MitoFates – Identifying Putative Mitochondrial Presequences and Cleavage Sites

MitoFates

:: DESCRIPTION

MitoFates predicts mitochondrial presequence, a cleavable localization signal located in N-terminal, and its cleaved position.

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MitoFates

:: MORE INFORMATION

Citation:

MitoFates: Improved Prediction of Mitochondrial Targeting Sequences and Their Cleavage Sites.
Yoshinori Fukasawa, Junko Tsuji, Szu-Chin Fu, Kentaro Tomii, Paul Horton and Kenichiro Imai.
Molecular & Cellular Proteomics, 14(4): 1113-1126, 2015

ScreenCap3 – Screening of Caspase-3 substrates and Cleavage site prediction

ScreenCap3

:: DESCRIPTION

ScreenCap3 is a web-based prediction method, to facilitate the discovery of novel caspase-3 substrates in human proteome.

::DEVELOPER

Computational Biology Research Center[CBRC]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteomics. 2014 Sep;14(17-18):2042-6. doi: 10.1002/pmic.201400002. Epub 2014 Aug 4.
ScreenCap3: Improving prediction of caspase-3 cleavage sites using experimentally verified noncleavage sites.
Fu SC, Imai K, Sawasaki T, Tomii K.

LabCaS – Prediction of the Calpain Substrate Cleavage Sites

LabCaS

:: DESCRIPTION

LabCaS  (Labeling Calpain substrate cleavage Sites) is a new computational approach for accurate prediction of the calpain substrate cleavage sites from amino acid sequences.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Proteins. 2013 Apr;81(4):622-34. doi: 10.1002/prot.24217. Epub 2012 Dec 24.
LabCaS: labeling calpain substrate cleavage sites from amino acid sequence using conditional random fields.
Fan YX1, Zhang Y, Shen HB.

HIVcleave – Predicting HIV Protease Cleavage Sites in Proteins

HIVcleave

:: DESCRIPTION

HIVcleave is a web-server for predicting HIV protease cleavage sites in proteins

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Anal Biochem. 2008 Apr 15;375(2):388-90. doi: 10.1016/j.ab.2008.01.012. Epub 2008 Jan 15.
HIVcleave: a web-server for predicting human immunodeficiency virus protease cleavage sites in proteins.
Shen HB1, Chou KC.

Cascleave 2.0 – Caspase Substrate Cleavage Site Prediction

Cascleave 2.0

:: 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

Structural Bioinformatics Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences,

:: SCREENSHOTS

Cascleave

:: REQUIREMENTS

  • WIndows/Linux/MacOsX
  • java

:: DOWNLOAD

 Cascleave

:: 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

NetChop 3.1b – Neural Network Predictions for Cleavage Sites of Human Proteasome

NetChop 3.1b

:: DESCRIPTION

NetChop produces neural network predictions for cleavage sites of the human proteasome.

NetChop has been trained on human data only, and will therefore presumably have better performance for prediction of the cleavage sites of the human proteasome. However, since the proteasome structure is quite conserved, we believe that the server is able to produce reliable predictions for at least the other mammalian proteasomes.

::DEVELOPER

CBS (Center for Biological Sequence Analysis),  Technical University of Denmark

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NetChop

:: MORE INFORMATION

Citation

The role of the proteasome in generating cytotoxic T cell epitopes: Insights obtained from improved predictions of proteasomal cleavage.
M. Nielsen, C. Lundegaard, O. Lund, and C. Kesmir. Immunogenetics., 57(1-2):33-41, 2005.