In Partnership with AOL
  • 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.
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  • 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.
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  • DisEMBL - Computational tool for sequence based prediction of intrinsic protein disorder and unstructured regions within a protein.
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  • 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.
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  • EpiC - Resource for the prediction of antigenicity combined with functional analysis of the target protein.
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  • 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.
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  • InterPro - A database built from Pfam, PRINTS and PROSITE.
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  • Isoelectric Point Estimator - Calculator with graphical user interface written in Qt library.
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  • JAligner - Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
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  • Jpred - Secondary protein structure prediction from amino acid sequence; based on a consensus from several methods including DSC, PHD, NNSSP, PREDATOR, ZPRED, and MULPRED.
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  • 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.
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  • 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.
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  • 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).
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  • 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.
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  • Munich Information Center for Protein Sequences (MIPS) - Bioinformatics research group offering organism specific information (Yeast, Cress) as well as search tools for public databases.
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  • PDBeMotif - Integrated resource, which provides information about ligands, sequence and structure motifs, their relative position and the neighbour environment.
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  • 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.
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  • 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.
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  • The ProCKSI Server - A decision support system for protein structure comparison. It provides tools for visualising, analysing, clustering and comparing results.
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  • 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.
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  • 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).
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  • 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.
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  • Proteomics Tools - Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB).
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  • 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.
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  • Protonet - Provides automatic hierarchical classification of proteins sequences.
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  • protSPHERE - Tool to organize and analyze BLAST protein-data. It's free to use for scientific purpose.
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  • 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.
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  • 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.
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  • Swiss-Model - Automated comparative protein modelling server to make protein modelling accessible to biochemists and molecular biologists worldwide - from GlaxoWellcome Experimental Research, Geneva, Switzerland.
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  • 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.
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  • TopMatch: Protein Structure Comparison - Public web service for the alignment and superposition of protein structures and the instant visualization of structural similarities.
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  • 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.
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  • 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.
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Last update: February 20, 2014 at 7:15:09 UTC - edit