Biomolecular simulation: a computational microscope for molecular biology.

By Ron O. Dror, Robert M. Dirks, J. P. Grossman, Huafeng Xu, David E. Shaw. Annual Review of Biophysics, 2012

1,126 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5823a81a97ace58e072cd8a7c1382ea27bad0e17

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

In Molecular Biology

Citations in the corpus

Outsmarting Quantum Chemistry Through Transfer Learning (2018, background): “For example, empirical potentials ( e.g. classical force fields) are commonly employed to enable large scale dynamical simulation such as protein folding 14 , ligand-protein docking 15 or the dynamics of dislocations in materials 16 .”
Meeting Review: Diffuse X-Ray Scattering to Model Protein Motions (2014, methodology): “Future avenues for achieving increased sampling include millisecond all-atom simulations (Dror et al., 2012), advanced sampling methods such as parallel tempering (Earl and Deem, 2005), and acceleration schemes such as Markov State Models (Pande et al., 2010).”
The power of coarse graining in biomolecular simulations (2013, methodology): “100 × 100 × 100 nm3 containing millions of particles; (2) allowing for the simulation of slow processes requiring time scales in the micro- to millisecond range; (3) enabling high-throughput studies, systematically exploring state conditions in thousands of parallel runs; (4) showing where details m”
Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer (2014, background): “I. INTRODUCTION Molecular dynamics (MD) simulations offer exceptional visibility into the behavior of biological macromolecules at an atomic level of detail [15].”
To Milliseconds and Beyond: Challenges in the Simulation of Protein Folding (2012, background): “Folding is rapid and complex, requiring atomic-level resolution at nanosecond timescales for a complete detailed picture — outside the hard limits of temporal and spatial resolution of most experimental techniques [4].”