Tag: Remote Homology

ProtRe-CN – Protein Remote Homology Detection

ProtRe-CN

:: DESCRIPTION

ProtRe-CN is a novel ranking method for protein remote homology detection by combining classification methods and network methods via Learning to Rank.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ProtRe-CN

:: MORE INFORMATION

Citation

Shao J, Chen J, Liu B.
ProtRe-CN: Protein Remote Homology Detection by Combining Classification Methods and Network Methods via Learning to Rank.
IEEE/ACM Trans Comput Biol Bioinform. 2021 Aug 30;PP. doi: 10.1109/TCBB.2021.3108168. Epub ahead of print. PMID: 34460380.

ProDec-BLSTM – Protein Remote Homology Detection based on Bidirectional Long Short-Term Memory

ProDec-BLSTM

:: DESCRIPTION

ProDec-BLSTM is a predictor of Protein remote homology detection based on bidirectional long short-term memory.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

ProDec-BLSTM

:: MORE INFORMATION

Citation

Li S, Chen J, Liu B.
Protein remote homology detection based on bidirectional long short-term memory.
BMC Bioinformatics. 2017 Oct 10;18(1):443. doi: 10.1186/s12859-017-1842-2. PMID: 29017445; PMCID: PMC5634958.

ProtDet-CCH – Protein Remote Homology Detection by combining Long Short-Term Memory and Ranking methods

ProtDet-CCH

:: DESCRIPTION

ProtDet-CCH is a Python package for Protein remote homology detection by combining Long Short-Term Memory and ranking methods

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

ProtDet-CCH i

:: MORE INFORMATION

Citation

Liu B, Li S.
ProtDet-CCH: Protein Remote Homology Detection by Combining Long Short-Term Memory and Ranking Methods.
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1203-1210. doi: 10.1109/TCBB.2018.2789880. Epub 2018 Jan 5. PMID: 29993950.

HITS-PR-HHblits – Protein Remote Homology Detection by Combining PageRank and Hyperlink-Induced Topic Search

HITS-PR-HHblits

:: DESCRIPTION

HITS-PR-HHblits is a web server of Protein Remote Homology Detection by Combining PageRank and Hyperlink-Induced Topic Search

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

HITS-PR-HHblits

:: MORE INFORMATION

Citation

Liu B, Jiang S, Zou Q.
HITS-PR-HHblits: protein remote homology detection by combining PageRank and Hyperlink-Induced Topic Search.
Brief Bioinform. 2018 Nov 7. doi: 10.1093/bib/bby104. Epub ahead of print. PMID: 30403770.

FUGUE 20160606 – Protein Structure Prediction using Remote Homology Detection

FUGUE 20160606

:: DESCRIPTION

FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure. Given a query sequence (or a sequence alignment), FUGUE scans a database of structural profiles, calculates the sequence-structure compatibility scores and produces a list of potential homologues and alignments.

::DEVELOPER

the Mizuguchi Laboratory.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FUGUE

:: MORE INFORMATION

Citation

J. Shi, T. L. Blundell, and K. Mizuguchi (2001).
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure- dependent gap penalties.
J. Mol. Biol., 310, 243-257.

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