How Fast-Folding Proteins Fold
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October 2011 |
Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field
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February 2015 |
Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator
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October 2004 |
A simple polarizable model of water based on classical Drude oscillators
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September 2003 |
Current Status of the AMOEBA Polarizable Force Field
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March 2010 |
Development of the Charmm Polarizable Force Field for Polypeptides Based on Drude Oscillators
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February 2011 |
The Amber biomolecular simulation programs
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January 2005 |
Comparison of multiple Amber force fields and development of improved protein backbone parameters
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November 2006 |
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
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May 1995 |
Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins
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December 2002 |
-Helical stabilization by side chain shielding of backbone hydrogen bonds
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February 2002 |
Conformational transition states of a β-hairpin peptide between the ordered and disordered conformations in explicit water
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October 2002 |
Energy landscape of a peptide consisting of α-helix, 3 10 -helix, β-turn, β-hairpin, and other disordered conformations
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journal
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June 2001 |
Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95
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July 2000 |
Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures
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January 1999 |
Accurate ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields
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June 1997 |
Residue-Specific α-Helix Propensities from Molecular Simulation
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March 2012 |
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
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July 2015 |
Molecular dynamics simulation of triclinic lysozyme in a crystal lattice: Molecular Dynamics of Crystal Lysozyme
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June 2015 |
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
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August 2012 |
Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides
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July 2009 |
Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association
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October 2014 |
Are Current Molecular Dynamics Force Fields too Helical?
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July 2008 |
Using J -Coupling Constants for Force Field Validation: Application to Hepta-alanine
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December 2011 |
Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities.
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July 1992 |
A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation
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June 2008 |
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
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April 1998 |
Balancing Solvation and Intramolecular Interactions: Toward a Consistent Generalized Born Force Field
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March 2006 |
ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
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October 2014 |
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
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May 2004 |
Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model
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July 2016 |
Water Model Tuning for Improved Reproduction of Rotational Diffusion and NMR Spectral Density
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journal
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May 2012 |
Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment
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journal
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October 2015 |
Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations
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journal
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February 2014 |
Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States
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journal
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December 2014 |
Residue-Specific Force Field Based on the Protein Coil Library. RSFF1: Modification of OPLS-AA/L
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May 2014 |
New Force Field on Modeling Intrinsically Disordered Proteins
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July 2014 |
ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins
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September 2016 |
Developing a molecular dynamics force field for both folded and disordered protein states
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May 2018 |
Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment
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journal
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June 2015 |
Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States
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April 2015 |
Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
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May 2014 |
Building Water Models: A Different Approach
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October 2014 |
General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins
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March 2019 |
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements
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March 2012 |
Advances in free-energy-based simulations of protein folding and ligand binding
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February 2016 |
Anton, a special-purpose machine for molecular dynamics simulation
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July 2008 |
Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent
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August 2014 |
Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations
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September 2015 |
Context-Independent, Temperature-Dependent Helical Propensities for Amino Acid Residues
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journal
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September 2009 |
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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journal
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August 2004 |
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
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November 2016 |
Stabilizing and Destabilizing Effects of Placing .beta.-Branched Amino Acids in Protein .alpha.-Helixes
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October 1994 |
The penultimate rotamer library
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January 2000 |
Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR Study
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February 2007 |
Residue-Specific Force Field Based on Protein Coil Library. RSFF2: Modification of AMBER ff99SB
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August 2014 |
Universal Implementation of a Residue-Specific Force Field Based on CMAP Potentials and Free Energy Decomposition
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journal
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June 2018 |
The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins
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May 2017 |
An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids
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August 2000 |
A new force field for molecular mechanical simulation of nucleic acids and proteins
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February 1984 |
An all atom force field for simulations of proteins and nucleic acids: An All Atom Force Field
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April 1986 |
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J . Am . Chem . Soc . 1995 , 117 , 5179−5197
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January 1996 |
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
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October 1993 |
Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme
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February 2006 |
Building Force Fields: An Automatic, Systematic, and Reproducible Approach
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May 2014 |
Empirical force fields for biological macromolecules: Overview and issues
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January 2004 |
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
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October 2003 |
A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects
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journal
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August 2012 |
Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization
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journal
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February 2013 |
110 Refinement of force field torsion parameters for nucleic acids based on inclusion of conformation-dependent solvation effects
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journal
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January 2013 |
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
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journal
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August 2011 |
Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields
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journal
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July 2015 |
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15
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journal
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April 2017 |
The Protein Data Bank
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January 2000 |
Comparison of simple potential functions for simulating liquid water
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July 1983 |
Improved Generalized Born Solvent Model Parameters for Protein Simulations
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March 2013 |
Generalized Born Model with a Simple, Robust Molecular Volume Correction
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December 2006 |
Structural insights for designed alanine-rich helices: Comparing NMR helicity measures and conformational ensembles from molecular dynamics simulation
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September 2008 |
Crystal Structure of a Ten-Amino Acid Protein
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November 2008 |
Raising the Speed Limit for β-Hairpin Formation
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journal
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August 2012 |
Evaluation of Backbone Proton Positions and Dynamics in a Small Protein by Liquid Crystal NMR Spectroscopy
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journal
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July 2003 |
Structure of ubiquitin refined at 1.8 Å resolution
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journal
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April 1987 |
Comparison of radiation-induced decay and structure refinement from X-ray data collected from lysozyme crystals at low and ambient temperatures
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journal
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June 1993 |
Development and testing of a general amber force field
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journal
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January 2004 |
Approximate solvent-accessible surface areas from tetrahedrally directed neighbor densities
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journal
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October 1999 |
Structure validation by Cα geometry: ϕ,ψ and Cβ deviation
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journal
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January 2003 |
CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software
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journal
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December 2009 |
Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions
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May 2009 |
Continuous surface charge polarizable continuum models of solvation. I. General formalism
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March 2010 |
Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions
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January 2006 |
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
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April 2010 |
Atomic charges derived from semiempirical methods
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May 1990 |
An approach to computing electrostatic charges for molecules
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April 1984 |
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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March 1977 |
Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations
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January 2004 |
Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning
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March 2015 |
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
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June 2013 |
On the Theory of Helix—Coil Transition in Polypeptides
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June 1961 |
Discussion: Jackknife, Bootstrap and Other Resampling Methods in Regression Analysis
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December 1986 |
Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data
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August 2009 |
Contact Electron‐Spin Coupling of Nuclear Magnetic Moments
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January 1959 |
Determination of φ and χ 1 Angles in Proteins from 13 C− 13 C Three-Bond J Couplings Measured by Three-Dimensional Heteronuclear NMR. How Planar Is the Peptide Bond?
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July 1997 |
Intrinsic backbone preferences are fully present in blocked amino acids
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January 2006 |
Modification of the Generalized Born Model Suitable for Macromolecules
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April 2000 |
Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation
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February 2014 |
Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results
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August 1982 |
General Framework for Studying the Dynamics of Folded and Nonfolded Proteins by NMR Relaxation Spectroscopy and MD Simulation
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April 2002 |
NMR Order Parameter Determination from Long Molecular Dynamics Trajectories for Objective Comparison with Experiment
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May 2014 |
Exploring Multiple Timescale Motions in Protein GB3 Using Accelerated Molecular Dynamics and NMR Spectroscopy
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April 2007 |
Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins
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May 2011 |
Crystallographic model validation: from diagnosis to healing
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October 2013 |
MolProbity: More and better reference data for improved all-atom structure validation: PROTEIN SCIENCE.ORG
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November 2017 |
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
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December 1983 |
Biopython: freely available Python tools for computational molecular biology and bioinformatics
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March 2009 |
Rotamers: To be or not to be?
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March 1993 |
Local Interactions in Protein Folding: Lessons from the α-Helix
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January 1997 |
All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination
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February 1997 |
Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model
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January 2006 |
A Helix Propensity Scale Based on Experimental Studies of Peptides and Proteins
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July 1998 |
The relation between the divergence of sequence and structure in proteins.
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April 1986 |
Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse
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November 2010 |
A general purpose model for the condensed phases of water: TIP4P/2005
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December 2005 |
Improved side-chain torsion potentials for the Amber ff99SB protein force field
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January 2010 |
N- and C-capping preferences for all 20 amino acids in α-helical peptides
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journal
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July 1995 |
Helix propagation and N-cap propensities of the amino acids measured in alanine-based peptides in 40 volume percent trifluoroethanol
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December 1996 |
Rotational diffusion anisotropy of human ubiquitin from 15N NMR relaxation
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December 1995 |
Structural Determinants of Protein Dynamics: Analysis of 15N NMR Relaxation Measurements for Main-Chain and Side-Chain Nuclei of Hen Egg White Lysozyme
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March 1995 |
Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation
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February 2007 |