P
Peter L. Freddolino
Researcher at University of Michigan
Publications - 104
Citations - 6523
Peter L. Freddolino is an academic researcher from University of Michigan. The author has contributed to research in topics: Biology & Gene. The author has an hindex of 35, co-authored 85 publications receiving 5376 citations. Previous affiliations of Peter L. Freddolino include Columbia University & University of Illinois at Urbana–Champaign.
Papers
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Journal ArticleDOI
Accelerating molecular modeling applications with graphics processors
John E. Stone,James C. Phillips,Peter L. Freddolino,David J. Hardy,Leonardo G. Trabuco,Klaus Schulten +5 more
TL;DR: An overview of recent advances in programmable GPUs is presented, with an emphasis on their application to molecular mechanics simulations and the programming techniques required to obtain optimal performance in these cases.
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Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus
TL;DR: This work presents an all-atom molecular dynamics simulation of a complete virus, the satellite tobacco mosaic virus, and demonstrates the stability of the entire virion and of the RNA core alone, while the capsid without RNA exhibits a pronounced instability.
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COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information
TL;DR: Large-scale benchmark tests show that the new hybrid COFACTOR approach significantly improves the function annotation accuracy of the former structure-based pipeline and other state-of-the-art functional annotation methods, particularly for targets that have no close homology templates.
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Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain
TL;DR: A ten-microsecond simulation of an incipient downhill-folding WW domain mutant along with measurement of a molecular time and activated folding time of 1.5 microseconds and 13.3 microseconds is reported.
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Challenges in protein-folding simulations
TL;DR: Recent progress in the simulation of three common model systems for protein folding is reviewed, and how recent advances in technology and theory are allowing protein folding simulations to address their current shortcomings is discussed.