Author

M. R. Shirts

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioengineering· 2 Biophysics· 2 Pharmacology & Toxicology· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 4 Approach:mechanistic / dynamical model· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:database / resource· 1 Research Focus:drug response / drug discovery· 1 Organism:plant (other)· 1 Research Focus:protein folding & dynamics· 1

Frequent Co-Authors

A. J. Friedman· 2 shared J. D. Chodera· 2 shared A. C. Leonard· 1 shared A. Dickson· 1 shared A. Rizzi· 1 shared B. L. de Groot· 1 shared B. M. Petersen· 1 shared D. A. Ramirez· 1 shared

Activity by Year

2017-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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2 shared papersBioengineering

A. J. Friedman

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

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

A. C. Leonard, A. J. Friedman, R. Chayer, B. M. Petersen, J. Kaar, M. R. Shirts, T. A. Whitehead

This study analyzes two engineered biosensors based on PYR1 to recognize different ligands, revealing binding mechanisms and computational methods for biosensor design.

bioRxiv · Mar 25, 2024Bioengineering

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

D. A. Ramirez, L. E. Hough, M. R. Shirts

This study shows coiled-coil domains can drive liquid-liquid phase separation in molecular models, with multimerization state playing a key role.

bioRxiv · May 31, 2023Biophysics

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

A. J. Friedman, H. M. Padgette, L. Kramer, E. T. Liechty, G. W. Donovan, J. M. Fox, M. R. Shirts

The paper investigates how nonpolar terpenoids selectively inhibit PTP1B over TCPTP by disrupting conserved allosteric networks, with differences in amino acid conservation at specific sites enabling this selectivity.

bioRxiv · Apr 17, 2023 · PreprintBioengineering

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

A. Rizzi, T. Jensen, D. R. Slochower, M. Aldeghi, V. Gapsys, D. Ntekoumes, S. Bosisio, M. Papadourakis, N. M. Henriksen, B. L. de Groot, Z. Cournia, A. Dickson, J. Michel, M. K. Gilson, M. R. Shirts, , J. D. Chodera

This study evaluates binding free energy calculation methods using the SAMPL6 challenge, finding variations in efficiency and reproducibility across different systems and methods.

bioRxiv · Jan 3, 2020Biophysics

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

G. Duarte Ramos Matos, D. Y. Kyu, H. H. Loeffler, J. D. Chodera, M. R. Shirts, D. Mobley

The paper updates the FreeSolv database with calculated solvation free energies, enthalpies, and entropies using a single protocol and provides input files for molecular simulations.

bioRxiv · Jan 30, 2017Pharmacology & Toxicology