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/bioinformatics/backtranslation.php

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

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

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

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

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://salilab.org/modbase

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

Protein Structure Prediction Using Web Resources
- SPORes is a website for protein structure prediction using the web browser as an interface to software that runs of web servers or other resources available over the world wide web.
- http://cgat.ukm.my/spores/

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

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.ebi.ac.uk/msd-srv/ssm

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

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

ELM - Functional Sites in Proteins
- 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.
- http://elm.eu.org

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

ESyPred3D
- 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://www.fundp.ac.be/urbm/bioinfo/esypred/

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.
- http://bioinfo3d.cs.tau.ac.il/MultiProt/

ConSurf
- 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://consurf.tau.ac.il/overview.html

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

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

UniProt
- UniProt (Universal Protein Resource) is a comprehensive 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.pir.uniprot.org/

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

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

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

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://au.expasy.org/spdbv/

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://swissmodel.expasy.org//SWISS-MODEL.html

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

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/

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/

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

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

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/

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/

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/

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

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/

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/

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

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/

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

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
- http://pir.georgetown.edu

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/

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) pr
- http://www.ebi.ac.uk/swissprot/