(Q37127872)

18 August 2017

PRIMO: A Transferable Coarse-grained Force Field for Proteins (English)

1 reference

18 August 2017

0 references

Parimal Kar

1

1 reference

18 August 2017

Srinivasa Murthy Gopal

2

1 reference

18 August 2017

Yi-Ming Cheng

3

1 reference

18 August 2017

Alexander Predeus

4

1 reference

18 August 2017

Michael Feig

5

1 reference

18 August 2017

1 August 2013

1 reference

Journal of Chemical Theory and Computation

18 August 2017

1 reference

18 August 2017

9

1 reference

18 August 2017

8

1 reference

18 August 2017

3769-3788

1 reference

PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties.

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

A generic force field for protein coarse-grained molecular dynamics simulation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

The coarse-grained OPEP force field for non-amyloid and amyloid proteins.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

How fast-folding proteins fold

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Molecular dynamics trajectory compression with a coarse-grained model

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Atomic-level characterization of the structural dynamics of proteins

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Extending the PRIME model for protein aggregation to all 20 amino acids

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

CHARMM: the biomolecular simulation program

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Systematic multiscale simulation of membrane protein systems

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

A systematic methodology for defining coarse-grained sites in large biomolecules

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Ten-microsecond molecular dynamics simulation of a fast-folding WW domain

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Protein folding by zipping and assembly

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Coarse-grained models for proteins

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Protein modeling and structure prediction with a reduced representation.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Recent advances in the development and application of implicit solvent models in biomolecule simulations

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Minimalist models for protein folding and design

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Absolute comparison of simulated and experimental protein-folding dynamics

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Tryptophan zippers: Stable, monomeric -hairpins

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Anisotropy of fluctuation dynamics of proteins with an elastic network model

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Three-helix-bundle protein in a Ramachandran model

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Atomic solvation parameters applied to molecular dynamics of proteins in solution

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Computer simulation of protein folding

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Is Alanine Dipeptide a Good Model for Representing the Torsional Preferences of Protein Backbones?

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Modeling Protein-Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Coarse-Grained Potentials for Local Interactions in Unfolded Proteins

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Folding thermodynamics of peptides

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Theoretical Studies of Protein Folding

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Hydrogen bonds, hydrophobicity forces and the character of the collapse transition

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Generic coarse-grained model for protein folding and aggregation.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Mechanosensitive membrane channels in action

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

A fast method for large-scale de novo peptide and miniprotein structure prediction.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Targeting the early steps of Abeta16-22 protofibril disassembly by N-methylated inhibitors: a numerical study.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Stability and dynamics of virus capsids described by coarse-grained modeling

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Temperature weighted histogram analysis method, replica exchange, and transition paths.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Improved treatment of the protein backbone in empirical force fields.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Assembly of a tetrameric alpha-helical bundle: computer simulations on an intermediate-resolution protein model

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

1H NMR studies of the solution conformations of an analogue of the C-peptide of ribonuclease A.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Flap opening dynamics in HIV-1 protease explored with a coarse-grained model

20 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Direct Observation of Protein Folding, Aggregation, and a Prion-like Conformational Conversion

4 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3755638

Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling

4 December 2018

1 reference

12 December 2020

Tests of the helix dipole model for stabilization of α-helices

1 reference

12 December 2020

Assessing the Quality of the OPEP Coarse-Grained Force Field

1 reference

12 December 2020

Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations

1 reference

12 December 2020

All-atom ab initio folding of a diverse set of proteins

1 reference

12 December 2020

A coarse-grained protein-protein potential derived from an all-atom force field

1 reference

12 December 2020

Peptide folding using multiscale coarse-grained models

1 reference

12 December 2020

A multiscale coarse-graining method for biomolecular systems

1 reference

12 December 2020

Conditional reversible work method for molecular coarse graining applications

1 reference

12 December 2020

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

1 reference

12 December 2020

G Protein-Coupled Receptors Self-Assemble in Dynamics Simulations of Model Bilayers

1 reference

12 December 2020

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

1 reference

12 December 2020

Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT400230Y

1 reference

release_j5x2lgmwmbd6tkellj5wkj6auq

18 August 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/j5x2lgmwmbd6tkellj5wkj6auq

24 November 2022

mapped directly with Wikidata item

1 reference

18 August 2017

PubMed publication ID

23997693

1 reference