Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Unknown venue

• Publication date

  2004-12-27

• Fields of study

  Biology, Chemistry, Computer Science

• Identifiers
  DOI 10.1016/J.CHEMPHYS.2004.08.002
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Improved treatment of the protein backbone in empirical force fields.

  2004cited by this paper
• PROTEIN FORCE-FIELD PARAMETERS OPTIMIZED WITH THE PROTEIN DATA BANK II: COMPARISONS OF FORCE FIELDS BY FOLDING SIMULATIONS OF SHORT PEPTIDES

  2004cited by this paper
• Comparisons of force fields for proteins by generalized-ensemble simulations

  2004cited by this paper
• Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments

  2003cited by this paper
• Force field influence on the observation of π-helical protein structures in molecular dynamics simulations

  2003cited by this paper
• Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides.

  2003cited by this paper
• Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system

  2003cited by this paper
• Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test

  2003cited by this paper
• Validation of an all-atom protein force field: From dipeptides to larger peptides

  2003cited by this paper
• Optimization of protein force-field parameters with the Protein Data Bank

  2003cited by this paper
• Molecular dynamics of C-peptide of ribonuclease A studied by replica-exchange Monte Carlo method and diffusion theory

  2003cited by this paper
• Free energy landscape of protein folding in water: Explicit vs. implicit solvent

  2003cited by this paper
• Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine “dipeptides” (Ace‐Ala‐Nme and Ace‐Gly‐Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

  2003cited by this paper
• Polyproline II structure in a sequence of seven alanine residues

  2002cited by this paper
• Modern protein force fields behave comparably in molecular dynamics simulations

  2002cited by this paper
• Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides†

  2001cited by this paper
• The free energy landscape for β hairpin folding in explicit water

  2001cited by this paper
• Exploring the energy landscape of a β hairpin in explicit solvent

  2001cited by this paper
• Dihedral angles of trialanine in D2O determined by combining FTIR and polarized visible Raman spectroscopy.

  2001cited by this paper
• Structure Determination of Trialanine in Water Using Polarization Sensitive Two-Dimensional Vibrational Spectroscopy

  2000cited by this paper
• Role of side-chains in the cooperative beta-hairpin folding of the short C-terminal fragment derived from streptococcal protein G.

  2000cited by this paper
• How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?

  2000cited by this paper
• Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus.

  2000cited by this paper
• Mechanisms and kinetics of beta-hairpin formation.

  2000cited by this paper
• Peptide free‐energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95

  2000cited by this paper
• Generalized-ensemble algorithms for molecular simulations of biopolymers.

  2000cited by this paper
• Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape

  2000cited by this paper
• Replica-exchange molecular dynamics method for protein folding

  1999cited by this paper
• Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques.

  1999cited by this paper
• Understanding beta-hairpin formation.

  1999cited by this paper
• Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G.

  1999cited by this paper
• Tertiary Structure Prediction of C-Peptide of Ribonuclease A by Multicanonical Algorithm

  1998cited by this paper
• Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A

  1998cited by this paper
• All-atom empirical potential for molecular modeling and dynamics studies of proteins.

  1998cited by this paper
• Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

  1998cited by this paper
• Energy landscape of a native protein: Jumping‐among‐minima model

  1998cited by this paper
• Folding dynamics and mechanism of β-hairpin formation

  1997cited by this paper
• Computer Simulation of Biomolecular Systems

  1997cited by this paper
• Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides

  1997cited by this paper
• Molecular dynamics, Langevin, and hybrid Monte Carlo simulations in multicanonical ensemble

  1996cited by this paper
• Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

  1996cited by this paper
• A second generation force field for the simulation of proteins

  1995cited by this paper
• RASMOL: biomolecular graphics for all.

  1995cited by this paper
• Complement assembly of two fragments of the streptococcal protein G B1 domain in aqueous solution

  1995cited by this paper
• Hydration of the partially folded peptide RN-24 studied by multidimensional NMR

  1995cited by this paper
• Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements.

  1995cited by this paper
• Exchange Monte Carlo Method and Application to Spin Glass Simulations

  1995cited by this paper
• Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides

  1994cited by this paper
• Raster3D Version 2.0. A program for photorealistic molecular graphics.

  1994cited by this paper
• A short linear peptide that folds into a native stable β-hairpin in aqueous solution

  1994cited by this paper
• THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method

  1992cited by this paper
• Presto(protein Engineering Simulator): A Vectorized Molecular Mechanics Program for Biopolymers

  1992cited by this paper
• Multicanonical ensemble: A new approach to simulate first-order phase transitions.

  1992cited by this paper
• A program to produce both detailed and schematic plots of protein structures

  1991cited by this paper
• Multicanonical algorithms for first order phase transitions

  1991cited by this paper
• Optimized Monte Carlo data analysis.

  1989cited by this paper
• 1H NMR studies of the solution conformations of an analogue of the C-peptide of ribonuclease A.

  1989cited by this paper
• A fast algorithm for rendering space-filling molecule pictures

  1988cited by this paper
• New Monte Carlo technique for studying phase transitions.

  1988cited by this paper
• Tests of the helix dipole model for stabilization of α-helices

  1987cited by this paper
• Nature of the charged-group effect on the stability of the C-peptide helix.

  1985cited by this paper
• Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

  1983cited by this paper
• Comparison of simple potential functions for simulating liquid water

  1983cited by this paper

• Depolarizing Effects in Hydrogen Bond Energy in 310-Helices Revealed by Quantum Chemical Analysis

  2022cites this paper
• Quantum chemical studies on hydrogen bonds in helical secondary structures

  2022cites this paper
• How to strike a conformational balance in protein force fields for molecular dynamics simulations?

  2021cites this paper
• Improvement of the Force Field for β-d-Glucose with Machine Learning

  2021cites this paper
• Protein structure predictions by enhanced conformational sampling methods

  2019cites this paper
• Developments and Applications of Coil-Library-Based Residue-Specific Force Fields for Molecular Dynamics Simulations of Peptides and Proteins.

  2019cites this paper
• Replica-Based Protein Structure Sampling Methods II: Advanced Hybrid Solvent TIGER2hs.

  2019cites this paper
• A test of AMBER force fields in predicting the secondary structure of α-helical and β-hairpin peptides

  2017cites this paper
• Are AMBER Force Fields and Implicit Solvation Models Additive? A Folding Study with a Balanced Peptide Test Set.

  2016cites this paper
• Density functional study of molecular interactions in secondary structures of proteins

  2016cites this paper
• An Updated Test of AMBER Force Fields and Implicit Solvent Models in Predicting the Secondary Structure of Helical, β-Hairpin, and Intrinsically Disordered Peptides.

  2016cites this paper
• Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment.

  2015cites this paper
• Force-Field Induced Bias in the Structure of Aβ21-30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields

  2015cites this paper
• Structural predictions of neurobiologically relevant G-protein coupled receptors and intrinsically disordered proteins.

  2015cites this paper
• Salt effects on hydrophobic‐core formation in folding of a helical miniprotein studied by molecular dynamics simulations

  2014cites this paper
• Protein Conformational Dynamics

  2014cites this paper
• How accurately do current force fields predict experimental peptide conformations? An adiabatic free energy dynamics study.

  2014cites this paper
• Residue-specific force field based on the protein coil library. RSFF1: modification of OPLS-AA/L.

  2014cites this paper
• Predicting conformational ensembles of the intrinsically disordered protein α-Synuclein via molecular simulation

  2014influential citation
• Insights into the binding of intrinsically disordered proteins from molecular dynamics simulation

  2014cites this paper
• Protein folding simulations by generalized-ensemble algorithms.

  2014cites this paper
• Residue-Speci fi c Force Field Based on the Protein Coil Library

  2014cites this paper
• On the foldability of tryptophan-containing tetra- and pentapeptides: an exhaustive molecular dynamics study.

  2013cites this paper
• The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development.

  2013cites this paper
• Improvement of the backbone-torsion-energy term in the force field for protein systems by the double Fourier series expansion

  2013cites this paper
• Microsecond folding experiments and simulations: a match is made.

  2013cites this paper
• Orbitales localisées pour les interactions intermoléculaires

  2012cites this paper
• Membrane Protein Simulations Using AMBER Force Field and Berger Lipid Parameters.

  2012cites this paper
• Extension of the AMBER force field to cyclic α,α dialkylated peptides.

  2012cites this paper
• Towards the physical basis of how intrinsic disorder mediates protein function.

  2012cites this paper
• Optimizations of Protein Force Fields

  2012cites this paper
• Amino-acid-dependent main-chain torsion-energy terms for protein systems.

  2012cites this paper
• Molecular Dynamics Simulations of Voltage-Gated Cation Channels: Insights on Voltage-Sensor Domain Function and Modulation

  2012cites this paper
• Molecular dynamics simulations of a new branched antimicrobial peptide: a comparison of force fields.

  2012cites this paper
• Water interaction differences determine the relative energetic stability of the polyproline II conformation of the alanine dipeptide in aqueous environments.

  2012cites this paper
• Remote thioredoxin recognition using evolutionary conservation and structural dynamics.

  2011cites this paper
• Effective All-Atom Potentials for Proteins

  2011cites this paper
• A THEORETICAL INVESTIGATION EXAMINING DNA CONFORMATIONAL CHANGES AND THEIR EFFECTS ON GLYCOSYLASE FUNCTION

  2011cites this paper
• Observation of two families of folding pathways of BBL.

  2011cites this paper
• Study of pH-dependent misfolding of surfactant protein C using state-of-the-art molecular modelling techniques

  2011cites this paper
• Rotational barriers in alkanes

  2011cites this paper
• Comparison between Molecular Dynamic Based and Knowledge Based Potentials for Protein Side Chains

  2010cites this paper
• Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations.

  2010cites this paper
• Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration.

  2010cites this paper
• Folding simulations of three proteins having all α-helix, all β-strand and α/β-structures

  2010cites this paper
• A replica-exchange approach to computing peptide conformational free energies

  2010cites this paper
• Determination method of the balance of the secondary-structure-forming tendencies of force fields

  2010cites this paper
• Intrinsically Disordered Proteins in a Physics-Based World

  2010cites this paper
• Nucleic Acids Structure Minitutorial

  2010cites this paper
• Controlling the secondary-structure-forming tendencies of proteins by a backbone torsion-energy term

  2010cites this paper
• Optimisation of OPLS–UA force-field parameters for protein systems using protein data bank

  2010cites this paper
• Design Of Next Generation Force Fields From AB Initio Computations: Beyond Point Charges Electrostatics

  2009cites this paper
• 3-10 and Pi-Helices: Stochastic Events on Sequence Space; Reasons and Implications of their Accidental Occurrences across Protein Universe

  2009cites this paper
• Force field‐dependant structural divergence revealed during long time simulations of Calbindin d9k

  2009cites this paper
• An effective all-atom potential for proteins

  2009cites this paper
• Force field bias in protein folding simulations.

  2009cites this paper
• Free-energy landscapes of proteins in solution by generalized-ensemble simulations.

  2009cites this paper
• Atomistic details of the disordered states of KID and pKID. Implications in coupled binding and folding.

  2009cites this paper
• Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures

  2009cites this paper
• Convergence and Heterogeneity in Peptide Folding with Replica Exchange Molecular Dynamics.

  2009cites this paper
• Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.

  2008cites this paper
• A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein–water interface as a determinant of pKavalues

  2008influential citation
• Ten-microsecond molecular dynamics simulation of a fast-folding WW domain.

  2008cites this paper
• Conformational sampling of peptides in cellular environments.

  2008cites this paper
• Protein folding, unfolding and aggregation studied using an all-atom model with a simplified interaction potential

  2008cites this paper
• The protein folding problem.

  2008cites this paper
• Long time and large size molecular dynamics simulations made feasible through new TeraGrid hardware and software

  2008cites this paper
• Molecular dynamics simulations on the oligomer-formation process of the GNNQQNY peptide from yeast prion protein Sup35.

  2007cites this paper
• Replica-exchange molecular dynamics simulation of diffracted X-ray tracking

  2007cites this paper
• Protein folding by zipping and assembly

  2007cites this paper
• Cooperative folding mechanism of a β‐hairpin peptide studied by a multicanonical replica‐exchange molecular dynamics simulation

  2006cites this paper
• PROFASI: A Monte Carlo simulation package for protein folding and aggregation

  2006cites this paper
• Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis

  2006cites this paper
• Modeling H3 histone N-terminal tail and linker DNA interactions.

  2006cites this paper
• Structures of a peptide fragment of β2‐microglobulin studied by replica‐exchange molecular dynamics simulations – Towards the understanding of the mechanism of amyloid formation

  2005cites this paper
• Secondary-Structure Design of Proteins by a Backbone Torsion Energy(Cross-disciplinary Physics and Related Areas of Science and Technology)

  2005cites this paper
• Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent.

  2005cites this paper
• Optimizations of Protein Force-Field Parameters with Protein Data Bank

  2005cites this paper
• Free energy landscape and folding mechanism of a β‐hairpin in explicit water: A replica exchange molecular dynamics study

  2005cites this paper
• Effects of the fixed end in single-molecule imaging techniques: A replica-exchange molecular dynamics simulation study

  2005cites this paper
• Implementing Advanced Force Fields for Simulation of Physical and Biological Processes

  year unknowncites this paper