Michael R. Shirts

Molecular Biology · 2000–2022

A researcher in the Science corpus: 10 papers; trusts 17 researchers and is trusted by 37 researchers here, as inferred from the citation graph.

Subfields

• Molecular Biology — 96 citations into it; #879 of 17,773 by trust here, #3,102 by citations
• Atomic and Molecular Physics, and Optics — 53 citations into it; #483 of 7,135 by trust here, #2,287 by citations
• Materials Chemistry — 45 citations into it; #7,133 of 11,513 by trust here, #4,987 by citations
• Spectroscopy — 28 citations into it
• Condensed Matter Physics — 16 citations into it
• Statistical and Nonlinear Physics — 10 citations into it; #1,366 of 10,127 by trust here, #3,382 by citations
• Computational Chemistry & Drug Discovery — 7 citations into it

Whom Michael R. Shirts trusts overall

Their strongest outbound trust, strongest first, inferred from their citations.

1. S. Plimpton
2. Charles H. Bennett
3. Berk Hess
4. Andrew Pohorille
5. A. W. Sousa da Silva
6. John D. Chodera
7. Vijay S. Pande
8. Eric F Darve
9. Giovanni Bussi
10. Massimiliano Bonomi

Who trusts Michael R. Shirts overall

1. David L. Mobley
2. Justin A. Lemkul
3. Jason Tyler Rolfe
4. Theofanis Karaletsos
5. Vijay S. Pande
6. Brooke E. Husic
7. Ken A. Dill
8. Wenbo Yu
9. Pavel V. Klimovich
10. Emiliano Brini

Papers from Michael R. Shirts's perspective

Ordered by how strongly the researchers Michael R. Shirts trusts endorse each paper. Same corpus, a different order for every researcher.

1. CHARMM: The biomolecular simulation program
2. Scalable molecular dynamics with NAMD
3. A smooth particle mesh Ewald method
4. Fast parallel algorithms for short-range molecular dynamics
5. Good practices in free-energy calculations. (Journal of Physical Chemistry B)
6. Calculating free energies using average force
7. How Fast-Folding Proteins Fold (Science)
8. Replica Exchange with Solute Scaling: A more efficient version of Replica Exchange with Solute Tempering (REST2) (Journal of Physical Chemistry B)
9. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
10. VMD: visual molecular dynamics.

Their papers

• Statistically optimal analysis of samples from multiple equilibrium states. (2008) — 1,757 citations
• Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. (2003) — 346 citations
• Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins (2003) — 607 citations
• COMPUTING: Screen Savers of the World Unite! (2000) — 541 citations
• Alchemical free energy methods for drug discovery: Progress and challenges (2011) — 538 citations
• Guidelines for the analysis of free energy calculations (2015) — 477 citations
• GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit (2013) — 7,077 citations
• Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0] (2022) — 294 citations
• Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset (2016) — 338 citations
• OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation (2012) — 656 citations