(Q35816082)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

title

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

Carlos X Hernández

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

Lee-Ping Wang

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

10

Vijay S Pande

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

2

Kyle A Beauchamp

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

1

Robert T McGibbon

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

Christian R Schwantes

7

object named as

Christian R Schwantes

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

author name string

Christoph Klein

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

Jason M Swails

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

Thomas J Lane

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

language of work or name

English

0 references

publication date

1 October 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

number of pages

5

1 reference

based on heuristic

inferred from page(s)

published in

Biophysical Journal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

volume

109

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

issue

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

page(s)

1528-1532

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

27 February 2020

Jupyter notebook file

1 reference

1 reference

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4623899/

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=4623899

EMMA: A Software Package for Markov Model Building and Analysis.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

iview: an interactive WebGL visualizer for protein-ligand complex.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

Best practices for scientific computing

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

To milliseconds and beyond: challenges in the simulation of protein folding

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

Pteros: fast and easy to use open-source C++ library for molecular analysis.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

LOOS: an extensible platform for the structural analysis of simulations.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

Scalable molecular dynamics with NAMD

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

Rapid calculation of RMSDs using a quaternion-based characteristic polynomial

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

VMD: visual molecular dynamics

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

Limits on variations in protein backbone dynamics from precise measurements of scalar couplings.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

Bio3d: an R package for the comparative analysis of protein structures.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

Hydrogen bonding in globular proteins

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4623899

ST-analyzer: a web-based user interface for simulation trajectory analysis

24 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26488642

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26488642

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Self-strengthening biphasic nanoparticle assemblies with intrinsic catch bonds

1 reference

19 May 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BPJ.2015.08.015

The molecular modeling toolkit: A new approach to molecular simulations

1 reference

19 May 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BPJ.2015.08.015

An efficient newton-like method for molecular mechanics energy minimization of large molecules

1 reference

19 May 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BPJ.2015.08.015

IPython: A System for Interactive Scientific Computing

1 reference

19 May 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BPJ.2015.08.015

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

19 May 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BPJ.2015.08.015

Matplotlib: A 2D Graphics Environment

1 reference

19 May 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BPJ.2015.08.015

Identifiers

DOI

10.1016/J.BPJ.2015.08.015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26488642%20AND%20SRC:MED&resulttype=core&format=json

27 February 2020

1 reference