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Cross-References: DNA/RNA Bioinformatics Genome Bioinformatics ==================================================================================== Protein Data Banks: BLAST Protein Data Bank (PDB) PIR SwissProt Human Protein Reference Database Biotools Annotated Protein Sequences: PIR SwissProt EMBOSS Enzyme Information: BRENDA Motifs, domains, patterns and patterns of your protein with other proteins in the database. Prosite (Database which can be searched by keywords, accession number and sequence information) Scan Prosite Tool (searches for patterns, profiles and motifs in both Tr-EMBL or Swiss-Prot) Phobius (transmembrane topology and signal peptide predictor) Pratt (use to discover patterns (small motifs or larger regions of sequence containing several motifs that are conserved in protein sequences) Blocks (searches for conserved part of a multiple sequence alignment that contains no residue insertions or deletions)Motif Scan (finds all the known motifs in a given sequence) Links to Motif Pattern DBs PRINTS (a compendium of protein fingerprints (group of conserved motifs used to characterize a protein family)) NCBICDD NCBICDD online server (Search by keyword or sequence for conserved protein domains among two different proteins) NCBI CDART (similar to NCBICDD above in that can take a FASTA amino acid sequence and find conserved domains in that sequence. Will also indicate which other proteins contain domains in your query sequence) Human Proteome Organization Protein Family Databases MOTIF SEARCH TMHMM (Prediction of transmembrane helices in proteins) Function/interactions/sequences: BLAST Protein Analysis Tools MIPS KEGG BioMolQuest Structure Generally: Protein Data Bank (PDB) (repository for structural information) PDBSUM (generate Wir and Lig plots) Expasy SwissPDViewer Protein Quarternary Structure (PQS) OCA NCBI Structure (data base of structures as well as tools for their visualization) SCOP (structural classification of proteins) BSM Group EBI UMass Duke Protein Purification Scheme Human Proteome Initiative European Biofinformatics Institute Human Proteome Org Georgetown Protein Structure Initiative (NIH) Structure Viewing: Molecular Vision Freeware RasTop DSViewer RasMol (download freeware) GCUA (Graphical Codon Usage Analyser) Structure Prediction: PSIPPED (submit protein sequence and predict its structure) JPred Structure Predict Predict Protein SOSUI (classification and secondary structure prediction of membrane proteins) Physical & Chemical Parameters from a Given Amino Acid Sequence Expasy (calculation of pI and MW from sequence) Expasy (identification of proteins based on pI and MW) ExPASy - ProtParam tool (generate an aa composition, pI, and MW) AACompldent Expasy tool (use the aa composition, pI and Mr estitmates) to identify possible proteins) ExPasy Randseq tool (generate a protein sequence from aa composition) Kendrick Labs (proteomics services with specialty in 2D) Nonlinear (software for 2D gel analysis) Microarray technology: Ebi Nonlinear 2D gel analysis: Proteome Works Melanie Danish Center 3D viewing: Rastop Protein Chemistry/Mass Spectometry: PROWL South Carolina SEQUEST Matrixscience MOWSE Expasy-peptident Predicted proteomes of completed genomes: EBI Protein Partial Sequence Searching: BlockSearcher Sequence Alignment/Evolutional Trees/phylogenetics: ClustalX download Clustalw LALign Clustalx Genedoc EBMnet Clustal W PIR Genomenet DOTLET (dot matrix) Dotter (dot matrix) Weblogo (This will create beautiful logos out of your multiple sequence alignment) Phylogeny Programs (this is a super site for links to various phylogeny programs) NJplot tree drawing (also comes with Clustal X download and is used to generate a phylogenic tree from the Clustal X multiple sequence alignment) Ghostview (use to convert poscriptfiles into other formats (e.g., jpg files, etc) Tree View (displays various phylogenic trees. Use after you have compared sequences using one of the alignment programs above like ClustalX) Phylodraw (creates phylogenetic trees from various multi alignment programs (e.g., Clustal W) Transcription Factors Transcription Factors (for eukaryotic transcription factors, their DNA binding sites and DNA-binding profiles. It is a commercial site, however, and costs money) rVISTA (transcription binding sties) Posttranslational Modifications Post-translational modifications: phosphorylation DB
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