MolAxis statistics

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Citations per year

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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


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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 in pipeline

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

[…] 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 […]


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MolAxis in publications

 (9)
PMCID: 5620967
PMID: 28979936
DOI: 10.1021/acscentsci.7b00211

[…] 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 […]

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

[…] 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 […]

PMCID: 5090048
PMID: 27693650
DOI: 10.1016/j.jmb.2016.09.021

[…] 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, […]

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

[…] to the overall single channel conductance. in order to better characterize the size of such lateral cavities, we submitted an average receptor configuration issuing from the md simulation to the molaxis webserver. displays the lateral channels and their corresponding diameter size, as provided by the molaxis analysis tool. since the maximum constriction point lies below the diameter of na+ […]

PMCID: 4514475
PMID: 26208301
DOI: 10.1371/journal.pone.0133011

[…] 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 […]


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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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