Conformational Preferences of an Intrinsically Disordered Protein Domain: A Case Study for Modern Force Fields

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CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins

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Intrinsically disordered proteins in cellular signalling and regulation

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Classification of Intrinsically Disordered Regions and Proteins

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Intrinsically Disordered Proteins and Intrinsically Disordered Protein Regions

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Developing a molecular dynamics force field for both folded and disordered protein states

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

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Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

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A flexible algorithm for calculating pair interactions on SIMD architectures

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Replica Exchange with Solute Scaling: A more efficient version of Replica Exchange with Solute Tempering (REST2)

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On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction

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Replica exchange with solute tempering: a method for sampling biological systems in explicit water.

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Systematic Validation of Protein Force Fields against Experimental Data

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Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment

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Relating sequence encoded information to form and function of intrinsically disordered proteins

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Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

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Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

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Hamiltonian replica exchange in GROMACS: a flexible implementation

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Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment

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Conformational propensities of intrinsically disordered proteins influence the mechanism of binding and folding

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Structure and Dynamics of an Unfolded Protein Examined by Molecular Dynamics Simulation

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Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

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New developments in force fields for biomolecular simulations

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Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

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Bayesian ensemble refinement by replica simulations and reweighting

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Computational and theoretical advances in studies of intrinsically disordered proteins

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Water models for biomolecular simulations

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Solution Structure of the KIX Domain of CBP Bound to the Transactivation Domain of c-Myb

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Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

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The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins

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Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

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Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing.

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Functional advantages of dynamic protein disorder

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Force field development and simulations of intrinsically disordered proteins

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Roles of Phosphorylation and Helix Propensity in the Binding of the KIX Domain of CREB-binding Protein by Constitutive (c-Myb) and Inducible (CREB) Activators

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Modeling Intrinsically Disordered Proteins with Bayesian Statistics

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On easy implementation of a variant of the replica exchange with solute tempering in GROMACS

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Comparison of force fields for Alzheimer's A: A case study for intrinsically disordered proteins

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Finding Our Way in the Dark Proteome

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Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States

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Helix nucleation kinetics from molecular simulations in explicit solvent

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

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Structure of the transition state for the binding of c-Myb and KIX highlights an unexpected order for a disordered system

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SESCA: Predicting Circular Dichroism Spectra from Protein Molecular Structures

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Remarkably Fast Coupled Folding and Binding of the Intrinsically Disordered Transactivation Domain of cMyb to CBP KIX

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Water Model Tuning for Improved Reproduction of Rotational Diffusion and NMR Spectral Density

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Computer Simulations of Intrinsically Disordered Proteins

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Experiments and simulations show how long-range contacts can form in expanded unfolded proteins with negligible secondary structure

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Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins

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Kirkwood–Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields

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Extended experimental inferential structure determination method in determining the structural ensembles of disordered protein states

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SAXS-Restrained Ensemble Simulations of Intrinsically Disordered Proteins with Commitment to the Principle of Maximum Entropy

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Secondary Structure of Rat and Human Amylin across Force Fields

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Extensive tests and evaluation of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins

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Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins

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Modulation of the intrinsic helix propensity of an intrinsically disordered protein reveals long-range helix-helix interactions.

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Balanced Amino-Acid-Specific Molecular Dynamics Force Field for the Realistic Simulation of Both Folded and Disordered Proteins

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The combined force field-sampling problem in simulations of disordered amyloid-β peptides

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Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations

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Effects of forcefield and sampling method in all-atom simulations of inherently disordered proteins: Application to conformational preferences of human amylin

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Rotational and Translational Diffusion of Proteins as a Function of Concentration

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Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs

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How accurate is circular dichroism-based model validation?

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Conformation dynamics of the intrinsically disordered protein c-Myb with the ff99IDPs force field

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Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid Experimental and Computational Approach

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AlphaFold, Artificial Intelligence (AI), and Allostery

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Folding Free Energy Landscape of Ordered and Intrinsically Disordered Proteins

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Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied?

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Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins

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The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins

Song, D., Luo, R., & Chen, H. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00135 · Cited by 198 · see citing works

Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D

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