GOMEP – Gene Ontology-based Missing Enzyme Predictor

GOMEP

:: DESCRIPTION

GOMEP Predicts Missing Enzymes using functional coherence scores of Gene Ontology (GO) terms

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

GOMEP

:: MORE INFORMATION

Citation

Sci Rep. 2016 Aug 24;6:31725. doi: 10.1038/srep31725.
Missing gene identification using functional coherence scores.
Chitale M, Khan IK, Kihara D

Phobius /PolyPhobius 1.05 – Combined Transmembrane Topology & Signal Peptide Predictor

Phobius /PolyPhobius 1.05

:: DESCRIPTION

Phobius /PolyPhobius is for prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein.

::DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Phobius

:: MORE INFORMATION

Citation:

Phobius is described in:

  • Lukas Käll, Anders Krogh and Erik L. L. Sonnhammer.
    A Combined Transmembrane Topology and Signal Peptide Prediction Method.
    Journal of Molecular Biology, 338(5):1027-1036, May 2004.
    (doi) (PubMed)

PolyPhobius is described in:

  • Lukas Käll, Anders Krogh and Erik Sonnhammer.
    An HMM posterior decoder for sequence feature prediction that includes homology information
    Bioinformatics, 21 (Suppl 1):i251-i257, June 2005.
    (doi) (PubMed)

 

ZincExplorer – Predictor of Protein Zinc-binding Sites

ZincExplorer

:: DESCRIPTION

ZincExplorer is a web server that could predict Zinc-binding sites from protein sequence.

::DEVELOPER

Ziding Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Mol Biosyst. 2013 Sep;9(9):2213-22. doi: 10.1039/c3mb70100j.
ZincExplorer: an accurate hybrid method to improve the prediction of zinc-binding sites from protein sequences.
Chen Z, Wang Y, Zhai YF, Song J, Zhang Z.

SPAR v1.0 – Predictor for self-interacting protein from Sequence Information

SPAR v1.0

:: DESCRIPTION

SPAR (Self-interacting Protein AnalyzeR) was a predictor for self-interacting protein from sequence information. Based on comprehensive analysis of a variety of physiochemical properties on self-interacting proteins, a new encoding scheme named RSI has been designed.

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SPAR

:: MORE INFORMATION

Citation

Amino Acids. 2016 Jul;48(7):1655-65. doi: 10.1007/s00726-016-2226-z.
SPAR: a random forest-based predictor for self-interacting proteins with fine-grained domain information.
Liu X, Yang S, Li C, Zhang Z, Song J.

Lypred – Predictor for Identifying Bacterial Cell Wall Lyase

Lypred

:: DESCRIPTION

The web-server Lypred was developed to predict Bacterial Cell Wall Lyase via pseudo amino acid composition.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Identification of Bacterial Cell Wall Lyases via Pseudo Amino Acid Composition.
Chen XX, Tang H, Li WC, Wu H, Chen W, Ding H, Lin H.
Biomed Res Int. 2016;2016:1654623. doi: 10.1155/2016/1654623.

iProEP – Predictor for Predicting Promoter

iProEP

:: DESCRIPTION

iProEP is a promoter prediction tools of five species: Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Bacillus subtilis, and Escherichia coli. The PseKNC and PCSF features were employed to formulate promoter samples.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iProEP: A Computational Predictor for Predicting Promoter.
Lai HY, Zhang ZY, Su ZD, Su W, Ding H, Chen W, Lin H.
Mol Ther Nucleic Acids. 2019 Sep 6;17:337-346. doi: 10.1016/j.omtn.2019.05.028.

RASP 1.90 – RApid Side-chain Predictor

RASP 1.90

:: DESCRIPTION

RASP is a RApid Side-chain Predictor. To achieve a much faster speed with a comparable accuracy to the best existing methods, the authors not only employ the clash elimination strategy of CIS-RR, but also carefully optimize energy terms and integrate different search algorithms. In comprehensive benchmark testings, RASP is over one order of magnitude faster (~ 40 times over CIS-RR) than the recently developed methods, while achieving comparable or even better accuracy.

::DEVELOPER

Zhichao (Chichau) MIAO

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  RASP

:: MORE INFORMATION

Citation:

Zhichao Miao,Yang Cao, Taijiao Jiang 2011
RASP:Rapid modeling of protein side-chain conformations
Bioinformatics (2011) 27 (22): 3117-3122.

MetalionRNA – Metal Ion Binding Site Predictor

MetalionRNA

:: DESCRIPTION

MetalionRNA is a novel bioinformatic method for predicting metal-binding sites in RNA structures.

::DEVELOPER

Bujnicki lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Computational methods for prediction of RNA interactions with metal ions and small organic ligands.
Philips A, Łach G, Bujnicki JM.
Methods Enzymol. 2015;553:261-85. doi: 10.1016/bs.mie.2014.10.057.

MetaSSPred – Balanced Secondary Structure Predictor

MetaSSPred

:: DESCRIPTION

MetaSSPred is a well-balanced Secondary Structure predictor

::DEVELOPER

Hoque’s Lab, University of New Orleans

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MetaSSPred

:: MORE INFORMATION

Citation

J Theor Biol. 2015 Nov 5;389:60-71. doi: 10.1016/j.jtbi.2015.10.015. [Epub ahead of print]
A balanced secondary structure predictor.
Nasrul Islam M, Iqbal S, Katebi AR, Tamjidul Hoque M