4.8 Article

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

Related references

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

CHARMM TIP3P Water Model Suppresses Peptide Folding by Solvating the Unfolded State

Sander Boonstra et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2016)

Article Biophysics

An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

Aaron M. Fluitt et al.

BIOPHYSICAL JOURNAL (2015)

Article Chemistry, Physical

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

Sarah Rauscher 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)

Review Cell Biology

Intrinsically disordered proteins in cellular signalling and regulation

Peter E. Wright et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)

Review Chemistry, Multidisciplinary

Single-Molecule Studies of Intrinsically Disordered Proteins

Marco Brucale et al.

CHEMICAL REVIEWS (2014)

Article Chemistry, Physical

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

Robert B. Best et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Physical

Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields

Karl T. Debiec et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2014)

Letter Multidisciplinary Sciences

Testing the validity of ensemble descriptions of intrinsically disordered proteins

Malene Ringkjobing Jensen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Chemistry, Physical

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

Peter Eastman et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

Automated Optimization of Potential Parameters

Michele Di Pierro 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)

Article Chemistry, Physical

Systematic Improvement of a Classical Molecular Model of Water

Lee-Ping Wang et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2013)

Article Chemistry, Multidisciplinary

NMR-Based Protein Potentials

Da-Wei Li et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2010)

Article Multidisciplinary Sciences

Charge interactions can dominate the dimensions of intrinsically disordered proteins

Sonja Mueller-Spaeth et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Review Chemistry, Multidisciplinary

CHARMM: The Biomolecular Simulation Program

B. R. Brooks et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Biochemistry & Molecular Biology

Examining Polyglutamine Peptide Length: A Connection between Collapsed Conformations and Increased Aggregation

Robert H. Walters et al.

JOURNAL OF MOLECULAR BIOLOGY (2009)

Article Chemistry, Physical

GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

Berk Hess et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)

Article Chemistry, Multidisciplinary

Highly populated turn conformations in natively unfolded Tau protein identified from residual dipolar couplings and molecular simulation

Marco D. Mukrasch et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)

Article Biophysics

Effects of denaturants on the dynamics of loop formation in polypeptides

Marco Buscaglia et al.

BIOPHYSICAL JOURNAL (2006)

Review Chemistry, Physical

Polarizable empirical force field for alkanes based on the classical drude oscillator model

IV Vorobyov et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2005)

Article Biochemistry & Molecular Biology

The protein coil library: A structural database of nonhelix, nonstrand fragments derived from the PDB

NC Fitzkee et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

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

Enhanced hairpin stability through loop design: The case of the protein G B1 domain hairpin

RM Fesinmeyer et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)

Review Chemistry, Multidisciplinary

Empirical force fields for biological macromolecules: Overview and issues

AD Mackerell

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Biochemistry & Molecular Biology

Structure validation by Cα geometry:: φ,ψ and Cβ deviation

SC Lovell et al.

PROTEINS-STRUCTURE FUNCTION AND GENETICS (2003)

Article Multidisciplinary Sciences

Measuring the rate of intramolecular contact formation in polypeptides

LJ Lapidus et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)