PocketMatch specifications

Information


Unique identifier OMICS_10541
Name PocketMatch
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Kalidas Yeturu <>

Publication for PocketMatch

PocketMatch in publications

 (8)
PMCID: 5842552
PMID: 29514608
DOI: 10.1186/s12885-018-4050-1

[…] of the molecular interactions are tabulated in table .fig. 18fig. 19table 6, furthermore, the binding pockets of both the targets were evaluated to understand their similarity and was assessed using pocketmatch (pm) [] that was executed through three aspects (a) representation of each site as sorted lists of distances between chosen points, (b) alignment of two sets of distance lists and (c) […]

PMCID: 5624866
PMID: 28970579
DOI: 10.1038/s41598-017-12471-8

[…] on the false negatives so as to minimize false positives. supplementary table  shows the number of proteins identified with different thresholds, whereas supplementary table  lists the highest pms (pocketmatch score) each of the 1,768 proteins share with the queried ntp motif. higher the pms, higher is the similarity and higher is the confidence., in order to understand how well our method […]

PMCID: 5376175
PMID: 25220818
DOI: 10.1038/srep06356

[…] motifs documented in prosite were scanned against each protein sequence in the proteome to identify possible binding sites., the binding sites obtained were compared using an in-house algorithm – pocketmatch (pm). pm computes shape descriptors of the pockets and compares sorted arrays of all-pair distance elements grouped into 90 combinations of chemical type pairs to calculate a combined […]

PMCID: 3395720
PMID: 22808064
DOI: 10.1371/journal.pone.0039808

[…] pipeline where the top 10 binding sites for each of these 57 proteins were identified using pocketdepth algorithm . the binding pockets of these proteins were then compared with human proteome using pocketmatch . of the 57 proteins, 31 proteins have high structural similarity with human proteome at binding site level whereas 26 proteins which do not have binding site similarity with human […]

PMCID: 3205055
PMID: 22073123
DOI: 10.1371/journal.pone.0027044

[…] of tb. validation for this part of the annotation pipeline has been carried out on the 312 protein test set. binding site prediction, comparison and ligand association computed using pocketdepth and pocketmatch were compared with that in their corresponding crystal structures (), which indicated that ligand associations and hence annotations were in most cases correct, when the detected […]


To access a full list of publications, you will need to upgrade to our premium service.

PocketMatch institution(s)
Bioinformatics Centre and Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India

PocketMatch reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PocketMatch