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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.
- 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.
- 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.
- Resource for the prediction of antigenicity combined with functional analysis of the target protein.
- 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.
- A database built from Pfam, PRINTS and PROSITE.
Isoelectric Point Estimator
- Calculator with graphical user interface written in Qt library.
- Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
- 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.
- 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).
- 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.
- 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.
The ProCKSI Server
- A decision support system for protein structure comparison. It provides tools for visualising, analysing, clustering and comparing results.
- 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.
- Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB).
- 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.
- Provides automatic hierarchical classification of proteins sequences.
- Tool to organize and analyze BLAST protein-data. It's free to use for scientific purpose.
- 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.
- 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.
- 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.
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 (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.
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