Protein Analysis from Sequence
|Search || Browse|
Bioinformatics & Genomics
Companies, Publishers, & Books
Compendiums & Lists of Resource Links
Compounds & Enzymes
Educational & Information Resources
Genomics & DNA Sequence Analysis
Hidden Markov Models
Major Sites & Organizations
Metabolic Pathway Databases & Related
Molecular Modeling & Visualization
Motif, Domain, Profile, Pattern, & Repeat Searches
Multiple Alignment & Phylogeny
Protein & Nucleic Acid Search Servers
Protein Analysis from Sequence
Sites with Multiple or Integrated Tools
Software Catalogues, Lists, & Downloads
|Opens resource in a 2nd browser window.|
AAA: Amino Acid Analysis Server
[EMBL-Heidelberg] Protein and amino acid identification in SwissProt and PIR using amino acid composition.
[ExPASY] A tool used to identify a protein from its amino acid composition.
[ExPASY] Compares the amino acid composition of a SWISS-PROT entry with all other SWISS-PROT entries to find the proteins whose amino acid compositions are closest to that of the selected entry.
[Martin, UCL] Tests an antibody sequence against the Kabat sequence database.
AMAS: Analyze Multiple Alignments of Protein Sequences
[EBI] Allows the identification of functional residues by comparison of sub-groups of sequences arranged on a tree.
[Institute of Biology and Chemistry of Proteins] (ANalyse THE PROTeins) This free software application integrates into a single package most of the methods designed forprotein sequence analysis. Methods include: Sequence information,Sequence edition, dot matrix plot,FASTA/BLAST, sites/signatures detection, physico-chemical profiles, secondary structure prediction, helical wheel projections, multiple alignments,prediction of signal peptide and cleavage sites, 3D display of molecules, amphiphilicity, andtitration curve.
Atlas of Protein Side-Chain Interactions
[Univ. College London] Atlas depicts how amino acid side-chains pack against one another. Presents all possible 400 pairwise interactions between the 20 side chains.
BCM Search Launcher: Pairwise Sequence Alignment
[Baylor College of Medicine] A site with multiple tools to align pairs of input sequences.
Biomolecular Structure and Modelling Group
[University College London] The BSM group brings together people who derive protein and carbohydrate structure information using crystallography or NMR, those who manage databases of this information, and analysts and modellers who examine these structures to try to derive principles of protein folding. Services are offered in the areas of protein sequence and stucture analysis. The group is the home of the CATH protein structure classification database.
[CBS] Predicts whether or not an amino acid sequence contains an N-terminal chloroplast transit peptide, cTP, and the probable site for cleavage of the transit peptide.
Clusters of Orthologous Groups
[NCBI] (COGs) A phylogenetic database (with a comparison search server incorporated) of orthologous proteins in many complete genomes.
[ExPASy] CombSearch is an attempt to provide a unified interface to query several protein identification tools accessible on the web. Includes PeptIdent, TagIdent, and MultiIdent from ExPASy, MS-Fit from ProteinProspector, Mowse from Imperial SERC Daresbury Laboratory, ProFound from PROWL, and Peptide Search from EMBL Protein & Peptide Group.
Computational Biology Tools
[Cornell Theory Center] This site provides several downloadable programs for analyzing protein sequences for predictions in the areas of folding, structure determination, energetics, and dynamics. It also is home to the LOOPP program (Learning, Observing and Outputting Protein Patterns), a program for potential optimization and alignments. LOOPP aligns sequence to sequence, sequence to structure, and structure to structure.
Computational Services at EMBL
[EMBL] Ties together sequence search and retrieval, alignment, data submission, comparison and prediction into one site. Also available are tools for structure verification and related software.
Compute pI/Mw tool
[ExPASY] A tool which allows the computation of the theoretical isoelectric point and molecular weight of a protein sequence.
CUBIC: Columbia University Bioinformatics Center
CUBIC contains a wealth of services, databases, articles and their data sets, and annotated bioinformatics links. It is the current home of PredictProtein and other services for protein analysis.
[Univ. of Tours] A program to generate peptide fragments by the enzymatic or chemical cleavage of a protein sequence entered by the user, and computes the theoretical masses to the generated peptides.
DARWIN Molecular Sequence Analysis
[CBRG] An interactive tool for peptide and nucleotide sequence analysis with a library of functions for sequence management and analysis, statistics, numerics, and graphics.
[National Cancer Institute] This software is for information analysis of protein and nucleic-acid sequences.
[CBS] Produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.
[Carlsberg Laboratory] Software for handling and analysis of nucleotide and protein sequences. This downloadable package also has special functions for EST and SAGE handling and analysis.
[Karolinska Institutet, Center for Genomics Research] Compares two related sequences and finds matches, creating a dotplot. Accompanying the dotplot are excellent statistics and user-friendly adjustment of thresholds. Download the program to run on Unix. A server version is available at http://www.hgmp.mrc.ac.uk/Registered/Option/dotter.html for registered users.
Electron Density Server
[Uppsala University] Electron density calculations are based on the Protein Data Bank entries and deposited structure factors. The electron density maps derived from the structure factors and coordinates aregenerated using the programs CNS or CCP4.
[Stanford Univ.] A protein identification tool allowing a protein sequence to be entered and submitted for identification.
[ExPASy] Predicts potential post-translational protein modifications (PTM) and finds potential single amino acid substitutions in peptides.
[European Bioinformatics Institute] “GeneQuiz is an integrated system for large-scale biological sequence analysis, that goes from a protein sequence to a biochemical function, using a variety of search and analysis methods and up-to-date protein and DNA databases.”
[Washington Univ., St. Louis] A protein sequence analysis tool that profiles hidden Markov models (profile HMMs) that can be used to do sensitive database searching using statistical descriptions of a sequence family’s consensus.
[Institute of Enzymology] Predicts transmembrane helices and topology of proteins.
Institute of Biology and Chemistry of Proteins
The aim of the research at the IBCP is to study proteins in their biological context. These studies are concerned with both intracellular and extracellular proteins of procaryotic and eucaryotic organisms dealing mainly with biosynthesis, maturation, and interactions. The IBCP is the home of Network Protein Sequence Analysis and software for protein sequence analysis.
[European Bioinformatics Institute] InterPro is an integrated documentation resource for protein families, domains andsites, developed initially as a means of rationalising the complementary efforts of thePROSITE, PRINTS, Pfam and ProDom database projects. Each combined InterProentry includes functional descriptions and literature references, and links are madeback to the relevant member database(s), allowing users to see at a glance whethera particular family or domain has associated patterns, profiles, fingerprints, etc.
ISREC Bioinformatics Group
[Swiss Institute for Experimental Cancer Research] “Our main field of research is the detection and assessment of similarity between distantly related protein and DNA sequences by means of ‘Generalized Profiles.’ We have developed and made available a program package that allows searches with a single sequence against a database of generalized profiles and vice versa.”
ISREC Software Homepage
[Swiss Institute for Experimental Cancer] This site provides a number of servers in the areas of sequence analysis, domain/motif searches, gene prediction, and prediction of protein features.
[Univ. of York] MacStripe will explore potential alpha-helical coiled coils in the sequence of a protein.