Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains (Q36426407)

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English	Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains	scientific article

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scholarly article

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Europe PubMed Central

PMC publication ID

14 August 2017

Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains (English)

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Europe PubMed Central

PMC publication ID

14 August 2017

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Klaus Schulten

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14 August 2017

author name string

Wei Han

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Europe PubMed Central

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14 August 2017

publication date

11 October 2012

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Europe PubMed Central

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14 August 2017

Journal of Chemical Theory and Computation

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Europe PubMed Central

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14 August 2017

8

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Europe PubMed Central

PMC publication ID

14 August 2017

11

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Europe PubMed Central

PMC publication ID

14 August 2017

4413-4424

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Europe PubMed Central

PMC publication ID

14 August 2017

PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification

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Parameterization of PACE Force Field for Membrane Environment and Simulation of Helical Peptides and Helix-Helix Association

1 reference

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

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How fast-folding proteins fold

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Recent progress in adaptive multiscale molecular dynamics simulations of soft matter.

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Multiscale coarse-graining of the protein energy landscape

1 reference

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Polarizable water model for the coarse-grained MARTINI force field

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Extracting rate coefficients from single-molecule photon trajectories and FRET efficiency histograms for a fast-folding protein.

1 reference

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Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein.

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Influence of side chain conformations on local conformational features of amino acids and implication for force field development

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Backbone additivity in the transfer model of protein solvation

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A force field for virtual atom molecular mechanics of proteins

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Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides

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Ab initio folding of proteins with all-atom discrete molecular dynamics

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Structure and energetics of the hydrogen-bonded backbone in protein folding.

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Recent advances in implicit solvent-based methods for biomolecular simulations

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30 September 2017

Coarse-grained models of protein folding: toy models or predictive tools?

1 reference

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Protein folding by zipping and assembly

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30 September 2017

The MARTINI force field: coarse grained model for biomolecular simulations

1 reference

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Multiscale modeling of biomolecular systems: in serial and in parallel

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A backbone-based theory of protein folding

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Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion

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Biomolecular modeling: Goals, problems, perspectives

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Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

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Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

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SimFold energy function for de novo protein structure prediction: consensus with Rosetta.

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Hairpin folding rates reflect mutations within and remote from the turn region

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Scalable molecular dynamics with NAMD

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Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes

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Molecular structure of the lecithin ripple phase

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Intrinsically unstructured proteins and their functions

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Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

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Folding thermodynamics of peptides

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Development of novel statistical potentials for protein fold recognition

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30 September 2017

Simulations of the role of water in the protein-folding mechanism

1 reference

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Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein

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Trp-cage: Folding free energy landscape in explicit water

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Free energy landscape of protein folding in water: Explicit vs. implicit solvent

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Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins

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Multiplexed-replica exchange molecular dynamics method for protein folding simulation

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Absolute comparison of simulated and experimental protein-folding dynamics

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30 September 2017

Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3507460

30 September 2017

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

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All-Atom Structure Prediction and Folding Simulations of a Stable Protein

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30 September 2017

Molecular dynamics simulations of biomolecules

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30 September 2017

Designing a 20-residue protein

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30 September 2017

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

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The interrelationships of side-chain and main-chain conformations in proteins.

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30 September 2017

Design and NMR analyses of compact, independently folded BBA motifs

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30 September 2017

Folding dynamics and mechanism of beta-hairpin formation

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30 September 2017

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30 September 2017

VMD: visual molecular dynamics

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30 September 2017

Fast events in protein folding: helix melting and formation in a small peptide.

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30 September 2017

Electrostatic screening of charge and dipole interactions with the helix backbone

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30 September 2017

A short linear peptide that folds into a native stable beta-hairpin in aqueous solution

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Interaction of the peptide bond with solvent water: a vapor phase analysis

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How robust are protein folding simulations with respect to force field parameterization?

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28 June 2018

Generic coarse-grained model for protein folding and aggregation.

1 reference

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28 June 2018

A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins

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28 June 2018

A coarse-grained protein force field for folding and structure prediction.

1 reference

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28 June 2018

Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions

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28 June 2018

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.

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21 September 2018

The MARTINI Coarse-Grained Force Field: Extension to Proteins.

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A new coarse-grained model for water: the importance of electrostatic interactions.

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21 September 2018

Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent

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Large-scale molecular dynamics simulations of self-assembling systems.

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21 September 2018

All-atom level direct folding simulation of a betabetaalpha miniprotein.

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21 September 2018

Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics.

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21 September 2018

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21 September 2018

Polyproline II helix is the preferred conformation for unfolded polyalanine in water

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21 September 2018

Additive transfer free energies of the peptide backbone unit that are independent of the model compound and the choice of concentration scale

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21 September 2018

Hydrophobic core malleability of a de novo designed three-helix bundle protein

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21 September 2018

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

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21 October 2018

Internal stark effect measurement of the electric field at the amino terminus of an alpha helix

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21 October 2018

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12 December 2020

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Reproducible Protein Folding with the Stochastic Tunneling Method

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12 December 2020

based on heuristic

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https://pubmed.ncbi.nlm.nih.gov/23204949

12 December 2020

based on heuristic

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Limited validity of group additivity for the folding energetics of the peptide group

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https://pubmed.ncbi.nlm.nih.gov/23204949

12 December 2020

based on heuristic

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Exploring the energy landscape of a beta hairpin in explicit solvent

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https://pubmed.ncbi.nlm.nih.gov/23204949

12 December 2020

based on heuristic

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Coarse-Grained Model of Proteins Incorporating Atomistic Detail of the Active Site

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https://pubmed.ncbi.nlm.nih.gov/23204949

12 December 2020

based on heuristic

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https://pubmed.ncbi.nlm.nih.gov/23204949

12 December 2020

based on heuristic

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Coarse-Grained Protein Model Coupled with a Coarse-Grained Water Model: Molecular Dynamics Study of Polyalanine-Based Peptides

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https://pubmed.ncbi.nlm.nih.gov/23204949

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based on heuristic

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Nearly symmetrical proteins: folding pathways and transition states

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https://pubmed.ncbi.nlm.nih.gov/23204949

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Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry

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based on heuristic

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Beta-hairpin folding simulations in atomistic detail using an implicit solvent model

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https://pubmed.ncbi.nlm.nih.gov/23204949

12 December 2020

based on heuristic

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PACE Force Field for Protein Simulations. 2. Folding Simulations of Peptides.

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https://pubmed.ncbi.nlm.nih.gov/23204949

12 December 2020

based on heuristic

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How large is an alpha-helix? Studies of the radii of gyration of helical peptides by small-angle X-ray scattering and molecular dynamics

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https://pubmed.ncbi.nlm.nih.gov/23204949

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations

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https://pubmed.ncbi.nlm.nih.gov/23204949

12 December 2020

based on heuristic

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Mechanism of helix induction by trifluoroethanol: a framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water

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https://pubmed.ncbi.nlm.nih.gov/23204949

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/CT300696C

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

14 August 2017

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