Cargando…

Improved side-chain torsion potentials for the Amber ff99SB protein force field

Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber...

Descripción completa

Detalles Bibliográficos
Autores principales:	Lindorff-Larsen, Kresten, Piana, Stefano, Palmo, Kim, Maragakis, Paul, Klepeis, John L, Dror, Ron O, Shaw, David E
Formato:	Texto
Lenguaje:	English
Publicado:	Wiley Subscription Services, Inc., A Wiley Company 2010
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/ https://www.ncbi.nlm.nih.gov/pubmed/20408171 http://dx.doi.org/10.1002/prot.22711

Ejemplares similares

Systematic Validation of Protein Force Fields against Experimental Data
por: Lindorff-Larsen, Kresten, et al.
Publicado: (2012)

Correction: Systematic Validation of Protein Force Fields against Experimental Data
por: Lindorff-Larsen, Kresten, et al.
Publicado: (2013)

Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations
por: Piana, Stefano, et al.
Publicado: (2012)

Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field
por: Yang, Darian T., et al.
Publicado: (2022)

FF12MC: A revised AMBER forcefield and new protein simulation protocol
por: Pang, Yuan‐Ping
Publicado: (2016)

Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein–Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF
por: He, Xibing, et al.
Publicado: (2020)

How well do force fields capture the strength of salt bridges in proteins?
por: Ahmed, Mustapha Carab, et al.
Publicado: (2018)

Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity
por: Jephthah, Stéphanie, et al.
Publicado: (2021)

Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine
por: Yildirim, Ilyas, et al.
Publicado: (2010)

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model
por: Debiec, Karl T., et al.
Publicado: (2016)

Evaluation of nine condensed-phase force fields of the GROMOS, CHARMM, OPLS, AMBER, and OpenFF families against experimental cross-solvation free energies
por: Kashefolgheta, Sadra, et al.
Publicado: (2021)

Comparing Molecular Dynamics Force Fields in the Essential Subspace
por: Martín-García, Fernando, et al.
Publicado: (2015)

Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised χ Torsions
por: Yildirim, Ilyas, et al.
Publicado: (2011)

Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range
por: Tesei, Giulio, et al.
Publicado: (2023)

Lipid14: The Amber Lipid Force Field
por: Dickson, Callum J., et al.
Publicado: (2014)

Similarity Measures for Protein Ensembles
por: Lindorff-Larsen, Kresten, et al.
Publicado: (2009)

Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations
por: Sborgi, Lorenzo, et al.
Publicado: (2015)

Mapping transiently formed and sparsely populated conformations on a complex energy landscape
por: Wang, Yong, et al.
Publicado: (2016)

Refinement of RNA Structures Using Amber Force Fields
por: Gray, Jonathon G., et al.
Publicado: (2021)

Robust AMBER Force Field Parameters for Glutathionylated Cysteines
por: Elftmaoui, Zineb, et al.
Publicado: (2023)

Combining Experiments and Simulations Using the Maximum Entropy Principle
por: Boomsma, Wouter, et al.
Publicado: (2014)

Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics
por: Wang, Yong, et al.
Publicado: (2017)

Torsion of the Ovary on Both Sides
por: Mankad, C. R.
Publicado: (1931)

S. A. ff. Dakin
Publicado: (1962)

Assessing the Current State of Amber Force Field Modifications for DNA
por: Galindo-Murillo, Rodrigo, et al.
Publicado: (2016)

Empirical Corrections to the Amber RNA Force Field with Target Metadynamics
por: Gil-Ley, Alejandro, et al.
Publicado: (2016)

Slow conformational changes in the rigid and highly stable chymotrypsin inhibitor 2
por: Gavrilov, Yulian, et al.
Publicado: (2023)

The ATP Synthase Subunits FfATPh, FfATP5, and FfATPb Regulate the Development, Pathogenicity, and Fungicide Sensitivity of Fusarium fujikuroi
por: Yang, Xin, et al.
Publicado: (2023)

Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods
por: Ahmed, Mustapha Carab, et al.
Publicado: (2021)

Correction to NMR of CCCC RNA Reveals a Right-Handed Helix and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics
por: Tubbs, Jason D., et al.
Publicado: (2013)

Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor
por: Escobedo, Albert, et al.
Publicado: (2019)

Transferable Force Field for Metal–Organic Frameworks from First-Principles: BTW-FF
por: Bristow, Jessica K., et al.
Publicado: (2014)

Mixing ReaxFF parameters for transition metal oxides using force-matching method
por: Włodarczyk, Adam, et al.
Publicado: (2021)

Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts
por: Crehuet, Ramon, et al.
Publicado: (2019)

Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field
por: Pabis, Anna, et al.
Publicado: (2014)

Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field
por: Fröhlking, Thorben, et al.
Publicado: (2022)

The Nuclear Magnetic Resonance of CCCC RNA Reveals a Right-Handed Helix, and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics
por: Tubbs, Jason D., et al.
Publicado: (2013)

Highlights of H→ff at the LHC
por: Chen, Xin
Publicado: (2019)

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
por: Cerutti, David S., et al.
Publicado: (2014)

Balanced Force Field ff03CMAP Improving the Dynamics Conformation Sampling of Phosphorylation Site
por: Zhong, Bozitao, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_g7u9sfdujs21beh5g9kskoq73o