- 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.
- BioInfoBank Meta Server - 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 - 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 - 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.
- EpiC - Resource for the prediction of antigenicity combined with functional analysis of the target protein.
- 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 - Calculator with graphical user interface written in Qt library.
- 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).
- 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.
- PDBeMotif - Integrated resource, which provides information about ligands, sequence and structure motifs, their relative position and the neighbour environment.
- 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.
- ProPred-I - An online service for predicting MHC binding regions in antigens. It also offers the proteasomal and immunoproteasomal filters to improve the applicability of results.
- Protein Information Resource - PIR is a non-redundant annotated protein sequence database, and analytical tools, maintained by collaboration of MIPS, in Munich and the Japanese International Protein Sequence Database (JIPID).
- 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.
- 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.
- protSPHERE - Tool to organize and analyze BLAST protein-data. It's free to use for scientific purpose.
- 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.
- Scansite - Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.
- 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-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 ProCKSI Server: Protein Comparison, Knowledge, Similarity and Information - ProCKSI is a decision support system for protein structure comparison. It provides tools for visualising, analysing, clustering and comparing results.
- TopMatch: Protein Structure Comparison - Public web service for the alignment and superposition of protein structures and the instant visualization of structural similarities.
- TRANSFAC-The Transcription Factor Database - 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.
- UniProt - 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.
- Wurst - A protein threading server using sequence profiles combined with a protein sequence to structure compatibility function based on Bayesian statistics.
Last update: Apr 28, 2012 18:35:07. Phy.org is a private web site, powered by the Open Directory Project.
