(Q42618711)

3 November 2017

MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories (English)

1 reference

3 November 2017

0 references

4

1 reference

3 November 2017

Axel Bidon-Chanal

2

0 references

author name string

Peter Schmidtke

series ordinal

1

1 reference

PubMed ID

21967761

3 November 2017

F Javier Luque

series ordinal

3

1 reference

PubMed ID

21967761

3 November 2017

language of work or name

English

0 references

publication date

3 October 2011

1 reference

3 November 2017

1 reference

3 November 2017

27

1 reference

3 November 2017

23

1 reference

3 November 2017

3276-3285

1 reference

Crystal structure of an Hsp90-nucleotide-p23/Sba1 closed chaperone complex

3 November 2017

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Pocketome via comprehensive identification and classification of ligand binding envelopes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Unveiling the full potential of flexible receptor docking using multiple crystallographic structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

PELE: Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Fast prediction and visualization of protein binding pockets with PASS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

CHARMM: the biomolecular simulation program

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

GRID-MD-A tool for massive simulation of protein channels.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

The Amber biomolecular simulation programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Finding gas migration pathways in proteins using implicit ligand sampling

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Improving structure-based function prediction using molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

MetaPocket: a meta approach to improve protein ligand binding site prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

VMD: visual molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

The many roles of computation in drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Pocket extraction on proteins via the Voronoi diagram of spheres.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Detection, delineation, measurement and display of cavities in macromolecular structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Fpocket: an open source platform for ligand pocket detection.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

In silico prediction of binding sites on proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Ensemble Docking from Homology Models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

The role of the distal histidine in myoglobin and haemoglobin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Ligand binding and conformational motions in myoglobin

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

UCSF Chimera--a visualization system for exploratory research and analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Scalable molecular dynamics with NAMD

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Recipes for the selection of experimental protein conformations for virtual screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Understanding and predicting druggability. A high-throughput method for detection of drug binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Watching a protein as it functions with 150-ps time-resolved x-ray crystallography

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Ligand migration in sperm whale myoglobin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Mapping the pathways for O2 entry into and exit from myoglobin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Binding site detection and druggability index from first principles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Novel procedure for modeling ligand/receptor induced fit effects.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Histidine E7 Dynamics Modulates Ligand Exchange between Distal Pocket and Solvent in AHb1 fromArabidopsis thaliana

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 A.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Characteristic physical properties and structural fragments of marketed oral drugs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

PocketPicker: analysis of ligand binding-sites with shape descriptors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Structure-activity relationships in purine-based inhibitor binding to HSP90 isoforms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

MolAxis: efficient and accurate identification of channels in macromolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Crystal structures of CO-, deoxy- and met-myoglobins at various pH values

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Transient Pockets on Protein Surfaces Involved in Protein−Protein Interaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

Stereochemistry of Cooperative Effects in Haemoglobin: Haem–Haem Interaction and the Problem of Allostery

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTR550

10.1093/BIOINFORMATICS/BTR550

21 January 2018

Identifiers

DOI

1 reference

journals/bioinformatics/SchmidtkeBLB11

3 November 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PubMed ID

21967761