Proteins

Swiss Institute for Experimental Cancer Reseach (ISREC). Searches a single protein sequence against currently available protein profile databases

EBI. Colorizes the residues of an entered protein sequence according to hydrophobicity or user defined characteristics

Swiss Institute for Experimental Cancer Research (ISREC). Collection of protein pattern search tools for the identification of functional domains within a user entered protein sequence or proteins containing a defined domain

IBM Research. Download the bio-dictionaries of seqlets (amino acid patterns) for completed genomes.

Fred Hutchinson Cancer Research Center (FHCRC). Provides access to search the BLOCKS and PRINTS databases of protein domains. BLOCKMAKER allows the alignment of sequences and construction of conserved blocks

CBS. Predicts the presence of transmembrane spanning helices within a submitted protein sequence

CBS. Neural network algorithms predict the presence and localization of signal peptides and the associated cleavage site

IBM. Tools for sequence pattern discovery from IBM Bioinformatics Group.

University of Manchester. Database of groups of conserved motifs used to characterise protein families (protein fingerprints)

EBI. Database of protein domains compiled from the integration of Pfam, PROSITE and PRINTS

ExPASy. Scans a sequence for the occurence of PROSITE patterns, or allows a user defined pattern to be used to scan the SWISS-PROT and TrEMBL protein databases

INRA, Toulouse. Database of protein domains constructed by clustering sequences aligned by PSI-Blast

SDSC. Searches protein and nucleotide database for the specific motifs that are defined by the user; MAST accepts MEME output as its input.

University of Bergen. Identifies protein patterns in unaligned protein sequences

NCBI. Database of conserved protein motifs and domains from Smart, Pfam and local NCBI resources with a Reverse Position Specific (RPS)-BLAST search interface.

UW BIR. Suite of command line driven resources for protein structure analysis.

EMBL. Protein structure motif classification based on an all-against-all structural alignment comparison on all entries within the Protein Database (PDB)

Elinor Adman, UW. Molecular visualization consultant for 3D protein structures.

European Molecular Biology Network. Predicts coiled-coil domains in an entered sequence based on a comparison to the coiled-coil domain database. The similarity score for the entered sequence is compared to globular and coiled-coil containing proteins to generate the prediction

NCI. Uses substitution matrices, secondary structure prediction, and contact capacity potentials to thread a sequence through sets of known protein structures

Institute for Molecular Biotechnology, Jena, Germany

PBIL. Queries a selectable set of secondary structure prediction resources and then outputs the consensus prediction.

MRC Centre for Protein Engineering, Cambridge. Database of protein structural elements. Classification of proteins into families and superfamilies based on common structural features

RCSB. Primary database archive of experimentally determined three-dimensional structures of biological macromolecules

ICRF. Protein fold recognition using sequence profiles coupled with secondary structure and solvation potential information

EBI. Secondary Structure prediction of either multiple aligned protein sequences or single protein submissions.

University of Cambridge. Database of experimentally determined organic and metallo-organic crystal structures with graphical search, retrieval, data manipulation and visualisation software

Glaxo Wellcome. 3D modelling tool that simultaneously presents multiple proteins to examine plausible interactions.

EMBL. Email service for the prediction of protein structure from submitted amino acid sequences. Includes secondary structure, solvent accessibility, transmembrane helices, multiple alignments, threading, fold recognition, remote homology detection, and evaluation of secondary structure prediction accuracy

UCL. Hierarchical classification of protein domain structures by class, architecture, topology and homologous superfamily.

NCBI. The NCBI database of NMR and x-ray crystalograph based 3D protein structures.

UCL. PDBsum gives a summary and structural analysis of the 3D PDB protein structure files.

Geneva Biomedical Research Institute, Glaxo Wellcome. A freely available automated comparative protein modelling server

This database contains the known enzyme structures that have been deposited in the Protein Data Bank (PDB).

ExPASy. Annotated database which assembles data on proteins identified on 2-D PAGE maps. Includes mapping procedures, physiological and pathological data, bibliographical references, 2-D PAGE images showing protein location, and cross-references to other federated 2-DE databases (ECO2DBASE, HSC-2DPAGE, YEPD) and SWISS-PROT

ExPASy. Molecular proteomics analysis tools for nucleotide translation, protein identification, primary sequence analysis, secondary and tertiary structure prediction, transmembrane region detection and sequence alignment

UW BIR. Suite of command line driven resources for protein structure analysis.

ExPASy. Multiple protein identification tools including peptide mass fingerprinting, amino acid composition, and peptide sequence tagging

MIPS. Protein extraction, description and analysis tool. Provides computational analysis of complete, experimental, and unfinished genomic sequences

Rockefeller and New York Universities

EMBL. Email service for the prediction of protein structure from submitted amino acid sequences. Includes secondary structure, solvent accessibility, transmembrane helices, multiple alignments, threading, fold recognition, remote homology detection, and evaluation of secondary structure prediction accuracy

ExPASy. A tool for the computation of the theoretical isolectric point and molecular weight for a list of SWISS-PROT entries or for a user entered sequence

EBI. Database of protein domains compiled from the integration of Pfam, PROSITE and PRINTS

ExPASy. Peptide Mass cleaves one or more protein sequences from the SWISS-PROT and/or TrEMBL databases or a user-entered protein sequence with a chosen enzyme, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the proteins of interest

ExPASy. ProtScale allows you to compute and represent the profile produced by any amino acid scale on a selected protein. Fifty predefined scales based on different chemical and physical properties of amino acids are provided from the literature, including one for antigenicity prediction ("Hphob./Welling & al" option)

Yale. Database of macromolecular motions visualized using movie renderings of protein subdomains with occurrence frequencies in microbial genomes.