| 3D-JIGSAW: 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: Combines sequence and structural information for predicting the structure and/or function of your protein sequence, and can detect remote homologies beyond PSI-Blast. |
| 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. |
| BioInfoBank Meta Server: The BioInfoBank Meta Server offers a gateway to well-benchmarked protein structure and function prediction methods. Structural models collected from the predictions servers are assesset using the powerfull 3D-jury consensus approach. |
| COLORADO3D: Service to aid visualisation of potential errors in protein structures. Free for academic users. |
| Combinatorial Extension of Polypeptides: Method for finding 3-D similarities in protein structures from the UCSD Supercomputer Center. |
| 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. |
| Dali server: The Dali server is a network service for comparing protein structures in 3D. |
| DisEMBL: Computational tool for sequence based prediction of intrinsic protein disorder and unstructured regions within a protein. |
| 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. |
| 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. |
| 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. |
| 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. |
| iMolTalk: 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.: A database built from Pfam, PRINTS and PROSITE. |
| Isoelectric Point Estimator: Calculated using the FASTA amino acid sequence and pKa values for. Allows consideration of post-translational modifications. |
| JAligner: Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment. |
| Jpred: Secondary protein structure prediction from amino acid sequence; based on a consensus from several methods including DSC, PHD, NNSSP, PREDATOR, ZPRED, and MULPRED. |
| 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. |
| 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. |
| 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). |
| Molecules To Go: Search engine for visualizing 3-D biomolecular models. From the Center for Molecular Modeling, NIH, Maryland. |
| MSDmotif: Service for protein sequence motifs detection. Search based on the small 3D motifs defined by J.Milner-White. |
| 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): Bioinformatics research group offering organism specific information (Yeast, Cress) as well as search tools for public databases. |
| NUMODs Motifs Finder: Finds Nuclease-Associated Modular DNA-binding Domains (NUMODs) in protein sequences |
| PDB Ligand Environment: Ligand search engine to EBI Macromolecule Structure Database. Provides PDB ID codes with further visualization and statistics charts. |
| 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. |
| 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. |
| PredictProtein Server: Most widely used server for analysing protein sequences, searching protein databases, and predicting protein structure - from Columbia Univ. |
| 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. |
| 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. |
| Proteomics Tools: Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB). |
| 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. |
| Protonet: Provides automatic hierarchical classification of proteins sequences. |
| 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. |
| SDSC molecular biology software: Server based software for molecule animation, x-ray crystal analysis and protein structure. Free downloads of software also available. |
| 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. |
| Swiss-Model: 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: 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: 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 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. |
| 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. |
| 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. |
| Wurst: A protein threading server using sequence profiles combined with a protein sequence to structure compatibility function based on Bayesian statistics. |
Classical
