PLUMED: A portable plugin for free-energy calculations with molecular dynamics
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Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and DynamicsMetadynamics studies of crystal nucleationAtomistic picture for the folding pathway of a hybrid-1 type human telomeric DNA G-quadruplexFree energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNAComputational study of synthetic agonist ligands of ionotropic glutamate receptorsComputational studies of the binding profile of phosphoinositide PtdIns (3,4,5) P₃ with the pleckstrin homology domain of an oomycete cellulose synthaseEvidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteinsThe Molecular Mechanism of Substrate Engagement and Immunosuppressant Inhibition of CalcineurinHuman immunoglobulin E flexes between acutely bent and extended conformations.Molecular mechanism of Aurora A kinase autophosphorylation and its allosteric activation by TPX2Crystal structure of the deglycating enzyme Amadoriase I in its free form and substrate-bound complexMultiple routes and milestones in the folding of HIV-1 protease monomerA catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulationsThe impact of small molecule binding on the energy landscape of the intrinsically disordered protein C-mycProtein dynamics of the HIF-2α PAS-B domain upon heterodimerization and ligand bindingThe free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discoveryLocating the route of entry and binding sites of benzocaine and phenytoin in a bacterial voltage gated sodium channelP-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscapeSecondary Structure of Rat and Human Amylin across Force FieldsSignaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonisTowards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational DynamicsBIN1/M-Amphiphysin2 induces clustering of phosphoinositides to recruit its downstream partner dynamin.Two-state dynamics of the SH3-SH2 tandem of Abl kinase and the allosteric role of the N-capALMOST: an all atom molecular simulation toolkit for protein structure determination.How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory.DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions.Funnel metadynamics as accurate binding free-energy methodPhosphate release coupled to rotary motion of F1-ATPase.Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein.The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning.The glycan role in the glycopeptide immunogenicity revealed by atomistic simulations and spectroscopic experiments on the multiple sclerosis biomarker CSF114(Glc)Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization.Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates.In situ data analytics and indexing of protein trajectories.Mechanistic insight into ligand binding to G-quadruplex DNAEvolutionary Divergence of the C-terminal Domain of Complexin Accounts for Functional Disparities between Vertebrate and Invertebrate ComplexinsMetadynamics simulation study on the conformational transformation of HhaI methyltransferase: an induced-fit base-flipping hypothesisLigand-induced modulation of the free-energy landscape of G protein-coupled receptors explored by adaptive biasing techniquesA robust nanoscale experimental quantification of fracture energy in a bilayer material systemThe five-to-six-coordination transition of ferric human serum heme-albumin is allosterically-modulated by ibuprofen and warfarin: a combined XAS and MD study
P2860
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P2860
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
description
article
@en
im Oktober 2009 veröffentlichter wissenschaftlicher Artikel
@de
wetenschappelijk artikel
@nl
наукова стаття, опублікована в жовтні 2009
@uk
name
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
@en
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
@nl
type
label
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
@en
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
@nl
prefLabel
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
@en
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
@nl
P2093
P50
P1476
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
@en
P2093
Davide Branduardi
Davide Provasi
Fabrizio Marinelli
Massimiliano Bonomi
Michele Parrinello
Ricardo A. Broglia
P304
P356
10.1016/J.CPC.2009.05.011
P577
2009-10-01T00:00:00Z