Micro Scale

Scansite 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 P… ProPred-I 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. EpiC EpiC- Resource for the prediction of antigenicity combined with functional analysis of the target protein. PDBeMotif PDBeMotif- Integrated resource, which provides information about ligands, sequence and structure motifs, their relative position and the neighbour environment. Isoelectric Point Estimator Isoelectric Point Estimator- Calculator with graphical user interface written in Qt library. The ProCKSI Server The ProCKSI Server- A decision support system for protein structure comparison. It provides tools for visualising, analysing, clustering and comparing results. TopMatch: Protein Structure Comparison TopMatch: Protein Structure Comparison- Public web service for the alignment and superposition of protein structures and the instant visualization of structural similarities. DisEMBL DisEMBL- Computational tool for sequence based prediction of intrinsic protein disorder and unstructured regions within a protein. MODBASE MODBASE- A database of annotated comparative protein structure models. The database includes fold assignments and alignments as well as information about putative ligand binding s… TRANSFAC-The Transcription Factor Database TRANSFAC-The Transcription Factor Database- A compilation of transcriptional regulatory protein factors and their cognate gene promoter elements along with DNA sequence search and… SSM 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 struct… Phyre- Protein Homology/analogY Recognition Engine 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. ELM - Functional Sites in Proteins ELM - Functional Sites in Proteins- Predicts functional sites (linear motifs) in proteins, such as post-translational modification sites, ligand motifs, and targeting signals. Con… PFP: Automated Function Prediction Server 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 ontologi… ESyPred3D 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… MultiProt 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… ConSurf 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 … UniProt 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 informati… Melanie II 2-D Analysis Software 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. Proteomics Tools Proteomics Tools- Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB). Jpred Jpred- Secondary protein structure prediction from amino acid sequence; based on a consensus from several methods including DSC, PHD, NNSSP, PREDATOR, ZPRED, and MULPRED. Protein Structure Prediction Server (PSIPRED) Protein Structure Prediction Server (PSIPRED)- 3D protein structure prediction from amino acid sequence. Includes MEMSAT for transmembrane topology prediction, GenTHREADER and mGe… 3D-PSSM Fold Recognition 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 beyo… ProtFun ProtFun- Ab initio predictions of protein function from protein sequence. The method works by integrating various predicted post-translational and localizational aspects of the pr… Molecular Biology Tools Online Molecular Biology Tools Online- Includes WebOligoMelt (Annealing temperature of oligonucleotides), Virtual Ribosome (translate nucleotide sequences into peptides), and SeqScanGrap… Protonet Protonet- Provides automatic hierarchical classification of proteins sequences. Munich Information Center for Protein Sequences (MIPS) Munich Information Center for Protein Sequences (MIPS)- Bioinformatics research group offering organism specific information (Yeast, Cress) as well as search tools for public data… InterPro InterPro- A database built from Pfam, PRINTS and PROSITE. Protein Information Resource 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 Int… SWISS-PROT + TrEMBL 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, …