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Protocols

MDpocket specifications

Information


Unique identifier OMICS_04154
Name MDpocket
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for MDpocket

MDpocket citations

 (25)
library_books

Identification of allosteric inhibitors of the ecto 5' nucleotidase (CD73) targeting the dimer interface

2018
PLoS Comput Biol
PMCID: 5805337
PMID: 29377887
DOI: 10.1371/journal.pcbi.1005943

[…] n interface, ) was the only pocket meeting all the druggability criteria previously defined, and was therefore selected as target binding site for virtual screening. As shown in , results obtained by MDpocket analyses indicated that the volume of this cavity is rather large and highly fluctuating (from 2815 to 4732 Å3) and also that the mean local hydrophobic density was increasing for several con […]

library_books

Involvement of arginine 878 together with Ca2+ in mouse aminopeptidase A substrate specificity for N terminal acidic amino acid residues

2017
PLoS One
PMCID: 5587309
PMID: 28877217
DOI: 10.1371/journal.pone.0184237

[…] and 1 fs per time step for 50,000,000 steps, generating a trajectory of 50 ns. Trajectory analyses were performed with VMD, pair interaction calculations with NAMD and ligand binding site volume with MDPOCKET. […]

library_books

Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis

2017
PMCID: 5620967
PMID: 28979936
DOI: 10.1021/acscentsci.7b00211

[…] POCKET, PocketFinder, POVME,), and molecular surfaces and probes (e.g., HOLE, SURFNET). Other algorithms analyze ensembles of structures, but usually require a preliminary structural alignment (e.g., MDpocket, PocketAnalizerPCA, Epock, Trj_cavity, and TRAPP). In this case, the resulting information may depend on the specific reference structure used for the alignment. Atom-based algorithms (e.g., […]

call_split

Unique residues in the ATP gated human P2X7 receptor define a novel allosteric binding pocket for the selective antagonist AZ10606120

2017
Sci Rep
PMCID: 5429621
PMID: 28389651
DOI: 10.1038/s41598-017-00732-5
call_split See protocol

[…] -31 G* approach. Simulations were run in at least two replicates for 50 ns using random number seeds for the Langevin thermostat and the initial velocity. Trajectories were analysed using cpptraj and MDpocket. For the wild type hP2X7R ten representative structures were extracted from the trajectories and used as starting conformations for ensemble ligand docking.Ensemble ligand docking of AZ106061 […]

library_books

Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling

2017
PeerJ
PMCID: 5410147
PMID: 28462022
DOI: 10.7717/peerj.3206

[…] mains low during the course of the simulation ( and ), with an increase corresponding to the c-terminal loop of the fungal model.The binding pockets of both receptor proteins were characterized using mdpocket in the fpocket software package (http://fpocket.sourceforge.net) (; ). Fpocket generates clusters of spheres to describe pockets identified in a given protein, while mdpocket allows for detec […]

library_books

Probing protein flexibility reveals a mechanism for selective promiscuity

2017
eLife
PMCID: 5446241
PMID: 28432789
DOI: 10.7554/eLife.22889.034

[…] The PyMOL Molecular Graphics System v1.7.4.0 was used for structure preparation and analysis (). Trajectories were analyzed using VMDv1.9.2 () and the MDpocket software package v2.0 (; ) for cavity detection and volume/surface area measurement. Measurements of PD-1 binding pocket occlusion, shown in and , were calculated from molecular dynamics sim […]

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MDpocket institution(s)
Departament de Fisicoquímica and Institut de Biomedicina, Universitat de Barcelona, Barcelona, Spain

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