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Protein Analysis


Protein Analysis
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3D-PSSM Fold Recognition Server open in new window
The 3D-PSSM server combines sequence and structural information for predicting the structure and/or function of your protein sequence, and can detect remote homologies beyond PSI-Blast.
(http://www.bmm.icnet.uk/~3dpssm/)

Combinatorial Extension of Polypeptides open in new window
Method for finding 3-D similarities in protein structures from the UCSD Supercomputer Center.
(http://cl.sdsc.edu/ce.html)

Entelechon Backtranslation tool open in new window
Online backtranslation tool for translating a protein sequence into a DNA sequence. The codon usage can be downloaded from a database and adjusted manually for each amino acid, if required. Java applet.
(http://www.entelechon.com/eng/backtranslation.html)

InterPro - The Integrated Resource of Protein Domains and Functional Sites. open in new window
A database built from Pfam, PRINTS and PROSITE.
(http://www.ebi.ac.uk/interpro/)

Munich Information Center for Protein Sequences (MIPS) open in new window
Bioinformatics research group offering organism specific information (Yeast, Cress) as well as search tools for public databases.
(http://mips.gsf.de/)

PredictProtein Server open in new window
Most widely used server for analysing protein sequences, searching protein databases, and predicting protein structure - from Columbia Univ.
(http://cubic.bioc.columbia.edu/predictprotein/)

Proteomics Analysis: Z3 and LabOnWeb's Z3OnWeb open in new window
Proteomic analysis for analyzing 2D-Gel images. Use Compugen's Z3 or Z3OnWeb utitlities for automatic spot detection and registration (=alignment) of protein gel images to match the spots.
(http://www.2dgels.com)

Proteomics Tools open in new window
Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB).
(http://www.expasy.ch/tools/)

Protonet open in new window
Provides automatic hierarchical classification of proteins sequences.
(http://www.protonet.cs.huji.ac.il)

Quaternary Structure Prediction open in new window
An experimental bioinformatics server. Classifies protein sequences as homodimers or non-homodimers. Applications: metabolic reconstruction, protein structure and function assignment, and drug-design.
(http://mericity.com/)

Swiss-Model open in new window
Automated comparative protein modelling server to make protein modelling accessible to biochemists and molecular biologists worldwide - from GlaxoWellcome Experimental Research, Geneva, Switzerland.
(http://www.expasy.ch/swissmod/SWISS-MODEL.html)

Swiss-Pdb Viewer open in new window
User-friendly interface allowing analysis of several proteins at once, including superimposition to deduce structural alignments, and compare active sites. From GlaxoWellcome Experimental Research, Geneva, Switzerland.
(http://www.expasy.ch/spdbv/)

SWISS-PROT + TrEMBL open in new window
The SWISS-PROT database contains high-quality annotation, is non-redundant and cross-referenced to many other databases. SWISS-PROT is accompanied by TrEMBL, a computer-annotated supplement, which contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database, which are not yet integrated into SWISS-PROT.
(http://www.ebi.ac.uk/swissprot/)

The Protein Information Resource open in new window
In collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japanese International Protein Sequence Database (JIPID) maintains the PIR-International Protein Sequence Database --- a comprehensive, annotated, and non-redundant set of protein sequence databases in which entries are classified into family groups and alignments of each group are available.
(http://pir.georgetown.edu)

Virtual Ribosome open in new window
Instantly convert your DNA sequence into peptide in three reading frames.
(http://www.aelfgar.com/sa/vr.html)


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