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Comparison of multiple Amber force fields and development of improved protein backbone parameters

Comparison of multiple Amber force fields and development of improved protein backbone parameters

http://www.wikidata.org/entity/Q27861040

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Collective dynamics underlying allosteric transitions in hemoglobin Structural model of the hUbA1-UbcH10 quaternary complex: in silico and experimental analysis of the protein-protein interactions between E1, E2 and ubiquitin A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies.Structures of the E46K mutant-type α-synuclein protein and impact of E46K mutation on the structures of the wild-type α-synuclein protein Correlation as a determinant of configurational entropy in supramolecular and protein systems Computational and functional characterization of Angiogenin mutations, and correlation with amyotrophic lateral sclerosis Side chain specificity of ADP-ribosylation by a sirtuin Mutations to a glycine loop in the catalytic site of human Lon changes its protease, peptidase and ATPase activities NMR solution structure of rat aβ(1-16): toward understanding the mechanism of rats' resistance to Alzheimer's disease Improved side-chain torsion potentials for the Amber ff99SB protein force field Taming the complexity of protein folding Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53 Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail Amyloid beta-protein monomer folding: free-energy surfaces reveal alloform-specific differences Structure-based discovery of opioid analgesics with reduced side effects.Physicochemical Properties of Ion Pairs of Biological Macromolecules A hybrid approach to simulation of electron transfer in complex molecular systems Dynamics, flexibility and ligand-induced conformational changes in biological macromolecules: a computational approach Synergistic applications of MD and NMR for the study of biological systems Role of substrate dynamics in protein prenylation reactions Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis A computational study of the glycine-rich loop of mitochondrial processing peptidase In silico analysis of conformational changes induced by mutation of aromatic binding residues: consequences for drug binding in the hERG K+ channel Two arginine residues suppress the flexibility of nucleosomal DNA in the canonical nucleosome core Mechanism of p27 Unfolding for CDK2 Reactivation.Two distinct states of the HAMP domain from sensory rhodopsin transducer observed in unbiased molecular dynamics simulations Structural dynamics as a contributor to error-prone replication by an RNA-dependent RNA polymerase.A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation Novel allosteric sites on Ras for lead generation A Barley Efflux Transporter Operates in a Na+-Dependent Manner, as Revealed by a Multidisciplinary Platform Detailed Per-residue Energetic Analysis Explains the Driving Force for Microtubule Disassembly CELLULOSE SYNTHASE INTERACTIVE1 Is Required for Fast Recycling of Cellulose Synthase Complexes to the Plasma Membrane in Arabidopsis Mussel adhesion is dictated by time-regulated secretion and molecular conformation of mussel adhesive proteins.Molecular dynamics study of the opening mechanism for DNA polymerase I Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue A new model for pore formation by cholesterol-dependent cytolysins Different inward and outward conduction mechanisms in NaVMs suggested by molecular dynamics simulations Insights in 17beta-HSD1 enzyme kinetics and ligand binding by dynamic motion investigation

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P2860

Comparison of multiple Amber force fields and development of improved protein backbone parameters

http://www.wikidata.org/entity/Q27861040

description

2006 nî lūn-bûn

@nan

2006 թուականի Նոյեմբերին հրատարակուած գիտական յօդուած

@hyw

2006 թվականի նոյեմբերին հրատարակված գիտական հոդված

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2006年の論文

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2006年論文

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2006年論文

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2006年論文

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2006年論文

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2006年論文

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2006年论文

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name

Comparison of multiple Amber f ...... ed protein backbone parameters

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Comparison of multiple Amber f ...... ed protein backbone parameters

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Comparison of multiple Amber f ...... ed protein backbone parameters

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Comparison of multiple Amber f ...... ed protein backbone parameters

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Comparison of multiple Amber f ...... ed protein backbone parameters

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Comparison of multiple Amber f ...... ed protein backbone parameters

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Comparison of multiple Amber f ...... ed protein backbone parameters

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Comparison of multiple Amber f ...... ed protein backbone parameters

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Comparison of multiple Amber f ...... ed protein backbone parameters

@en

P2093

Adrian Roitberg

http://www.w3.org/2001/XMLSchema#string

Asim Okur

http://www.w3.org/2001/XMLSchema#string

Bentley Strockbine

http://www.w3.org/2001/XMLSchema#string

Carlos Simmerling

http://www.w3.org/2001/XMLSchema#string

Robert Abel

http://www.w3.org/2001/XMLSchema#string

Viktor Hornak

http://www.w3.org/2001/XMLSchema#string

P2860

Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations

PISCES: recent improvements to a PDB sequence culling server

Tryptophan zippers: Stable, monomeric -hairpins

Designing a 20-residue protein

Structure of ubiquitin refined at 1.8 A resolution

The Amber biomolecular simulation programs

The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure

Analysis and prediction of the different types of beta-turn in proteins

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

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712-25

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scholarly article

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232922

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10.1002/PROT.21123

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3

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65

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6813457

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16981200

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4805110

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