(Q29615867)

21 June 2017

title

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit (English)

1 reference

21 June 2017

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10

David van der Spoel

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Pär Bjelkmar

Pär Bjelkmar

5

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Peter M Kasson

Peter M Kasson

9

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Erik Lindahl

Erik Lindahl

12

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Jeremy C Smith

Jeremy C Smith

8

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Michael R. Shirts

7

Michael R Shirts

1 reference

21 June 2017

Sander Pronk

1

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21 June 2017

Szilárd Páll

2

1 reference

21 June 2017

Roland Schulz

3

1 reference

21 June 2017

Per Larsson

4

1 reference

21 June 2017

Rossen Apostolov

6

1 reference

21 June 2017

Berk Hess

11

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=23407358

21 June 2017

language of work or name

1 reference

30 April 2017

publication date

13 February 2013

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21 June 2017

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21 June 2017

volume

29

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21 June 2017

issue

7

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21 June 2017

page(s)

845-854

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maintained by WikiProject

21 June 2017

WikiProject Software

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cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

The free energy landscape of small molecule unbinding

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Everything you wanted to know about Markov State Models but were afraid to ask

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

CHARMM: the biomolecular simulation program

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

The MARTINI force field: coarse grained model for biomolecular simulations

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Scalable molecular dynamics with NAMD

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

The Amber biomolecular simulation programs

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Development and testing of a general amber force field

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Exploring protein native states and large-scale conformational changes with a modified generalized born model

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

VMD: visual molecular dynamics

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Dynamics of folded proteins

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Virus capsid dissolution studied by microsecond molecular dynamics simulations

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

GROMACS molecule & liquid database

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

How fast-folding proteins fold

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Microsecond simulations indicate that ethanol binds between subunits and could stabilize an open-state model of a glycine receptor

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Atomistic folding simulations of the five-helix bundle protein λ(6−85).

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Transition networks for modeling the kinetics of conformational change in macromolecules

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

The GROMOS software for biomolecular simulation: GROMOS05.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

A high-performance parallel-generalized Born implementation enabled by tabulated interaction rescaling

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

Protein folding kinetics and thermodynamics from atomistic simulations.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605599

The Origin of Layer Structure Artifacts in Simulations of Liquid Water

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23407358

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Refinement of protein conformations using a macromolecular energy minimization procedure

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23407358

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTT055

1 reference

journals/bioinformatics/PronkPSLBASSKSHL13

21 June 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

OpenCitations bibliographic resource ID

28 January 2021

31792

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=23407358

30 April 2017

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

31792

1 reference