How robust are protein folding simulations with respect to force field parameterization?
about
Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulationsThe Internal Dynamics of Fibrinogen and Its Implications for Coagulation and AdsorptionComparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations.High-resolution crystal structure of human protease-activated receptor 1Structure and dynamics of the M3 muscarinic acetylcholine receptorAtypical OmpR/PhoB Subfamily Response Regulator GlnR of Actinomycetes Functions as a Homodimer, Stabilized by the Unphosphorylated Conserved Asp-focused Charge InteractionsCold denaturation of a protein dimer monitored at atomic resolutionA structural ensemble of a ribosome-nascent chain complex during cotranslational protein folding.When fast is better: protein folding fundamentals and mechanisms from ultrafast approachesDistance-Based Configurational Entropy of Proteins from Molecular Dynamics SimulationsExploring early stages of the chemical unfolding of proteins at the proteome scaleThe SH2 domain regulates c-Abl kinase activation by a cyclin-like mechanism and remodulation of the hinge motionSecondary Structure of Rat and Human Amylin across Force FieldsEnhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolinA molecular interpretation of 2D IR protein folding experiments with Markov state modelsSystematic validation of protein force fields against experimental dataAn Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase.CHARMM36 all-atom additive protein force field: validation based on comparison to NMR dataFormulation of probabilistic models of protein structure in atomic detail using the reference ratio method.Assessing the effect of dynamics on the closed-loop protein-folding hypothesisProtein folding and de novo protein design for biotechnological applicationsForce Field for Peptides and Proteins based on the Classical Drude OscillatorElectronic polarization stabilizes tertiary structure prediction of HP-36.Protein structure prediction: assembly of secondary structure elements by basin-hopping.Enhanced Sampling of Coarse-Grained Transmembrane-Peptide Structure Formation from Hydrogen-Bond Replica Exchange.Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition.pmx: Automated protein structure and topology generation for alchemical perturbations.Comparing molecular dynamics force fields in the essential subspace.Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations.Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides.DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions.The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer.Coarse-Grained Models for Protein-Cell Membrane Interactions.An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass.Solvent effect on the folding dynamics and structure of E6-associated protein characterized from ab initio protein folding simulations.Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.Protein structure prediction using global optimization by basin-hopping with NMR shift restraints.Misplaced helix slows down ultrafast pressure-jump protein foldingJoyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data.Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.
P2860
Q21134160-417CB896-AAAF-49ED-9FE7-88CAFDF4AE7EQ27318502-EB1875C2-F432-4DE4-BA7D-163DD36CBBD5Q27337348-2CA1B823-C705-4438-B52D-2924BF14C9DEQ27675402-82111731-A2EE-4397-8AE7-9A9FE1D06245Q27677433-41344B36-2D9B-46F2-9AA2-9FA520CAD05BQ27683358-06FAFA6A-A110-4596-B470-3F077A843ABEQ27683967-DF00DFB1-27E2-4FA8-B651-843FB149EE52Q27704200-05751710-BB6D-4441-840D-B0F08A251F03Q28080003-C4563EAA-50EA-447B-B99D-92A3256CDDEBQ28383547-4C82A9F5-F79E-4B21-8F7C-F095A2C9A4D8Q28536903-1398D74D-6779-4324-803F-5C86E02DB1C4Q28543640-085F2953-3F90-4C3C-B69B-4F3A41A6230DQ28546876-B8924ECF-3177-4220-AE9F-1B39C4C8C2A7Q28601123-BAED446C-7F4B-42E5-AC06-9F8B2D537A9CQ28660159-6B359433-ECCD-4846-B6FC-D7218DEF5D87Q28731830-CF13D5DF-0275-4628-B0E1-91697E00F035Q30152729-E1E69A5A-B2CF-43B1-A272-06E9ADE296BEQ30351917-E7D8D0E6-258D-4691-8615-0926BAEE09CCQ30352752-E938CB8F-551A-4223-93CA-2435C551D78EQ30355826-7B6F5507-BDBC-4535-8B34-A35EAB9796C9Q30355936-5599D77C-94F4-4174-81F9-A008F1A1DFC7Q30358273-4CE68327-3A16-4682-B779-CBA539034F4CQ30361195-278EF351-C337-4E88-ACD1-143264780806Q30365048-A2CB4FCA-A0D5-46BE-B021-204D9F13212CQ30367786-43DC7E59-0800-4F69-B1AE-5E930A17E331Q30368111-B119CEE9-B47B-4F45-9E59-08F3FA3F9D92Q30369502-2BA49D46-EE00-4897-8A25-8F8E22314A38Q30373070-943ED831-A595-4D8F-836E-EF3F0ED1BF76Q30377837-30C82F03-88FA-47B1-B476-3A644029F7B8Q30388784-66D5EF2F-38EE-478E-8603-016D2C09C3F5Q30392650-5C9AC688-B52F-46E6-AB6C-A0C858FEFAC1Q30396819-CF540174-C871-470B-BAAE-89B18A35136CQ30398145-2D9CA253-FA63-4FC6-B8E5-A800DA2DBDEBQ30402785-D3EF4CAB-90DB-4A4B-B7B0-EA76F84AFB60Q30415112-253BB43F-3AC0-4E6C-8A8C-21C1A8FB5A70Q30415550-05D127E9-30BA-420C-B3F9-0B374228B84DQ30425947-84F37EB4-28D6-420D-A591-07DE924988ADQ30539947-D42D6961-9FFF-4236-88A9-DCC6615ECA44Q30587280-23514F00-10FD-4592-8756-58DE8C9E2742Q30804944-1B4256BA-ADDE-496A-97B2-CCCC4AADEA44
P2860
How robust are protein folding simulations with respect to force field parameterization?
description
2011 nî lūn-bûn
@nan
2011年の論文
@ja
2011年論文
@yue
2011年論文
@zh-hant
2011年論文
@zh-hk
2011年論文
@zh-mo
2011年論文
@zh-tw
2011年论文
@wuu
2011年论文
@zh
2011年论文
@zh-cn
name
How robust are protein folding simulations with respect to force field parameterization?
@en
How robust are protein folding simulations with respect to force field parameterization?
@nl
type
label
How robust are protein folding simulations with respect to force field parameterization?
@en
How robust are protein folding simulations with respect to force field parameterization?
@nl
prefLabel
How robust are protein folding simulations with respect to force field parameterization?
@en
How robust are protein folding simulations with respect to force field parameterization?
@nl
P2860
P1433
P1476
How robust are protein folding simulations with respect to force field parameterization?
@en
P2093
David E Shaw
Stefano Piana
P2860
P356
10.1016/J.BPJ.2011.03.051
P407
P577
2011-05-01T00:00:00Z