PCP 1.0 – Protein Complex Prediction

PCP 1.0

:: DESCRIPTION

PCP is a sofware that searches for cliques in the modified network, and merge cliques to form clusters using a “partial clique merging” method. Experiments show that (1) the use of indirect interactions and topological weight to augment protein-protein interactions can be used to improve the precision of clusters predicted by various existing clustering algorithms; and (2) our complex-finding algorithm performs very well on interaction networks modified in this way. Since no other information except the original PPI network is used, the would be very useful for protein complex prediction, especially for prediction of novel protein complexes.

::DEVELOPER

Limsoon Wong Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • C++ Compiler
  • Perl

:: DOWNLOAD

 PCP

:: MORE INFORMATION

Citation:

J Bioinform Comput Biol. 2008 Jun;6(3):435-66.
Using indirect protein-protein interactions for protein complex prediction.
Chua HN, Ning K, Sung WK, Leong HW, Wong L.

PhyloPFP – Gene Ontology Prediction Using Phylogenomics

PhyloPFP

:: DESCRIPTION

PhyloPFP is a phylogenomics based protein function prediction server

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Mar 1;35(5):753-759. doi: 10.1093/bioinformatics/bty704.
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences.
Jain A, Kihara D.

SUPRB 1.0 – Threading Strucuture Prediction

SUPRB 1.0

:: DESCRIPTION

SUPRB (threading with Suboptimal alignment-based PRoBabilistic residue contact information) is a threading strucuture prediction algorithm which employs suboptimal alignments.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SUPRB

:: MORE INFORMATION

Citation

Proteins. 2011 Jan;79(1):315-34. doi: 10.1002/prot.22885.
Effect of using suboptimal alignments in template-based protein structure prediction.
Chen H1, Kihara D.

SUBWAI 1.0 – Protein Structure Prediction program

SUBWAI 1.0

:: DESCRIPTION

SUBWAI (SUBoptimal Weighted AlIgnment) is the protein structure prediction program based on threading strategy with SPAD.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SUBWAI

:: MORE INFORMATION

Citation

Proteins. 2008 May 15;71(3):1255-74.
Estimating quality of template-based protein models by alignment stability.
Chen H1, Kihara D.

TAPIR 1.2 – Prediction of Plant microRNA Targets

TAPIR 1.2

:: DESCRIPTION

TAPIR is a web server designed for the prediction of plant microRNA targets. The server offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much slower but guarantees to find less perfectly paired miRNA – target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA – target duplex having a large loop, making them undetectable by traditional tools.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl
  • Bioperl
  • ViennaRNA library + perl modules

:: DOWNLOAD

 TAPIR

:: MORE INFORMATION

Citation

Bonnet, E., He, Y., Billiau, K., Van de Peer, Y. (2010)
TAPIR, a web server for the prediction of plant microRNA targets, including target mimics.
Bioinformatics 26, 1566-1568.

Cascleave – Caspase Substrate Cleavage Site Prediction

Cascleave

:: DESCRIPTION

Cascleave is a novel tool developed using Java program for the high-throughput in silico identification of substrate cleavage sites for various caspases from the amino acid sequences of the substrates.

::DEVELOPER

Cascleave team

:: SCREENSHOTS

Cascleave

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets.
Wang M, Zhao XM, Tan H, Akutsu T, C Whisstock J, Song J.
Bioinformatics (2014) 30 (1): 71-80. doi: 10.1093/bioinformatics/btt603

Concavity 0.1 – Ligand Binding Site Prediction from Protein Sequence and Structure

Concavity 0.1

:: DESCRIPTION

Concavity predicts ligand-binding sites from structure.

::DEVELOPER

John A. Capra , Thomas Funkhouser , Mona Singh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 Concavity

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2009 Dec;5(12):e1000585. doi: 10.1371/journal.pcbi.1000585. Epub 2009 Dec 4.
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
Capra JA1, Laskowski RA, Thornton JM, Singh M, Funkhouser TA.

SAINT2 – Cotranslational Protein Structure prediction

SAINT2

:: DESCRIPTION

SAINT2 is a fragment-based de novo protein structure prediction software. It is based on the notion that some proteins fold as they are being synthesised, which is known as the cotranslational protein folding hypothesis.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOs/ Linux

:: DOWNLOAD

SAINT2

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Apr 1;34(7):1132-1140. doi: 10.1093/bioinformatics/btx722.
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.
de Oliveira SHP, Law EC, Shi J, Deane CM.

TCRBuilder – Multi-state T-cell Receptor Structure prediction

TCRBuilder

:: DESCRIPTION

TCRBuilder is a TCR structure prediction algorithm.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Front Immunol. 2019 Oct 15;10:2454. doi: 10.3389/fimmu.2019.02454. eCollection 2019.
Comparative Analysis of the CDR Loops of Antigen Receptors.
Wong WK, Leem J, Deane CM.

FREAD 3.0.1 – Database Search Loop Structure Prediction protocol

FREAD 3.0.1

:: DESCRIPTION

FREAD is a database search loop structure prediction protocol. Loops are generally located in the protein’s surface and they are known to be notoriously difficult to predict.The basic assumption of FREAD is that local sequence similarity may determine the backbone structure of a local protein structure if it is constrained within anchor structures.

::DEVELOPER

Oxford Protein Informatics Group (OPIG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

FREAD

Citation

FREAD revisited: Accurate loop structure prediction using a database search algorithm.
Choi Y, Deane CM.
Proteins. 2010 May 1;78(6):1431-40. doi: 10.1002/prot.22658.