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Protocols

ProMate specifications

Information


Unique identifier OMICS_08143
Name ProMate
Interface Web user interface
Restrictions to use None
Input data ID, file
Input format PDB
Computer skills Basic
Stability Stable
Maintained No

Publication for ProMate

ProMate citations

 (27)
library_books

Molecular characterization of HIV 1 Nef and ACOT8 interaction: insights from in silico structural predictions and in vitro functional assays

2016
Sci Rep
PMCID: 4772117
PMID: 26927806
DOI: 10.1038/srep22319

[…] alculated using the APBS program. The CPORT (Consensus Prediction Of interface Residues in Transient complex) bioinformatic tool, a consensus method combining six interface web servers (WHISHY, PIER, ProMate, cons-PPISP, SPIDER and PINUP), was used as interface prediction program. The Nef/ACOT8 docking model was then performed using the HADDOCK (High Ambiguity Driven biomolecular DOCKing) version […]

library_books

Risk of lung cancer in patients with gastro esophageal reflux disease: a population based cohort study

2016
PeerJ
PMCID: 5178340
PMID: 28028458
DOI: 10.7717/peerj.2753

[…] athways (; ; ) and further result in malignant transformation. In addition, based on the studies investigating the pathogenesis of Barrett’s esophagus and esophageal carcinoma, both acid and bile can promate carcinogenesis through the induction of DNA damage and the influence of cell proliferation and apoptosis (; ). These pathogenesis may happen in the respiratory tract, and contribute to the dev […]

library_books

Structural neighboring property for identifying protein protein binding sites

2015
BMC Syst Biol
PMCID: 4565107
PMID: 26356630
DOI: 10.1186/1752-0509-9-S5-S3

[…] Our method is compared to ProMate and PINUP. The test data is originally used by ProMate [], including 57 unbound proteins and their complexes. The results are reported in Table . The overall Fnat values for our method, PINUP […]

library_books

Progress and challenges in predicting protein interfaces

2015
Brief Bioinform
PMCID: 4719070
PMID: 25971595
DOI: 10.1093/bib/bbv027

[…] t position in the MSA are interface or non-interface. HomPPI implicitly takes advantage of binding site conservation of the homologous complexes. It performs better than 3D classifier methods such as ProMate [], PIER [], meta-PPISP [], cons-PPISP [] and PSIVER [].A combination of sequence and structure conservation scores was introduced in IBIS []. Initially, homologous complexes with at least 30% […]

library_books

Algorithmic approaches to protein protein interaction site prediction

2015
PMCID: 4338852
PMID: 25713596
DOI: 10.1186/s13015-015-0033-9

[…] ds, as in WHISCYMATE [] and Combined BindML [].More integrative approaches utilize meta-predictors, which combine multiple predictors into a single output score. Meta-PPISP [] combines cons-PPISP [], Promate [], and PINUP [] via a linear regression model taking local environment into account.By adding SPPIDER [] and PPI-PRED [] to that list, metaPPI [] uses the frequency with which its constituent […]

library_books

Drug Like Protein–Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology

2014
Mol Inform
PMCID: 4160817
PMID: 25254076
DOI: 10.1002/minf.201400040

[…] equire the structure of the protein(s). Some methods use empirical scoring functions like ODA (see for review the literature[]), other approaches use sequence conservation among other parameters like Promate,[] while others make use of machine learning techniques like SPPIDER.[] Meta-servers, combining different tools have also been developed such as meta-PPISP.[] Protein interface can also be pro […]

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ProMate institution(s)
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel

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