Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.

By Vijay S. Pande, I. Baker, Jarrod Chapman, S. P. Elmer, S. Khaliq, Stefan M. Larson, Young Min Rhee, Michael R. Shirts, Christopher D. Snow, Eric J. Sorin and 1 more. Biopolymers, 2003

346 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bb7754ca4bff4401b1b483d66f74265c505fccd6

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Citations in the corpus

Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. (2005, methodology): “Still, a distributed computing effort can greatly advance computational studies of protein and nucleic acid folding (Pande et al., 2003; Snow et al., 2002; Sorin et al., 2004, 2003; Zagrovic et al., 2001) as well as the validation of solute and solvent force-field accuracy and applicability (Rhee…”
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters (2006, background): “Several other research groups have deployed significant computational resources either to run a large number of separate MD simulations, each of limited duration [ 31 ], or to parallelize the simulation of extremely large biochemical systems [29, 46].”
Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, background): “Thus, numerous simulations are started from the same initial condition and run in parallel on diﬀerent computers, and when one escapes from the energy minimum, all the simulations are stopped and started from the new productive conﬁguration (Pande et al., 2003).”
Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome (2006, neutral): “A closer connection between the simulated and experimental timescales of folding is to be expected in (atomically detailed) simulations of protein folding events that do not make such assumptions, such as the massive distributed computing simulations pioneered by the Pande group [60,61] and those th”
Anton, a special-purpose machine for molecular dynamics simulation (2007, background): “…quickly with distance that they can typically be neglected for pairs of particles separated by more than some cutoff radius , usually chosen between 5 and 15 Å. Neglecting electrostatic interactions beyond a cutoff, however, leads to serious artifacts in explicit solvent simulations [7, 23].”
The protein folding 'speed limit'. (2004, neutral): “1 300 [16] [22,91,108–119] N68H/K65Nle 35 1.”