Related references
Note: Only part of the references are listed.Systematic Differences between Current Molecular Dynamics Force Fields To Represent Local Properties of Intrinsically Disordered Proteins
Lei Yu et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2021)
Methylguanidinium at the Air/Water Interface: A Simulation Study with the Drude Polarizable Force Field
Jian Zhu et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2021)
Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties
Giulio Tesei et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)
Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field
Yudong Qiu et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)
Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations
Felix Kummerer et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)
OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space
Chao Lu et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)
Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins
Fang-Yu Lin et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2020)
SASBDB: Towards automatically curated and validated repository for biological scattering data
Alexey G. Kikhney et al.
PROTEIN SCIENCE (2020)
Development of a Force Field for the Simulation of Single-Chain Proteins and Protein-Protein Complexes
Stefano Piana et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution
Chuan Tian et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Balanced Amino-Acid-Specific Molecular Dynamics Force Field for the Realistic Simulation of Both Folded and Disordered Proteins
Lei Yu et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics
Cristina Paissoni et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins
Dong Song et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
Richard T. Bradshaw et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field
Fang-Yu Lin et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
A Preorganized Electric Field Leads to Minimal Geometrical Reorientation in the Catalytic Reaction of Ketosteroid Isomerase
Yufan Wu et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)
Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens
Christian Devereux et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
A fast and high-quality charge model for the next generation general AMBER force field
Xibing He et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
On the faithfulness of molecular mechanics representations of proteins towards quantum-mechanical energy surfaces
Gerhard Koenig et al.
INTERFACE FOCUS (2020)
Toward Prediction of Electrostatic Parameters for Force Fields That Explicitly Treat Electronic Polarization
Esther Heid et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Development and Testing of the OPLS-AA/M Force Field for RNA
Michael J. Robertson et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems
Frederic Celerse et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Fluctuations of Electric Fields in the Active Site of the Enzyme Ketosteroid Isomerase
Valerie Vaissier Welborn et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)
Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins
Sheng Yang et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)
Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields
Fang-Yu Lin et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)
Intrinsically disordered protein-specific force field CHARMM36IDPSFF
Hao Liu et al.
CHEMICAL BIOLOGY & DRUG DESIGN (2018)
Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator
Fang-Yu Lin et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)
AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids
Changsheng Zhang et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
Insights into Stabilizing Forces in Amyloid Fibrils of Differing Sizes from Polarizable Molecular Dynamics Simulations
Darcy S. Davidson et al.
JOURNAL OF MOLECULAR BIOLOGY (2018)
Developing a molecular dynamics force field for both folded and disordered protein states
Paul Robustelli et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Improvements to the AMOEBA Force Field by Introducing Anisotropic Atomic Polarizability of the Water Molecule
Akshaya K. Das et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Jing Huang et al.
NATURE METHODS (2017)
PCDDB: new developments at the Protein Circular Dichroism Data Bank
Lee Whitmore et al.
NUCLEIC ACIDS RESEARCH (2017)
The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins
Dong Song et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site
Lu Wang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15
Lee-Ping Wang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
An optimized charge penetration model for use with the AMOEBA force field
Joshua A. Rockers et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2017)
ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost
J. S. Smith et al.
CHEMICAL SCIENCE (2017)
Computational and theoretical advances in studies of intrinsically disordered proteins
Robert B. Best
CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)
OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins
Edward Harder et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications
Justin A. Lemkul et al.
CHEMICAL REVIEWS (2016)
Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model
Karl T. Debiec et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements
Wesley K. Lay et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization
Mark S. Miller et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
A Critical Test of the Electrostatic Contribution to Catalysis with Noncanonical Amino Acids in Ketosteroid Isomerase
Yufan Wu et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)
Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations
Gerhard Koenig et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2015)
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
James A. Maier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States
Stefano Piana et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
SASBDB, a repository for biological small-angle scattering data
Erica Valentini et al.
NUCLEIC ACIDS RESEARCH (2015)
Induction of Peptide Bond Dipoles Drives Cooperative Helix Formation in the (AAQAA)3 Peptide
Jing Huang et al.
BIOPHYSICAL JOURNAL (2014)
Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations
Stefano Piana et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)
ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
David S. Cerutti et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model
Jing Huang et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)
Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for Escherichia coli Dihydrofolate Reductase
C. Tony Liu et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)
Extreme electric fields power catalysis in the active site of ketosteroid isomerase
Stephen D. Fried et al.
SCIENCE (2014)
Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data
Lee-Ping Wang et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
Pedro E. M. Lopes et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins
Yue Shi et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
Jing Huang et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)
Biomolecular Simulation: A Computational Microscope for Molecular Biology
Ron O. Dror et al.
ANNUAL REVIEW OF BIOPHYSICS, VOL 41 (2012)
New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field
Maria M. Reif et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone φ, ψ and Side-Chain χ1 and χ2 Dihedral Angles
Robert B. Best et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Systematic Validation of Protein Force Fields against Experimental Data
Kresten Lindorff-Larsen et al.
PLOS ONE (2012)
How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?
Stefano Piana et al.
BIOPHYSICAL JOURNAL (2011)
Definition and testing of the GROMOS force-field versions 54A7 and 54B7
Nathan Schmid et al.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2011)
Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules
Pengyu Ren et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
NMR-Based Protein Potentials
Da-Wei Li et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2010)
Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data
Oliver F. Lange et al.
BIOPHYSICAL JOURNAL (2010)
Accounting for Polarization Cost When Using Fixed Charge Force Fields. I. Method for Computing Energy
William C. Swope et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Current Status of the AMOEBA Polarizable Force Field
Jay W. Ponder et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions
Yun Luo et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2010)
Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization
Shina C. L. Kamerlin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Improved side-chain torsion potentials for the Amber ff99SB protein force field
Kresten Lindorff-Larsen et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Atomic-Level Characterization of the Structural Dynamics of Proteins
David E. Shaw et al.
SCIENCE (2010)
Are current molecular dynamics force fields too helical?
Robert B. Best et al.
BIOPHYSICAL JOURNAL (2008)
Understanding the dielectric properties of liquid amides from a polarizable force field
Edward Harder et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
BioMagResBank
Eldon L. Ulrich et al.
NUCLEIC ACIDS RESEARCH (2008)
Polarizable empirical force field for the primary and secondary alcohol series based on the classical drude model
Victor M. Anisimov et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Additive and classical drude polarizable force fields for linear and cyclic ethers
Igor Vorobyov et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Polarizable empirical force field for aromatic compounds based on the classical drude oscillator
Pedro E. M. Lopes et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Comparison of multiple amber force fields and development of improved protein backbone parameters
Viktor Hornak et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Atomic level anisotropy in the electrostatic modeling of lone pairs for a polarizable force field based on the classical Drude oscillator
Edward Harder et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
Protein Circular Dichroism Data Bank (PCDDB): Data bank and website design
Lee Whitmore et al.
CHIRALITY (2006)
XML-based IUPAC standard for experimental, predicted, and critically evaluated thermodynamic property data storage and capture (thermoML) (IUPAC recommendations 2006)
M Frenkel et al.
PURE AND APPLIED CHEMISTRY (2006)
Improved treatment of the protein backbone in empirical force fields
AD MacKerell et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)
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
AD Mackerell et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
C Oostenbrink et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
Y Duan et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm
G Lamoureux et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds
IJ Chen et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
LD Schuler et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2001)
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
GA Kaminski et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2001)