(Q30387121)

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Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.

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scholarly article

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Europe PubMed Central

PMC publication ID

13 September 2017

Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics. (English)

1 reference

Europe PubMed Central

PMC publication ID

13 September 2017

molecular dynamics simulation

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Harold A. Scheraga

6

object named as

Harold A Scheraga

1 reference

Europe PubMed Central

PMC publication ID

13 September 2017

1

object named as

Adam Liwo

1 reference

Europe PubMed Central

PMC publication ID

13 September 2017

Stanislaw Oldziej

2

object named as

Stanisław Ołdziej

1 reference

Europe PubMed Central

PMC publication ID

13 September 2017

Cezary Czaplewski

3

object named as

Cezary Czaplewski

1 reference

Europe PubMed Central

PMC publication ID

13 September 2017

author name string

Dana S Kleinerman

4

1 reference

Europe PubMed Central

PMC publication ID

13 September 2017

Philip Blood

5

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Europe PubMed Central

PMC publication ID

13 September 2017

publication date

1 March 2010

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Europe PubMed Central

PMC publication ID

13 September 2017

Journal of Chemical Theory and Computation

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Europe PubMed Central

PMC publication ID

13 September 2017

6

1 reference

Europe PubMed Central

PMC publication ID

13 September 2017

3

1 reference

Europe PubMed Central

PMC publication ID

13 September 2017

890-909

1 reference

Europe PubMed Central

PMC publication ID

13 September 2017

Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II

1 reference

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20 June 2018

An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Long-timescale molecular dynamics simulations of protein structure and function.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

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

1 reference

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20 June 2018

Accelerating molecular dynamic simulation on graphics processing units

1 reference

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20 June 2018

Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field

1 reference

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20 June 2018

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

1 reference

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20 June 2018

Folding pathway of the b1 domain of protein G explored by multiscale modeling

1 reference

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20 June 2018

Multiscale modeling of biomolecular systems: in serial and in parallel

1 reference

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20 June 2018

Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

1 reference

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20 June 2018

Protein-Folding Dynamics: Overview of Molecular Simulation Techniques

1 reference

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20 June 2018

Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Protein folding-simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Molecular dynamics: survey of methods for simulating the activity of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Scalable molecular dynamics with NAMD

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

How well can simulation predict protein folding kinetics and thermodynamics?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Coarse-grained models for proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

The protein folding 'speed limit'.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

All-atom simulations of protein folding and unfolding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Coarse-grained sequences for protein folding and design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Multiplexed-replica exchange molecular dynamics method for protein folding simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Protein unfolding pathways explored through molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Low-energy structures of two dipeptides and their relationship to bend conformations.

1 reference

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20 June 2018

Molecular dynamics simulations of the unfolding of an alpha-helical analogue of ribonuclease A S-peptide in water

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Molecular dynamics simulations of helix denaturation

1 reference

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Characterization of "native" apomyoglobin by molecular dynamics simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Dynamics of folded proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

20 June 2018

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839251

26 November 2018

Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function.

1 reference

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26 November 2018

Thermal folding and mechanical unfolding pathways of protein secondary structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/20305729

12 December 2020

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Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state

1 reference

https://pubmed.ncbi.nlm.nih.gov/20305729

12 December 2020

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Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains

1 reference

https://pubmed.ncbi.nlm.nih.gov/20305729

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I.

1 reference

https://pubmed.ncbi.nlm.nih.gov/20305729

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

1 reference

https://pubmed.ncbi.nlm.nih.gov/20305729

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based on heuristic

inferred from PubMed ID database lookup

Molecular dynamics simulations of the unfolding of apomyoglobin in water

1 reference

https://pubmed.ncbi.nlm.nih.gov/20305729

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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10.1021/CT9004068

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Europe PubMed Central

PMC publication ID

13 September 2017

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24 November 2022

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1 reference

Europe PubMed Central

PMC publication ID

13 September 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

13 September 2017

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