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Scalable Molecular Dynamics with NAMD
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The article was published on 2012-12-14 and is currently open access. It has received 13375 citations till now.read more
Citations
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Journal ArticleDOI
Mechanisms of membrane binding of small GTPase K-Ras4B farnesylated hypervariable region.
Hyunbum Jang,Hyunbum Jang,Sherwin J. Abraham,Sherwin J. Abraham,Tanmay S. Chavan,Tanmay S. Chavan,Ben Hitchinson,Lyuba Khavrutskii,Lyuba Khavrutskii,Nadya I. Tarasova,Ruth Nussinov,Ruth Nussinov,Ruth Nussinov,Vadim Gaponenko +13 more
TL;DR: The mechanism illuminates the roles of HVR modifications in K-Ras4B targeting microdomains of the plasma membrane and suggests an additional function for HVR in regulation of Ras signaling.
Proceedings ArticleDOI
Modeling and tolerating heterogeneous failures in large parallel systems
TL;DR: This work model each component and construct integrated failure models given the component us age of common supercomputing applications and shows that these application-centric models provide more accurate reliability estimates compared to general models, which improves the efficacy of fault-tolerant algorithms.
Journal ArticleDOI
Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration.
TL;DR: An equivalent methodology based on thermodynamic integration to substantially improve the speed, accuracy, precision, and reliability of calculated relative binding free energies is described.
Journal ArticleDOI
Structural Basis of the Potential Binding Mechanism of Remdesivir to SARS-CoV-2 RNA-Dependent RNA Polymerase.
TL;DR: It is suggested that remdesivir can potentially act as a SARS-CoV-2 RNA-chain terminator, effectively stopping its RNA replication, with key residues also identified for future lead optimization and/or drug resistance studies.
Journal ArticleDOI
Multiscale methods in drug design bridge chemical and biological complexity in the search for cures
TL;DR: This Perspective discusses how emerging data-rich, physics-based multiscale approaches are of the cusp of realizing long-promised impact in the discovery, design and development of novel therapeutics, and highlights emerging methods and applications.
References
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Journal ArticleDOI
Generalized Gradient Approximation Made Simple
TL;DR: A simple derivation of a simple GGA is presented, in which all parameters (other than those in LSD) are fundamental constants, and only general features of the detailed construction underlying the Perdew-Wang 1991 (PW91) GGA are invoked.
Journal ArticleDOI
Self-Consistent Equations Including Exchange and Correlation Effects
Walter Kohn,L. J. Sham +1 more
TL;DR: In this paper, the Hartree and Hartree-Fock equations are applied to a uniform electron gas, where the exchange and correlation portions of the chemical potential of the gas are used as additional effective potentials.
Journal ArticleDOI
VMD: Visual molecular dynamics
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
Journal ArticleDOI
Density-functional exchange-energy approximation with correct asymptotic behavior.
TL;DR: This work reports a gradient-corrected exchange-energy functional, containing only one parameter, that fits the exact Hartree-Fock exchange energies of a wide variety of atomic systems with remarkable accuracy, surpassing the performance of previous functionals containing two parameters or more.
Fast parallel algorithms for short-range molecular dynamics
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
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