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Protien databases (9)

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3D-JIGSAW - http://www.bmm.icnet.uk/~3djigsaw/
Automated comparative (homology) protein modelling, including an interactive mode which highlights known domains and allows users to select and align templates.

3D-PSSM Fold Recognition - http://www.sbg.bio.ic.ac.uk/~3dpssm/
Combines sequence and structural information for predicting the structure and/or function of your protein sequence, and can detect remote homologies beyond PSI-Blast.

BioInfoBank Meta Server - http://meta.bioinfo.pl/submit_wizard.pl
Offers a gateway to well-benchmarked protein structure and function prediction methods. Structural models collected from the predictions servers are assessed using the powerful 3D-jury consensus approach.

COLORADO3D - http://asia.genesilico.pl/colorado3d/
Service to aid visualisation of potential errors in protein structures. Free for academic users.

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

Dali server - http://www.ebi.ac.uk/dali/
The Dali server is a network service for comparing protein structures in 3D.

ELM - Functional Sites in Proteins - http://elm.eu.org
Predicts functional sites (linear motifs) in proteins, such as post-translational modification sites, ligand motifs, and targeting signals. Context-based rules and logical filters are applied to improve predictions.

Entelechon Backtranslation tool - http://www.entelechon.com/bioinformatics/backtranslation.php
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.

ESyPred3D - http://www.fundp.ac.be/urbm/bioinfo/esypred/
ESyPred3D is an automated homology modeling program getting benefit of the increased alignment performances of a new alignment strategy using neural networks. The final three dimensional structure is built using the modeling package MODELLER.

http://consurf.tau.ac.il/overview.html - http://consurf.tau.ac.il/overview.html
Identifies functionally important regions on the surface of a protein or domain, of known three-dimensional (3D) structure using the phylogenetic relations between close sequence homologues.

http://dis.embl.de - http://dis.embl.de
Computational tool for sequence based prediction of intrinsic protein disorder and unstructured regions within a protein.

http://salilab.org/modbase - http://salilab.org/modbase
A database of annotated comparative protein structure models. The database includes fold assignments and alignments as well as information about putative ligand binding sites, SNP annotation, and protein-protein interactions.

http://www.cbs.dtu.dk/services/ProtFun/ - http://www.cbs.dtu.dk/services/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.compbio.dundee.ac.uk/~www-jpred/ - http://www.compbio.dundee.ac.uk/~www-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.ebi.ac.uk/msd-srv/ssm - http://www.ebi.ac.uk/msd-srv/ssm
Provides interactive service for matching protein structures in 3D and looking for structural homologues in PDB and SCOP databases, as well as in user-uploaded sets of structures.

http://www.pir.uniprot.org/ - http://www.pir.uniprot.org/
UniProt (Universal Protein Resource) is a catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.

http://www.zbh.uni-hamburg.de/wurst - http://www.zbh.uni-hamburg.de/wurst
A protein threading server using sequence profiles combined with a protein sequence to structure compatibility function based on Bayesian statistics.

iMolTalk - http://i.moltalk.org
Provides protein structure information such as structural alignment, residue contact, protein-protein interfaces, contact maps and general information extraction.

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

Isoelectric Point Estimator - http://www.nihilnovus.com/Palabra.html
Calculated using the FASTA amino acid sequence and pKa values for. Allows consideration of post-translational modifications.

JAligner - http://jaligner.sourceforge.net/
Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.

Melanie II 2-D Analysis Software - http://au.expasy.org/melanie/
Powerful, state-of-the-art, 2-D analysis software package with user-friendly interface from the Swiss Institute of Bioinformatics.

Molecular Biology Tools Online - http://mbt.biobitfield.com/
Includes WebOligoMelt (Annealing temperature of oligonucleotides), Virtual Ribosome (translate nucleotide sequences into peptides), and SeqScanGraph (graph melting temperature along nucleotide chain).

Molecules To Go - http://molbio.info.nih.gov/cgi-bin/pdb/
Search engine for visualizing 3-D biomolecular models. From the Center for Molecular Modeling, NIH, Maryland.

MSDmotif - http://www.ebi.ac.uk/msd-srv/msdmotif/
Service for protein sequence motifs detection. Search based on the small 3D motifs defined by J.Milner-White.

MultiProt - http://bioinfo3d.cs.tau.ac.il/MultiProt/
Service for detecting the multiple structural alignments of proteins. Uses the common geometrical cores between the input molecules. Does not require that all the input molecules participate in the alignment.

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

NUMODs Motifs Finder - http://bioinfo.weizmann.ac.il/~naaman1/NUMODs/
Finds Nuclease-Associated Modular DNA-binding Domains (NUMODs) in protein sequences

PDB Ligand Environment - http://www.ebi.ac.uk/msd-srv/msdsite
Ligand search engine to EBI Macromolecule Structure Database. Provides PDB ID codes with further visualization and statistics charts.

PFP: Automated Function Prediction Server - http://dragon.bio.purdue.edu/pfp/
Accepts a single query protein sequence and returns the most probable Gene Ontology functional annotations in each of the three ontologies.

Phyre- Protein Homology/analogY Recognition Engine - http://www.sbg.bio.ic.ac.uk/phyre/
Phyre is a free for academics service for predicting the 3-dimensional structure of a protein amino acid sequence.

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

Protein Structure Prediction Server (PSIPRED) - http://bioinf.cs.ucl.ac.uk/psipred/
3D protein structure prediction from amino acid sequence. Includes MEMSAT for transmembrane topology prediction, GenTHREADER and mGenTHREADER for fold recognition.

Proteomics Tools - http://www.expasy.org/tools/
Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB).

Protonet - http://www.protonet.cs.huji.ac.il
Provides automatic hierarchical classification of proteins sequences.

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

Swiss-Model - http://swissmodel.expasy.org//SWISS-MODEL.html
Automated comparative protein modelling server to make protein modelling accessible to biochemists and molecular biologists worldwide - from GlaxoWellcome Experimental Research, Geneva, Switzerland.

Swiss-Pdb Viewer - http://au.expasy.org/spdbv/
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.

SWISS-PROT + TrEMBL - http://www.ebi.ac.uk/swissprot/
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.

The ProCKSI Server: Protein Comparison, Knowledge, Similarity and Information - http://www.procksi.net
ProCKSI is a decision support system for protein structure comparison. It provides tools for visualising, analysing, clustering and comparing results.

The Protein Information Resource - http://pir.georgetown.edu
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. An annotated, and non-redundant set of protein sequence databases in which entries are classified into family groups and alignments of each group are available.

TopMatch: Protein Structure Comparison - http://topmatch.services.came.sbg.ac.at
Public web service for the alignment and superposition of protein structures and the instant visualization of structural similarities.

TRANSFAC-The Transcription Factor Database - http://www.gene-regulation.com/pub/databases.html#transfac
A compilation of transcriptional regulatory protein factors and their cognate gene promoter elements along with DNA sequence search and analysis programs - from GBF, Braunschweig, Germany.

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