Category: Protein Sequence Analysis

PSORTb 3.0.3 / PSORT / PSORT II /WoLF PSORT 0.2 – Prediction of Protein Localization sites for Bacterial Sequences / Eukaryotic Sequences/ Plant Sequences

PSORTb 3.0.3 / PSORT / PSORT II /WoLF PSORT 0.2

:: DESCRIPTION

PSORTb (for “bacterial” PSORT) is a high-precision localization prediction method for bacterial proteins.PSORTb has remained the most precise bacterial protein subcellular localization (SCL) predictor since it was first made available in 2003.  PSORTb version improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories. It is the first SCL predictor specifically geared for all prokaryotes, including archaea and bacteria with atypical membrane/cell wall topologies.

PSORT is a computer program for the prediction of protein localization sites in cells. It receives the information of an amino acid sequence and its source orgin, e.g., Gram-negative bacteria, as inputs. Then, it analyzes the input sequence by applying the stored rules for various sequence features of known protein sorting signals. Finally, it reports the possiblity for the input protein to be localized at each candidate site with additional information.

PSORT II is a new version of PSORT for eukaryotic sequences.

WoLF PSORT (an update of PSORT II for fungi/animal/plant sequences)

::DEVELOPER

Brinkman Laboratory, Simon Fraser University /  Kenta Nakai

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PSORTb

:: MORE INFORMATION

Citation

N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao, S.C. Sahinalp, M. Ester, L.J. Foster, and F.S.L. Brinkman (2010)
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
Bioinformatics 26(13):1608-1615.

Proteins. 1991;11(2):95-110.
Expert system for predicting protein localization sites in gram-negative bacteria.
Nakai K, Kanehisa M.

Proc Int Conf Intell Syst Mol Biol. 1997;5:147-52.
Better prediction of protein cellular localization sites with the k nearest neighbors classifier.
Horton P, Nakai K.

Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, & Kenta Nakai,
“WoLF PSORT: Protein Localization Predictor“,
Nucleic Acids Research, doi:10.1093/nar/gkm259, 2007.

iPSORT / caml-iPSORT 20100316 – Subcellular Localization Site Predictor for N-terminal Sorting Signals

iPSORT / caml-iPSORT 20100316

:: DESCRIPTION

iPSORT is a subcellular localization site predictor for N-terminal sorting signals. Given a protein sequence , it will predict whether it contains a Signal Peptide (SP), Mitochondrial Targeting Peptide (mTP), or Chloroplast Transit Peptide (cTP).

caml-iPSORT is the command line version of iPSORT

::DEVELOPER

Hideo Bannai 

:: REQUIREMENTS

:: DOWNLOAD

  caml-iPSORT

:: MORE INFORMATION

Citation

Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., and Miyano, S.,
Extensive feature detection of N-terminal protein sorting signals,
Bioinformatics, 18(2) 298–305, 2002.

ELM / iELM 1.0 – Investigation of Functional Sites in Protein Sequences with Eukaryotic Linear Motif database

ELM / iELM 1.0

:: DESCRIPTION

The ELM (Eukaryotic Linear Motif) resource  provides the biological community with a comprehensive database of known experimentally validated motifs, and an exploratory tool to discover putative linear motifs in user-submitted protein sequences.

The iELM (interactions of Eukaryotic Linear Motif) web server provides a resource for predicting the function and positional interface for a subset of interactions mediated by short linear motifs (SLiMs).

::DEVELOPER

Gibson Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Holger Dinkel et al.
ELM — the database of eukaryotic linear motifs
Nucl. Acids Res. (2012) 40 (D1): D242-D251.

iELM – a web server to explore short linear motif-mediated interactions.
Weatheritt RJ, Jehl P, Dinkel H, Gibson TJ. (2012).
Nucleic Acids Res. 2012 Jul

IDRBP-PPCT – Identifying Nucleic Acid-binding Proteins

IDRBP-PPCT

:: DESCRIPTION

IDRBP-PPCT is a new computational predictor which was proposed by combining PPCT ( Position-Specific Scoring Matrix (PSSM) and Position-Specific Frequency Matrix (PSFM) Cross Transformation) and a two-layer framework based on the random forest algorithm to identify DBPs, RBPs and DRBPs.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Wang N, Zhang J, Liu B.
IDRBP-PPCT: Identifying nucleic acid-binding proteins based on Position-Specific Score Matrix and Position-Specific Frequency Matrix Cross Transformation.
IEEE/ACM Trans Comput Biol Bioinform. 2021 Mar 29;PP. doi: 10.1109/TCBB.2021.3069263. Epub ahead of print. PMID: 33780341.

PreTP-EL – Prediction of Therapeutic Peptides based on Ensemble Learning

PreTP-EL

:: DESCRIPTION

PreTP-EL is a predictor which has been proposed via employing the ensemble learning approach to fuse the different features and machine learning techniques in order to capture the different characteristics of various therapeutic peptides.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Guo Y, Yan K, Lv H, Liu B.
PreTP-EL: prediction of therapeutic peptides based on ensemble learning.
Brief Bioinform. 2021 Nov 5;22(6):bbab358. doi: 10.1093/bib/bbab358. PMID: 34459488.

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.

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.

GLYCO – Quantify Glycan Shielding of Glycosylated Proteins

GLYCO

:: DESCRIPTION

GLYCO (GLYcan COverage) is a program to calculate glycan coverage of glycoproteins (e.g., number of glycan atoms per protein surface residues/epitope residues).

::DEVELOPER

Myungjin Lee

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

GLYCO

:: MORE INFORMATION

Citation:

Lee M, Reveiz M, Rawi R, Kwong PD, Chuang GY.
GLYCO: a tool to quantify glycan shielding of glycosylated proteins.
Bioinformatics. 2021 Nov 23:btab791. doi: 10.1093/bioinformatics/btab791. Epub ahead of print. PMID: 34864901.

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

:: 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.

PepNovo 20120423 – De novo Sequencing of low Precision MS/MS Data

PepNovo 20120423

:: DESCRIPTION

PepNovo is a de novo sequencing algorithm for MS/MS spectra. PepNovo accepts MS/MS spectra in the following formats: dta,mgf,mzxml. This version of PepNovo is optimized for ion-trap mass spectromtetry that uses CID fragmentation (charges 1-3, dominant b/y ladders).

::DEVELOPER

Ari Frank

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows

:: DOWNLOAD

 PepNovo

:: MORE INFORMATION

Citation:

Predicting Intensity Ranks of Peptide Fragment Ions
Frank, A.M.
J. Proteome Research, 8:2226-2240, 2009

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