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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
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Journal ArticleDOI
Rapid parameterization of small molecules using the Force Field Toolkit.
TL;DR: The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error‐prone tasks, and graphical user interface design.
Journal ArticleDOI
Effect of KRAS Oncogene Substitutions on Protein Behavior: Implications for Signaling and Clinical Outcome
Nathan T. Ihle,Lauren Averett Byers,Edward S. Kim,Pierre Saintigny,J. Jack Lee,George R. Blumenschein,Anne Tsao,Suyu Liu,Jill E. Larsen,Jing Wang,Lixia Diao,Kevin R. Coombes,Lu Chen,Shuxing Zhang,Mena Abdelmelek,Ximing Tang,Vassiliki A. Papadimitrakopoulou,John D. Minna,Scott M. Lippman,Waun Ki Hong,Roy S. Herbst,Ignacio I. Wistuba,John V. Heymach,Garth Powis +23 more
TL;DR: Molecular modeling studies showed that different conformations imposed by mutant KRas may lead to altered association with downstream signaling transducers, and implies that therapeutic interventions may need to take into account the specific mutants expressed by the tumor.
Journal ArticleDOI
GPU-accelerated molecular modeling coming of age
TL;DR: The development of molecular modeling algorithms that leverage GPU computing, the advances already made and remaining issues to be resolved, and the continuing evolution of GPU technology that promises to become even more useful to molecular modeling are surveyed.
Journal ArticleDOI
X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel
Hugues Nury,Catherine Van Renterghem,Catherine Van Renterghem,Yun Weng,Alphonso Tran,Marc Baaden,Virginie Dufresne,Virginie Dufresne,Jean-Pierre Changeux,Jean-Pierre Changeux,James M. Sonner,Marc Delarue,Marc Delarue,Pierre-Jean Corringer,Pierre-Jean Corringer +14 more
TL;DR: Molecular dynamics simulations, performed on the wild type (WT) and two GLIC mutants, highlight differences in mobility of propofol in its binding site and help to explain these effects, and provide a novel structural framework for the design of general anaesthetics and of allosteric modulators of brain pLGICs.
Journal ArticleDOI
Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations
TL;DR: An overview of current RBFE implementations, highlighting recent advances and remaining challenges, along with examples that emphasize practical considerations for obtaining reliable RBFE results is presented, with a focus on real-world drug discovery 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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