4.6 Review

Integration of experimental data and use of automated fitting methods in developing protein force fields

Related references

Note: Only part of the references are listed.
Article Chemistry, Physical

Systematic Differences between Current Molecular Dynamics Force Fields To Represent Local Properties of Intrinsically Disordered Proteins

Lei Yu et al.

Summary: This study compared the performance of four recent molecular dynamics force fields on simulating intrinsically disordered proteins, revealing substantial differences between these force fields at the individual residue level. The study highlighted limitations of current force fields and showed that incorporating coil library information, as demonstrated by ff99SBnmr2, can significantly improve performance and sampling realism.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

Article Chemistry, Physical

Methylguanidinium at the Air/Water Interface: A Simulation Study with the Drude Polarizable Force Field

Jian Zhu et al.

Summary: The study found that methylguanidinium accumulates at the air/water interface, mostly adopting a tilted conformation, and has different interface preferences compared to guanidinium ions. Analysis of induced dipole moments revealed how ions adjust their charge distribution at the interface and highlighted the impact of molecular polarizability anisotropy on ion orientation. Results underscore the importance of explicitly considering electronic polarization effects in modeling interfacial properties.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

Article Multidisciplinary Sciences

Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties

Giulio Tesei et al.

Summary: Researchers have found that many intrinsically disordered proteins (IDPs) can participate in the formation of membraneless organelles in the cell. Investigating the phase behavior of IDPs through molecular simulations requires an accurate description of intramolecular and intermolecular interactions. By developing a coarse-grained model based on experimental data, the model accurately reproduces the conformational propensities of IDPs.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Chemistry, Physical

Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field

Yudong Qiu et al.

Summary: The study presents a methodology for defining and optimizing a general force field, successfully deriving the small-molecule force field Parsley. By optimizing parameters with quantum chemical data, the force field demonstrates similar accuracy to other general force fields in predicting liquid properties and binding free energies.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

Article Chemistry, Physical

Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations

Felix Kummerer et al.

Summary: Researchers propose an approach to integrate side-chain NMR relaxation measurements with molecular dynamics simulations to study the structure and dynamics of proteins. They apply the method to T4 lysozyme and demonstrate how it can combine the accuracy of NMR measurements with molecular models of protein dynamics from simulations.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

Article Chemistry, Physical

OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space

Chao Lu et al.

Summary: The development and validation of the OPLS4 force field, which builds upon previous work with OPLS3e, improved model accuracy on challenging regimes of drug-like chemical space. A novel parametrization strategy for charged species was introduced, leading to improved accuracy on benchmarks assessing small-molecule solvation and protein-ligand binding.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

Article Chemistry, Multidisciplinary

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)

Article Biochemistry & Molecular Biology

SASBDB: Towards automatically curated and validated repository for biological scattering data

Alexey G. Kikhney et al.

PROTEIN SCIENCE (2020)

Article Chemistry, Physical

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)

Article Chemistry, Physical

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)

Article Chemistry, Physical

Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics

Cristina Paissoni et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Chemistry, Medicinal

Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins

Dong Song et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Chemistry, Medicinal

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)

Article Chemistry, Physical

Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field

Fang-Yu Lin et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Chemistry, Multidisciplinary

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)

Article Chemistry, Physical

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)

Article Chemistry, Physical

A fast and high-quality charge model for the next generation general AMBER force field

Xibing He et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

Article Chemistry, Physical

Toward Prediction of Electrostatic Parameters for Force Fields That Explicitly Treat Electronic Polarization

Esther Heid et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

Article Chemistry, Physical

Development and Testing of the OPLS-AA/M Force Field for RNA

Michael J. Robertson et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

Article Chemistry, Multidisciplinary

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)

Article Chemistry, Medicinal

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)

Article Chemistry, Medicinal

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)

Article Biochemistry & Molecular Biology

Intrinsically disordered protein-specific force field CHARMM36IDPSFF

Hao Liu et al.

CHEMICAL BIOLOGY & DRUG DESIGN (2018)

Article Chemistry, Medicinal

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator

Fang-Yu Lin et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)

Article Chemistry, Physical

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids

Changsheng Zhang et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Article Biochemistry & Molecular Biology

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)

Article Multidisciplinary Sciences

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)

Article Chemistry, Physical

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)

Article Biochemical Research Methods

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Jing Huang et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

PCDDB: new developments at the Protein Circular Dichroism Data Bank

Lee Whitmore et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Chemistry, Medicinal

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)

Article Chemistry, Physical

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)

Article Chemistry, Physical

An optimized charge penetration model for use with the AMOEBA force field

Joshua A. Rockers et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2017)

Article Chemistry, Multidisciplinary

ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost

J. S. Smith et al.

CHEMICAL SCIENCE (2017)

Article Biochemistry & Molecular Biology

Computational and theoretical advances in studies of intrinsically disordered proteins

Robert B. Best

CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)

Article Chemistry, Physical

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)

Article Chemistry, Physical

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)

Article Chemistry, Physical

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)

Article Chemistry, Multidisciplinary

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)

Article Biochemistry & Molecular Biology

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)

Article Chemistry, Physical

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)

Article Chemistry, Physical

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

Stefano Piana et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2015)

Article Biochemistry & Molecular Biology

SASBDB, a repository for biological small-angle scattering data

Erica Valentini et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

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)

Article Chemistry, Physical

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

David S. Cerutti et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Multidisciplinary

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)

Article Multidisciplinary Sciences

Extreme electric fields power catalysis in the active site of ketosteroid isomerase

Stephen D. Fried et al.

SCIENCE (2014)

Article Chemistry, Physical

Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data

Lee-Ping Wang et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

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)

Article Chemistry, Physical

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

Yue Shi et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Multidisciplinary

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

Jing Huang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)

Review Biophysics

Biomolecular Simulation: A Computational Microscope for Molecular Biology

Ron O. Dror et al.

ANNUAL REVIEW OF BIOPHYSICS, VOL 41 (2012)

Article Chemistry, Physical

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)

Article Multidisciplinary Sciences

Systematic Validation of Protein Force Fields against Experimental Data

Kresten Lindorff-Larsen et al.

PLOS ONE (2012)

Article Biophysics

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

Nathan Schmid et al.

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2011)

Article Chemistry, Physical

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

Pengyu Ren et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Article Chemistry, Multidisciplinary

NMR-Based Protein Potentials

Da-Wei Li et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2010)

Article Chemistry, Physical

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)

Article Chemistry, Physical

Current Status of the AMOEBA Polarizable Force Field

Jay W. Ponder et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2010)

Article Chemistry, Physical

Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions

Yun Luo et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2010)

Article Multidisciplinary Sciences

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)

Article Biochemistry & Molecular Biology

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

Kresten Lindorff-Larsen et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Multidisciplinary Sciences

Atomic-Level Characterization of the Structural Dynamics of Proteins

David E. Shaw et al.

SCIENCE (2010)

Article Biophysics

Are current molecular dynamics force fields too helical?

Robert B. Best et al.

BIOPHYSICAL JOURNAL (2008)

Article Chemistry, Physical

Understanding the dielectric properties of liquid amides from a polarizable force field

Edward Harder et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2008)

Article Biochemistry & Molecular Biology

BioMagResBank

Eldon L. Ulrich et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Chemistry, Physical

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)

Article Chemistry, Physical

Additive and classical drude polarizable force fields for linear and cyclic ethers

Igor Vorobyov et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)

Review Chemistry, Physical

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)

Article Biochemistry & Molecular Biology

Comparison of multiple amber force fields and development of improved protein backbone parameters

Viktor Hornak et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)

Article Chemistry, Medicinal

Protein Circular Dichroism Data Bank (PCDDB): Data bank and website design

Lee Whitmore et al.

CHIRALITY (2006)

Article Chemistry, Multidisciplinary

Improved treatment of the protein backbone in empirical force fields

AD MacKerell et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)

Article Chemistry, Multidisciplinary

Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds

IJ Chen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)

Article Chemistry, Multidisciplinary

An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase

LD Schuler et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2001)