(Q27312694)

26 June 2017

title

QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts (English)

1 reference

molecular dynamics simulation

26 June 2017

main subject

0 references

7

Klaus Schulten

Klaus

Schulten

1 reference

26 June 2017

5

James C Phillips

James C

Phillips

1 reference

26 June 2017

2

Rafael C Bernardi

Rafael C

Bernardi

1 reference

26 June 2017

João V Ribeiro

1

João V

Ribeiro

1 reference

26 June 2017

Till Rudack

series ordinal

3

author given names

Till

author last names

Rudack

1 reference

26 June 2017

John E Stone

series ordinal

4

author given names

John E

author last names

Stone

1 reference

26 June 2017

Peter L Freddolino

series ordinal

6

author given names

Peter L

author last names

Freddolino

1 reference

26 June 2017

language of work or name

English

0 references

publication date

24 May 2016

1 reference

26 June 2017

1 reference

26 June 2017

volume

6

1 reference

26 June 2017

page(s)

26536

1 reference

Creative Commons Attribution 4.0 International

26 June 2017

copyright license

start time

24 May 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Energy barriers and driving forces in tRNA translocation through the ribosome

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

I-TASSER: a unified platform for automated protein structure and function prediction

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

21 March 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

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

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Scalable molecular dynamics with NAMD

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

VMD: visual molecular dynamics

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Comparative protein modelling by satisfaction of spatial restraints

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Dynamics of folded proteins

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Molecular dynamics study of enhanced Man5B enzymatic activity

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Comparison of simple potential functions for simulating liquid water

21 March 2017

1 reference

https://api.crossref.org/works/10.1038/SREP26536

Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics

22 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Mapping Mechanical Force Propagation through Biomolecular Complexes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Molecular dynamics simulations of large macromolecular complexes.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Impact of M36I polymorphism on the interaction of HIV-1 protease with its substrates: insights from molecular dynamics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Ultrastable cellulosome-adhesion complex tightens under load

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Enhanced sampling techniques in molecular dynamics simulations of biological systems

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

A theoretical view of protein dynamics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Rapid parameterization of small molecules using the Force Field Toolkit

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

The gating mechanism of the human aquaporin 5 revealed by molecular dynamics simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

The structural dynamics of the flavivirus fusion peptide-membrane interaction

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Ras and GTPase-activating protein (GAP) drive GTP into a precatalytic state as revealed by combining FTIR and biomolecular simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Parallel Generalized Born Implicit Solvent Calculations with NAMD.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units-Radial Distribution Function Histogramming

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Applications of computational science for understanding enzymatic deconstruction of cellulose

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

MUFOLD: A new solution for protein 3D structure prediction

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Molecular dynamics simulations of the complete satellite tobacco mosaic virus

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Modelling enzyme reaction mechanisms, specificity and catalysis.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Steered molecular dynamics and mechanical functions of proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Theory of protein folding: the energy landscape perspective

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Molecular dynamics study of unbinding of the avidin-biotin complex

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

Hybrid QM/MM Molecular Dynamics Study of Benzocaine in a Membrane Environment: How Does a Quantum Mechanical Treatment of Both Anesthetic and Lipids Affect Their Interaction.

28 September 2017

1 reference

Polarization effects and charge transfer in the KcsA potassium channel.

21 January 2018

1 reference

Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing

21 January 2018

1 reference

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

21 January 2018

1 reference

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

Progress towards automated Kepler scientific workflows for computer-aided drug discovery and molecular simulations

21 January 2018

1 reference

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions

21 January 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4877583

21 January 2018

CHARMM-GUI: a web-based graphical user interface for CHARMM

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27216779

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Cellulose degradation in the human gut: Ruminococcus champanellensis expands the cellulosome paradigm

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27216779

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/SREP26536

1 reference

Dimensions Publication ID

26 June 2017

1006222502

0 references

OpenCitations bibliographic resource ID

1409957

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1409957

1 reference