Journal ArticleDOI
Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease.
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TLDR
The emergence of compensatory drug-resistant mutations in HIV-1 protease challenges the common view of the reaction mechanism of this enzyme by performing classical and ab initio molecular dynamics simulations on a complex between the enzyme and a peptide substrate.About:
This article is published in Journal of Molecular Biology.The article was published on 2002-05-31. It has received 140 citations till now. The article focuses on the topics: Active site & HIV-1 protease.read more
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A Perspective on Enzyme Catalysis
TL;DR: A case study for the enzyme dihydrofolate reductase provides evidence for coupled networks of predominantly conserved residues that influence the protein structure and motion that have important implications for the origin and evolution of enzymes, as well as for protein engineering.
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Is allostery an intrinsic property of all dynamic proteins
TL;DR: It is argued that all (nonfibrous) proteins are potentially allosteric, and experimental observations validating this view of protein allostery are reviewed.
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An NMR perspective on enzyme dynamics.
TL;DR: Binding of substrate can lead to the repositioning of catalytic groups, effectively bridging the dynamic processes of substrate binding and catalysis.
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Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions.
TL;DR: 1. Reactive Flux Method 3156 6.6.1.
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Anisotropic network model: systematic evaluation and a new web interface
TL;DR: Residue fluctuations in globular proteins are shown to be more accurately predicted than those in nonglobular proteins, and core residues are more accurately described than solvent-exposed ones.
References
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Journal ArticleDOI
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
TL;DR: Numerical calculations on a number of atoms, positive ions, and molecules, of both open- and closed-shell type, show that density-functional formulas for the correlation energy and correlation potential give correlation energies within a few percent.
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.
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The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
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Molecular dynamics with coupling to an external bath.
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
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Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
TL;DR: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms.