SecretomeP 2.0 – Prediction of Non-classical Protein Secretion

SecretomeP 2.0

:: DESCRIPTION

SecretomeP server produces ab initio predictions of non-classical i.e. not signal peptide triggered protein secretion. The method queries a large number of other feature prediction servers to obtain information on various post-translational and localizational aspects of the protein, which are integrated into the final secretion prediction.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SecretomeP

:: MORE INFORMATION

Citation

Feature based prediction of non-classical and leaderless protein secretion
J. Dyrløv Bendtsen, L. Juhl Jensen, N. Blom, G. von Heijne and S. Brunak
Protein Eng. Des. Sel., 17(4):349-356, 2004

PSIPRED 4.02 – Accurate Protein Secondary Structure Prediction

PSIPRED 4.02

:: DESCRIPTION

PSIPRED (Position Specific Iterated Prediction) is a highly accurate method for protein secondary structure prediction.

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PSIPRED

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W349-57. doi: 10.1093/nar/gkt381. Epub 2013 Jun 8.
Scalable web services for the PSIPRED Protein Analysis Workbench.
Buchan DW1, Minneci F, Nugent TC, Bryson K, Jones DT.

Bioinformatics. 2000 Apr;16(4):404-5.
The PSIPRED protein structure prediction server.
McGuffin LJ, Bryson K, Jones DT.

CSS-Palm 4.0 – Palmitoylation Site Prediction with a Clustering and Scoring Strategy

CSS-Palm 4.0

:: DESCRIPTION

CSS-Palm is a computer program for palmitoylation site prediction, Clustering and Scoring Strategy for Palmitoylation Sites Prediction.The program’s prediction performance is encouraging with highly positive Jack-Knife validation results (sensitivity 82.16% and specificity 83.17% for cut-off score 2.6).

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

:: REQUIREMENTS

  • WIndows / Linux / MacOsX
  • Java

:: DOWNLOAD

 CSS-Palm

:: MORE INFORMATION

Citation

CSS-Palm 2.0: an updated software for palmitoylation sites prediction
Jian Ren, Longping Wen, Xinjiao Gao, Changjiang Jin, Yu Xue and Xuebiao Yao.
Protein Engineering, Design and Selection.2008 21(11):639-644

ddbRNA – RNA Secondary Structure Prediction

ddbRNA

:: DESCRIPTION

ddbRNA is a software for detection of conserved secondary structures in multiple alignments.

::DEVELOPER

di Bernardo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 ddbRNA

:: MORE INFORMATION

Citation

Bioinformatics. 2003 Sep 1;19(13):1606-11.
ddbRNA: detection of conserved secondary structures in multiple alignments.
di Bernardo D, Down T, Hubbard T.

iWRAP – Prediction of Cancer-related Protein-protein Interactions

iWRAP

:: DESCRIPTION

iWRAP is a threading program for identifying the putative interface between two protein sequences. iWRAP is based on RAPTOR, which is a single domain threading program. iWRAP considers only the interface of the template to predict interacting residues in a pair of query sequences. iWRAP uses the open-source optimization library (COIN-OR) to minimize the threading energy function.

::DEVELOPER

Raghavendra Hosur (rhosur@mit.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  iWRAP

:: MORE INFORMATION

Citation

J Mol Biol. 2011 Feb 4;405(5):1295-310. doi: 10.1016/j.jmb.2010.11.025.
iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions.
Hosur R, Xu J, Bienkowska J, Berger B.

SLPFA – Subcellular Location Prediction with Frequency and Alignment

SLPFA

:: DESCRIPTION

SLPFA is a predictor for subcellular location prediction of proteins by feature vectors based on amino acid composition (frequency) and sequence alignment. 90.96% of overall accuracy was obtained through fivefold cross validation tests with TargetP plant data sets.

SLPFA is an improved subcellular location predictor of SLP-Local

::DEVELOPER

Akutsu Laboratory (Laboratory of Mathematical Bioinformatics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2007 Nov 30;8:466.
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition.
Tamura T, Akutsu T.

DeepIDP-2L – Protein intrinsically Disordered Region Prediction

DeepIDP-2L

:: DESCRIPTION

DeepIDP-2L is a web server for protein intrinsically disordered region prediction by combining convolutional attention network and hierarchical attention network

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Tang YJ, Pang YH, Liu B.
DeepIDP-2L: protein intrinsically disordered region prediction by combining convolutional attention network and hierarchical attention network.
Bioinformatics. 2021 Dec 2:btab810. doi: 10.1093/bioinformatics/btab810. Epub ahead of print. PMID: 34864847.

TRAP 3.05 – Transcription factor Affinity Prediction

TRAP 3.05

:: DESCRIPTION

TRAP (Transcription factor Affinity Prediction) calculates the affinity of transcription factors for DNA sequences on the basis of a biophysical model. This method has proven to be useful for several applications, including for determining the putative target genes of a given factor. This protocol covers two other applications: (i) determining which transcription factors have the highest affinity in a set of sequences (illustrated with chromatin immunoprecipitation–sequencing (ChIP-seq) peaks), and (ii) finding which factor is the most affected by a regulatory single-nucleotide polymorphism.

::DEVELOPER

TRAP Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • R Package

:: DOWNLOAD

  TRAP

:: MORE INFORMATION

Citation

Morgane Thomas-Chollier, Andrew Hufton, Matthias Heinig, Sean O’Keeffe, Nassim El Masri, Helge G Roider, Thomas Manke and Martin Vingron.
Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.
Nature Protocols, 3;6(12):1860-9. (2011)

SPOCS 1.0.10 – Graph-based Ortholog/Paralog Prediction tool

SPOCS 1.0.10

:: DESCRIPTION

SPOCS (Species Paralogy and Orthology Clique Solver) is a graph-based ortholog/paralog prediction tool that will predict orthologs and paralogs given a set of prokaryotic proteomes (the set of proteins encoded by a genome). The software will take a set of protein fasta files (one per species genome), and an optional additional fasta to serve as an outgroup (a species that should be more distantly related to the species of interest than any of the species of interest are to each other).

::DEVELOPER

Computational Biology & Bioinformatics ,Pacific Northwest National Laboratory

:: SCREENSHOTS

SPOCS

:: REQUIREMENTS

  • Linux/ MacOsX
  • C++ Compiler
  • NCBI BLAST

:: DOWNLOAD

 SPOCS

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 15;29(20):2641-2. doi: 10.1093/bioinformatics/btt454.
SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.
Curtis DS, Phillips AR, Callister SJ, Conlan S, McCue LA.