(Q30400556)

14 October 2017

Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces (English)

1 reference

14 October 2017

Michele Seeber

1

0 references

Stefanie Muff

object named as

Stefanie Muff

4

0 references

F Fanelli

object named as

Francesca Fanelli

8

0 references

Amedeo Caflisch

7

object named as

Amedeo Caflisch

1 reference

14 October 2017

Angelo Felline

2

1 reference

14 October 2017

Francesco Raimondi

3

1 reference

14 October 2017

Ran Friedman

5

1 reference

14 October 2017

Francesco Rao

6

1 reference

14 October 2017

29 November 2010

1 reference

Journal of Computational Chemistry

14 October 2017

1 reference

14 October 2017

32

1 reference

14 October 2017

6

1 reference

14 October 2017

1183-1194

1 reference

CHARMM: the biomolecular simulation program

14 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

Intra and inter-molecular communications through protein structure network.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

Alpha-Helix folding in the presence of structural constraints.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

Complex network analysis of free-energy landscapes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

Biskit--a software platform for structural bioinformatics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

Residues crucial for maintaining short paths in network communication mediate signaling in proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

The Amber biomolecular simulation programs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

A network representation of protein structures: implications for protein stability.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

WEBnm@: a web application for normal mode analyses of proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

Hidden complexity of free energy surfaces for peptide (protein) folding

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

Estimating mutual information

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

DSSPcont: Continuous secondary structure assignments for proteins.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

Exploring expression data: identification and analysis of coexpressed genes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

Identification of side-chain clusters in protein structures by a graph spectral method.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

CATH--a hierarchic classification of protein domain structures

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

VMD: visual molecular dynamics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3151548

Wordom: a program for efficient analysis of molecular dynamics simulations.

14 July 2018

1 reference

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

21 January 2018

1 reference

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

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

21 January 2018

1 reference

Continuum secondary structure captures protein flexibility

21 January 2018

1 reference

ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations

21 January 2018

1 reference

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

21 January 2018

1 reference

Predictions of protein flexibility: first-order measures

21 January 2018

1 reference

Hinge-bending motion in citrate synthase arising from normal mode calculations.

21 January 2018

1 reference

A note on two problems in connexion with graphs

21 January 2018

1 reference

Anisotropic network model: systematic evaluation and a new web interface.

21 January 2018

1 reference

One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers.

21 January 2018

1 reference

Small-world view of the amino acids that play a key role in protein folding.

21 January 2018

1 reference

Slow folding of cross-linked alpha-helical peptides due to steric hindrance

21 January 2018

1 reference

Interpreting correlated motions using normal mode analysis.

21 January 2018

1 reference

Identification of the protein folding transition state from molecular dynamics trajectories.

21 January 2018

1 reference

Bulky side chains and non-native salt bridges slow down the folding of a cross-linked helical peptide: a combined molecular dynamics and time-resolved infrared spectroscopy study

21 January 2018

1 reference

Free-energy landscapes of proteins in the presence and absence of force

21 January 2018

1 reference

Network Analysis of Protein Structures Identifies Functional Residues

21 January 2018

1 reference

Uncovering the topology of configuration space networks

21 January 2018

1 reference

Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein

21 January 2018

1 reference

12 December 2020

Generalized correlation for biomolecular dynamics

1 reference

12 December 2020

The protein folding network

1 reference

12 December 2020

Software news and updates. Carma: a molecular dynamics analysis program

1 reference

12 December 2020

Essential Dynamics: A Tool for Efficient Trajectory Compression and Management

1 reference

12 December 2020

Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved

1 reference

12 December 2020

Estimation of protein folding probability from equilibrium simulations

1 reference

12 December 2020

Small-world network approach to identify key residues in protein-protein interaction

1 reference

12 December 2020

Hierarchical clustering schemes

1 reference

12 December 2020

Identifiers

DOI

10.1002/JCC.21688

1 reference

journals/jcc/SeeberFRMFRCF11

14 October 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

14 October 2017

PubMed publication ID

21387345

1 reference