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MolAxis specifications

Information


Unique identifier OMICS_04160
Name MolAxis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format PDB
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Eitan Yaffe

Information


Unique identifier OMICS_04160
Name MolAxis
Interface Web user interface
Restrictions to use None
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Eitan Yaffe

Publications for MolAxis

MolAxis citations

 (13)
library_books

Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis

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

[…] ing its potentially druggable binding pockets.There are already a number of algorithms that can detect protein binding pockets in static structures., Some of these rely on the Voronoi diagrams (e.g., MolAxis, MOLE), grids (e.g., POCKET, PocketFinder, POVME,), and molecular surfaces and probes (e.g., HOLE, SURFNET). Other algorithms analyze ensembles of structures, but usually require a preliminary […]

library_books

Interactive exploration of ligand transportation through protein tunnels

2017
BMC Bioinformatics
PMCID: 5333178
PMID: 28251878
DOI: 10.1186/s12859-016-1448-0

[…] solutions often focus on detection of possible ligand transportation paths through the protein, called tunnels. These solutions are mostly based on the geometric analysis, e.g., CAVER [], MOLE [], or MolAxis []. Figure shows an example of small ligand passing through a tunnel computed by CAVER algorithm and visualized using CAVER Analyst []. The tunnel is colored with respect to the hydrophobicit […]

library_books

MOMP from Campylobacter jejuni Is a Trimer of 18 Stranded β Barrel Monomers with a Ca2 + Ion Bound at the Constriction Zone

2016
J Mol Biol
PMCID: 5090048
PMID: 27693650
DOI: 10.1016/j.jmb.2016.09.021

[…] triction, is predominantly negatively charged (). The pore axis is slightly offset, relative to the membrane normal. When viewed from the extracellular face, L7 sits above the entrance. Analysis with MolAxis reveals that the constriction zone narrows to a radius of 2.6 Å. The constriction zone, like the protein, has an elliptical, not circular, shape. On one surface of the constriction zone, Tyr3 […]

library_books

Pathways and Barriers for Ion Translocation through the 5 HT3A Receptor Channel

2015
PLoS One
PMCID: 4605793
PMID: 26465896
DOI: 10.1371/journal.pone.0140258

[…] The HOLE[] program and the MolAxis[] webserver were used to analyze pore dimension and fenestrations. RMSF and B-factors were calculated using the ptraj[] software tool. RMSD, ion density and coordination analyses were performe […]

call_split

A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation

2015
PLoS One
PMCID: 4514475
PMID: 26208301
DOI: 10.1371/journal.pone.0133011
call_split See protocol

[…] onstriction point between Leu9′ and Leu16′, 10 Å long, ); iii) the pore radius, computed using the web-based implementation of a method to compute molecular channels [] (http://bioinfo3d.cs.tau.ac.il/MolAxis/) in the configuration obtained by averaging over the last 100 ns portion of each trajectory; iv) the orientation of the five M2 helices and the quaternary twist angle between the LBD and TMD […]

call_split

Ensemble Generation and the Influence of Protein Flexibility on Geometric Tunnel Prediction in Cytochrome P450 Enzymes

2014
PLoS One
PMCID: 4067289
PMID: 24956479
DOI: 10.1371/journal.pone.0099408
call_split See protocol

[…] conformations of all ensembles were prepared for tunnel calculation by removing the hydrogen atoms, solvent, ions and ligand (if present). Tunnels were calculated in each structure using the programs MolAxis and Caver3.0. Both programs identify and report tunnels as a series of spheres with the radius of each sphere being defined as the distance to the nearest protein atom. The smallest sphere, wh […]


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MolAxis institution(s)
School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Department of Human Genetics, Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel

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