| Directory > Science > Biology > Bioinformatics > Online Services > Protein Analysis Jpred
Secondary protein structure prediction from amino acid sequence; based on a consensus from several
methods including DSC, PHD, NNSSP, PREDATOR, ZPRED, and MULPRED.
http://www.compbio.dundee.ac.uk/~www-jpred/
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Protein Structure Prediction Server (PSIPRED)
3D protein structure prediction from amino acid sequence. Includes MEMSAT for transmembrane
topology prediction, GenTHREADER and mGenTHREADER for fold recognition.
http://bioinf.cs.ucl.ac.uk/psipred/
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Betapred
Prediction of beta turns and their types using statistical algorithms. 5 different methods
including Chou-Fasman, Thornton's PRs, Gorbturn, and a consensus of all methods.
http://imtech.res.in/raghava/betatpred
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PDB Ligand Environment
Ligand search engine to EBI Macromolecule Structure Database. Provides PDB ID codes with further
visualization and statistics charts.
http://www.ebi.ac.uk/msd-srv/msdsite
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JAligner
Java Applet for an implementation of Smith-Waterman algorithm for pairwise biological sequence
alignment using dynamic programming (extended to support affine gap penalties) download or launch
from site.
http://foobox.com/~ahmed/jaligner
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3D-PSSM Fold Recognition
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.sbg.bio.ic.ac.uk/~3dpssm/
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3D-JIGSAW
Automated comparative (homology) protein modelling, including an interactive mode which highlights
known domains and allows users to select and align templates.
http://www.bmm.icnet.uk/~3djigsaw/
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ProtFun
Ab initio predictions of protein function from protein sequence. The method works by integrating
various predicted post-translational and localizational aspects of the proteins submitted.
http://www.cbs.dtu.dk/services/ProtFun/
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EMBL Bioinformatic Harvester
Collection of human (swall) proteins, crossreferences to major prediction servers. Supported
predictions from: smart, string, blast, swall, mapview, sosui, ipsort and ncbi conserved domains.
http://harvester.embl.de
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Molecular Biology Tools Online
Includes WebOligoMelt (Annealing temperature of oligonucleotides), Virtual Ribosome (translate
nucleotide sequences into peptides), and SeqScanGraph (graph melting temperature along nucleotide
chain).
http://mbt.biobitfield.com/
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PredictProtein Server
Most widely used server for analysing protein sequences, searching protein databases, and
predicting protein structure - from Columbia Univ.
http://cubic.bioc.columbia.edu/predictprotein/
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Protonet
Provides automatic hierarchical classification of proteins sequences.
http://www.protonet.cs.huji.ac.il
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Entelechon Backtranslation tool
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
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Munich Information Center for Protein Sequences (MIPS)
Bioinformatics research group offering organism specific information (Yeast, Cress) as well as
search tools for public databases.
http://mips.gsf.de/
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Combinatorial Extension of Polypeptides
Method for finding 3-D similarities in protein structures from the UCSD Supercomputer Center.
http://cl.sdsc.edu/ce.html
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Proteomics Tools
Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB).
http://www.expasy.ch/tools/
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InterPro - The Integrated Resource of Protein Domains and Functional Sites.
A database built from Pfam, PRINTS and PROSITE.
http://www.ebi.ac.uk/interpro/
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The Protein Information Resource
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
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Swiss-Model
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
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Proteomics Analysis: Z3 and LabOnWeb's Z3OnWeb
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
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Swiss-Pdb Viewer
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/
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Quaternary Structure Prediction
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/
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SWISS-PROT + TrEMBL
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/
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