_x000D_ _x000D_ _x000D_ _x000D_ ANTHEPROT
_x000D_ [Institute of Biology and Chemistry of Proteins] (ANalyse THE PROTeins) This free software application integrates into a single package most of the methods designed for_x000D_protein sequence analysis. Methods include: Sequence information,_x000D_Sequence edition, dot matrix plot,_x000D_FASTA/BLAST, sites/signatures detection, physico-chemical profiles, secondary structure prediction, helical wheel projections, multiple alignments,_x000D_prediction of signal peptide and cleavage sites, 3D display of molecules, amphiphilicity, and_x000D_titration curve._x000D_ _x000D_ _x000D_
_x000D_ [more info][11236]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ BandScan
_x000D_ [Glyko] Protein gel image acquisition, documentation, and analysis._x000D_ _x000D_
_x000D_ [more info][11237]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ BCM Search Launcher: General Protein Sequence/Pattern Searches
_x000D_ [Baylor College of Medicine] A site with multiple tools to search a protein sequence for patterns._x000D_
_x000D_ [more info][12330]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ BLITZ
_x000D_ [EMBL] BLITZ performs comparisons of protein sequences against the SWISS-PROT protein sequence database using the Smith and Waterman best local similarity algorithm._x000D_
_x000D_ [more info][10439]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ Block Maker
_x000D_ [Fred Hutchinson Cancer Research Center] “Block Maker finds conserved blocks in a group of two or more unaligned protein sequences, which are assumed to be related, using two different algorithms. At least_x000D_two protein sequences must be provided to make blocks.”_x000D_
_x000D_ [more info][12159]_x000D_ _x000D_

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_x000D_ _x000D_ _x000D_ _x000D_ The Brutlag Bioinformatics Group
_x000D_ [Stanford University] This group is interested in the_x000D_problems of predicting biological function of genes and proteins from their primary sequence (sometimes known as functional genomics), predicting structure of protein and DNA from its sequence, and understanding how and when genes are expressed. This site links to tools being developed toward these interests._x000D_
_x000D_ [more info][11035]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ CAME: Center of Applied Molecular Engineering
_x000D_ [Institute of Chemistry and Biochemistry, University of Salzburg] CAME offers a variety of internet services such as: a protein structure superimposition server [ProSup], the structural genome annotation for C. elegans [WILMA], and a protein structure analysis tool [PROSAII]._x000D_
_x000D_ [more info][11227]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ Computational Biology Tools
_x000D_ [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._x000D_ _x000D_
_x000D_ [more info][12374]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ Dali
_x000D_ [EBI] Service for comparing protein structures in 3D. Protein structure coordinates are submitted for comparison against entries in the Protein Data Bank._x000D_
_x000D_ [more info][10498]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ DNA vs Protein
_x000D_ [The Sanger Centre] Compares a protein sequence or a protein profile-HMM to genomic DNA. It uses the ‘GeneWise’ class of algorithms to provide a combined homology and gene prediction alignment of the protein to the DNA sequence._x000D_
_x000D_ [more info][10359]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ DOCK
_x000D_ [UCSF] DOCK addresses the problem of “docking” molecules to each other. It explores ways in which two molecules, such as a drug and an enzyme or protein receptor, might fit together._x000D_ _x000D_
_x000D_ [more info][11295]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ eMOTIF
_x000D_ [Stanford Univ.] Ranks the motifs that it finds by both their specificity (expected false postives) and the number of supplied sequences that it covers (true positives). The twenty highest-scoring motifs are returned. This site also contains several other tools for sequence alignment and similarity searching, protein function identification and genome analysis._x000D_
_x000D_ [more info][10447]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ eMOTIF Identify
_x000D_ [Stanford Univ.] A protein identification tool allowing a protein sequence to be entered and submitted for identification._x000D_
_x000D_ [more info][10454]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ Entrez
_x000D_ [National Center for Biotechnology Information] Provides a General search for nucleotide sequences, protein sequences, biomolecule 3D structures, genomes, taxonomy or literature._x000D_
_x000D_ [more info][10360]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ Finding 3-D Similarity in Protein Structures
_x000D_ [San Diego Supercomputing Center] This site provides two methods for comparing 3D protein structures, and structure neighbor databases derived from them. Combinatorial Extension (CE) determines an optimal alignment between aligned fragment pairs (AFPs). AFPs are_x000D_determined from local geometry averaged over 8 C alpha positions. Heuristics are used to prevent a combinatorial_x000D_explosion. Final alignments are by dynamic programming. Compound Likeness (CL) uses a probabalistic approach to comparing a wide variety of properties._x000D_
_x000D_ [more info][12223]_x000D_ _x000D_

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_x000D_ _x000D_ _x000D_ _x000D_ FSSP ftp Site
_x000D_ [EBI] The FSSP database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB)._x000D_ _x000D_
_x000D_ [more info][12240]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ GeneFIND: Gene Family Identification Network Design
_x000D_ [Protein Information Resource] A database search system combining search/alignment tools and the ProClass database. Output includes global and motif scores, alignments to the best-matched members of the Pro-Site protein groups and PIR superfamilies, motif pattern matches, and links to the corresponding ProClass family records._x000D_
_x000D_ [more info][10449]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ GeneQuiz
_x000D_ [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.”_x000D_
_x000D_ [more info][12004]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ GeneScape Portal
_x000D_ [CuraGen] This commercial sites offers a fully integrated genomics suite of_x000D_services, including discovery-oriented software for SeqCalling with sequence and SNP data, GeneCalling with gene expression data, PathCalling with protein -protein interactions and pathways, a pharmacogenomics database of drug profiles, and SNPCalling with our database of 200,000 cSNPs (gene-based single nucleotide polymorphisms)._x000D_
_x000D_ [more info][12370]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ HMMER 2.1.1
_x000D_ [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._x000D_ _x000D_
_x000D_ [more info][10452]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ HMMTOP
_x000D_ [Institute of Enzymology] Predicts transmembrane helices and topology of proteins._x000D_
_x000D_ [more info][10453]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ ISREC Software Homepage
_x000D_ [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._x000D_
_x000D_ [more info][12367]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ JOY Software
_x000D_ [University of Cambridge] JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features._x000D_ _x000D_ _x000D_
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_x000D_ _x000D_ _x000D_ _x000D_ LAMA: Local Alignment of Multiple Alignments
_x000D_ [Fred Hutchinson Cancer Research Center] This program compares multiple protein sequence alignments with each other. The program can search databases of such multiple alignments. The search is for sequence similarities between conserved regions of protein families._x000D_
_x000D_ [more info][10455]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ LifeSeq
_x000D_ [Incyte Gemomics] LifeSeq provides fee access to Incyte’s human gene sequence databases, complete with integrated bioinformatics tools._x000D_
_x000D_ [more info][12201]_x000D_ _x000D_

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_x000D_ _x000D_ _x000D_ _x000D_ Ligand-Protein Contacts & Contacts of Structural Units
_x000D_ [Weizmann Institute] LPC analyzes the interatomic contacts in ligand-protein complexes, and CSU analyzes the interatomic contacts in PDB protein entries._x000D_
_x000D_ [more info][12254]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ LIGPLOT
_x000D_ [Univ. College London] A program for automatically plotting protein-ligand interactions. The interactions shown are those mediated by hydrogen bonds and hydrophobic contacts._x000D_ _x000D_
_x000D_ [more info][11306]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ LOCK
_x000D_ [Stanford University] A server that provides a hierarchical protein structure superposition._x000D_
_x000D_ [more info][12308]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ MassSearch
_x000D_ [CBRG] A tool for searching SwissProt or EMBL by protein mass after digestion._x000D_
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_x000D_ _x000D_ _x000D_ _x000D_ Match-Box
_x000D_ [University of Namur] “The Match-Box software proposes protein sequence alignment tools based on strict statistical criteria. The Match-Box program is particularly suitable for finding and aligning conserved structural motives, in particular in protein core.”_x000D_
_x000D_ [more info][12160]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ MEME
_x000D_ [San Diego Supercomputing Center] Discovers motifs (highly conserved regions) in groups of related DNA or protein sequences using MEME and searches sequence databases using motifs using MAST._x000D_
_x000D_ [more info][11261]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ META Server
_x000D_ [Columbia University Bioinformatics Center] This server submits your protein sequence to other servers through one interface. Analyses are in the areas of protein structure and function._x000D_
_x000D_ [more info][12366]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ MOTIF: Searching Protein and Nucleic Acid Sequence Motifs
_x000D_ [Genome Net] Finds protein motifs in query sequence and gives structural information on the found motifs._x000D_
_x000D_ [more info][11998]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ MultiIdent tool
_x000D_ [ExPASy] Identifies proteins using pI, MW, amino acid composition, sequence tag, and peptide mass fingerprinting data._x000D_
_x000D_ [more info][10459]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ OCA?
_x000D_ [Weizmann Institute] OCA? is a browser/database for retrieving rich content annotation on structure and function for proteins found in the Protein Data Bank._x000D_
_x000D_ [more info][12232]_x000D_ _x000D_

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_x000D_ _x000D_ _x000D_ _x000D_ PClass
_x000D_ [Stanford University] A protein structure classification tool that ranks an input protein using its PDB file in a heirarchical classification of 600 representative structures from_x000D_the PDB._x000D_
_x000D_ [more info][12246]_x000D_

_x000D_ _x000D_ _x000D_ _x000D_ PDB at a Glance
_x000D_ [National Institutes of Health] PDB At A Glance consists of a set of pre-defined biochemically meaningful search contexts (accessed by keyword) that represent the entire territory of the database._x000D_
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