutoff Dependence in Alchemical Free Energies

Journal of Chemical Theory and Computation(2025)10.1021/acs.jctc.5c00646

N/A

0DataRank · unranked

3 citations

Yalda Ramezani, Sumit Sharma, Michael R. Shirts, Lindsey M. Whitmore

Nonspecific interactions can lead to liquid-liquid phase separation in coiled-coil protein models

Biophysical Journal(2025)10.1016/j.bpj.2025.11.027

N/A

0DataRank · unranked

2 citations

Anastasia Shrimpton, Michael R. Shirts, Loren E. Hough, Dominique Ramirez

Computational design of dynamic biosensors for emerging synthetic opioids

Zenodo (CERN European Organization for Nuclear Research)(2025)10.5281/zenodo.15298584

N/A

0DataRank · unranked

1 citations

Lenert-Mondou, Chase, Chayer, Rachel, Samuel D. Swift, Zachary T. Baumer, Delaney, Ryan +10 more

Nonspecific interactions can lead to liquid-liquid phase separation in coiled-coil proteins models

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.09.653163

N/A

0DataRank · unranked

0 citations

Anastasia Shrimpton, Michael R. Shirts, Loren E. Hough, Dominique Ramirez

Computational design of dynamic biosensors for emerging synthetic opioids

Zenodo (CERN European Organization for Nuclear Research)(2025)10.5281/zenodo.15298585

N/A

0DataRank · unranked

0 citations

Lenert-Mondou, Chase, Chayer, Rachel, Samuel D. Swift, Zachary T. Baumer, Delaney, Ryan +10 more

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

Journal of Computer-Aided Molecular Design(2020)10.1007/s10822-020-00290-5

N/A

0DataRank · unranked

136 citations

Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes +12 more

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

ChemRxiv(2020)10.26434/chemrxiv.13082561.v2

N/A

0DataRank · unranked

31 citations

Daniel G. A. Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan +13 more