Protein Analysis from Sequence

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2nd Window Opens resource in a 2nd browser window.

2nd Window AAA: Amino Acid Analysis Server
[EMBL-Heidelberg] Protein and amino acid identification in SwissProt and PIR using amino acid composition.
[more info][10430]

2nd Window AACompIdent tool
[ExPASY] A tool used to identify a protein from its amino acid composition.
[more info][10431]

2nd Window AACompSim tool
[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.
[more info][10432]

2nd Window AbCheck
[Martin, UCL] Tests an antibody sequence against the Kabat sequence database.
[more info][10377]

2nd Window 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.
[more info][11235]

2nd Window ANTHEPROT
[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.
[more info][11236]

2nd Window 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.
[more info][10435]

2nd Window BCM Search Launcher: Pairwise Sequence Alignment
[Baylor College of Medicine] A site with multiple tools to align pairs of input sequences.
[more info][12332]

2nd Window 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.
[more info][12373]

2nd Window ChloroP v1.1
[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.
[more info][10443]

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2nd Window Clusters of Orthologous Groups
[NCBI] (COGs) A phylogenetic database (with a comparison search server incorporated) of orthologous proteins in many complete genomes.
[more info][12200]

2nd Window CombSearch
[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.
[more info][11947]

2nd Window 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.
[more info][12374]

2nd Window 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.
[more info][12520]

2nd Window Compute pI/Mw tool
[ExPASY] A tool which allows the computation of the theoretical isoelectric point and molecular weight of a protein sequence.
[more info][10444]

2nd Window 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.
[more info][11956]

2nd Window CUTTER
[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.
[more info][10445]

2nd Window 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.
[more info][12065]

2nd Window Delila
[National Cancer Institute] This software is for information analysis of protein and nucleic-acid sequences.
[more info][11246]

2nd Window DictyOGlyc 1.1
[CBS] Produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.
[more info][10446]

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2nd Window DNATools
[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.
[more info][11249]

2nd Window Dotter
[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 for registered users.
[more info][13604]

2nd Window 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.
[more info][13767]

2nd Window eMOTIF Identify
[Stanford Univ.] A protein identification tool allowing a protein sequence to be entered and submitted for identification.
[more info][10454]

2nd Window FindMod tool
[ExPASy] Predicts potential post-translational protein modifications (PTM) and finds potential single amino acid substitutions in peptides.
[more info][10448]

2nd Window GeneQuiz
[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.”
[more info][12004]

2nd Window HMMER 2.1.1
[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.
[more info][10452]

2nd Window HMMTOP
[Institute of Enzymology] Predicts transmembrane helices and topology of proteins.
[more info][10453]

2nd Window 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.
[more info][12150]

2nd Window InterPro
[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.
[more info][13762]

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2nd Window 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.”
[more info][12510]

2nd Window 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.
[more info][12367]

2nd Window MacStripe
[Univ. of York] MacStripe will explore potential alpha-helical coiled coils in the sequence of a protein.
[more info][11259]

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