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Computational Biology Resource Center

Protein Domain Searches

Various Domain finding and Cell Sorting Signal Servers available via the Internet

  • Simple Modular Architecture Research Tool-SMART S.M.A.R.T.
  • Protein Domain-PRODOM BLAST Search Form ProDom
  • ProfileScan Server ISREC
  • Prosite Scanning ExPASY site PROSITE-ExPASY
  • PRINTS/PROFILE database query PRINT/PROSITE
  • Protein Identification-Stanford IDENTIFY-form IDENTIFY
  • ProtoMap a classification of SwissProt PROTOMAP
  • Protein Topology-Home Page Protein Topology
  • San Diego SuperComputer Seqweb Login Page ProfileSearching
  • MEME Home-Multiple EM Motif Elicitation-Finds motifs MEME
  • BlockMaker Home-Finds MOTIFS links to MAST Search BLOCKMAKER
  • Motif Alignment Search Tool MAST v3.0 Linked from MEME or BlockMaker M.A.S.T.
  • Molecular Information Agent M.I.A
  • Protein Family Search via Hidden Markov Models PFAM PFAM
  • PSORT Search form for predicting protein localization sites in cells PSORT
  • ChloroP Search form for predicting protein localization sites in chloroplasts. ChloroP

    The ChloroP server predicts the presence of chloroplast transit peptides (cTP) in protein sequences and the location of potential cTP cleavage sites.

  • TargetP Search form for predicting (via neural net method) putative protein mitochondrial and plastid localization sites in cells. TargetP.

    TargetP is a method for predicting the subcellular location of proteins by identifying the presence of N-terminal presequences, such as chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP), or secretory pathway signal peptide (SP). Provided on this site are intructions, output format, data sets, predictions of A. thaliana and H. sapiens sets, abstract of paper describing the prediction of localization, and references. Made available on the Web by the Center for Biological Sequence Analysis at the Technical University of Denmark.

  • MITOP Search form for predicting protein localization sites in cells MITOP.

    MitoProt calculates the N-terminal protein region that can support a Mitochondrial Targeting Sequence and the cleavage site. A complete description of the method to make the prediction is available in: M.G. Claros, P. Vincens. Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur. J. Biochem. 241, 779-786 (1996).

  • SignalP Search form for predicting protein localization sites in cells SignalP

    The SignalP World Wide Web server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.

  • PREDOTAR Search form for predicting (via neural net method) putative protein mitochondrial and plastid localization sites in cells. PREDOTAR.

    Predotar recognizes the N-terminal targeting sequences of classically targeted mitochondrial and chloroplast precursor proteins. It cannot recognize organellar proteins from internal sequences, nor can it work with short N-terminal segments. Therefore Predotar will refuse to give a result if the submitted sequence lacks an N-terminal methionine or if the sequence is shorter than 60 amino acids long. Predotar also cannot recognize organellar proteins that are targeted to organelles in ways that do not involve the classical matrix/stromal import pathway. Therefore Predotar will fail to recognize many or all outer membrane proteins, and many inter-membrane space and inner membrane proteins. For example, typical well-known mitochondrial proteins like cytochrome c and the adenine nucleotide translocator are not recognised by Predotar.

  • Bipartite-nuclear localization signals. bp-NLS

Updated by ESH August 13, 2012

 
 
 

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