eMatchSite specifications

Information


Unique identifier OMICS_10538
Name eMatchSite
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data two protein structures
Input format PDB
Output data A single file that containing: numerical scores for the constructed alignment of binding sites, aligned residue pairs with the corresponding Cα-Cα distances, transformation matrices to superpose the second protein onto the first protein, and the coordinates of the second protein upon the superposition of two binding sites.
Output format PDB
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability No
Requirements
zlib, gzstream, libsvm
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Additional information


http://brylinski.cct.lsu.edu/content/ematchsite-manual

Information


Unique identifier OMICS_10538
Name eMatchSite
Interface Web user interface
Restrictions to use None
Input data two protein structures
Input format PDB
Output data A single file that containing: numerical scores for the constructed alignment of binding sites, aligned residue pairs with the corresponding Cα-Cα distances, transformation matrices to superpose the second protein onto the first protein, and the coordinates of the second protein upon the superposition of two binding sites.
Output format PDB
Programming languages C++
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Additional information


http://brylinski.cct.lsu.edu/content/ematchsite-manual

Publications for eMatchSite

eMatchSite citations

 (2)
library_books

Large scale computational drug repositioning to find treatments for rare diseases

2018
NPJ Syst Biol Appl
PMCID: 5847522
PMID: 29560273
DOI: 10.1038/s41540-018-0050-7

[…] an diseases. Comparing ligand-binding sites in protein structures is among the most promising computational techniques to inform drug repurposing efforts. In this study, we demonstrate that combining eMatchSite with structure-based virtual screening enhances the accuracy of the detection of similar binding pockets. This promising methodology was employed to match drug-binding pockets from DrugBank […]

library_books

Large scale detection of drug off targets: hypotheses for drug repurposing and understanding side effects

2017
PMCID: 5408384
PMID: 28449705
DOI: 10.1186/s40360-017-0128-7

[…] sed to find targets related to observed side-effects for 656 drugs [].There are a number of target-based methods for the detection of binding-site similarities []. Among these, SOIPPA [], CavBase [], eMatchSite [], IsoCleft [, ] and IsoMIF [, ]. Such methods can be used to predict protein function from structure [–], understand promiscuity within a protein family [, ], assess drugability [], and e […]

eMatchSite institution(s)
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
eMatchSite funding source(s)
Supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R35GM119524.

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