Difference between revisions of "Bioinformatics links"
From Christoph's Personal Wiki
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*[http://www.molmovdb.org/ MolMovDB] — Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis. | *[http://www.molmovdb.org/ MolMovDB] — Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis. | ||
*[http://scop.berkeley.edu/ SCOP: Structural Classification of Proteins] | *[http://scop.berkeley.edu/ SCOP: Structural Classification of Proteins] | ||
| + | *[http://ekhidna.biocenter.helsinki.fi/dali/start Dali Fold Classification] — based on exhaustive, all-against-all 3D structure comparison of protein structures in the Protein Data Bank | ||
| + | *[http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ PDBsum] — provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank | ||
| + | *[http://blocks.fhcrc.org/ BLOCKS] — a service for biological sequence analysis | ||
*[http://wikiomics.org/wiki/Searching_for_3D_functional_sites_in_a_protein_structure Searching for 3D functional sites in a protein structure] | *[http://wikiomics.org/wiki/Searching_for_3D_functional_sites_in_a_protein_structure Searching for 3D functional sites in a protein structure] | ||
*[[wikipedia:Structural genomics]] | *[[wikipedia:Structural genomics]] | ||
Revision as of 01:38, 16 June 2007
Contents
Databases
General
- European Bioinformatics Institute — portal for research and services in bioinformatics, with databases of nucleic acid and protein sequences, and macromolecular structures - from the EMBL, Hinxton UK.
- NCBI/GenBank (USA) — offers many important databases (PubMed, GenBank, OMIM) and some tools.
- DDBJ (Japan)
Genomes
Lists of genomes in progress
- Genome projects
- http://wit.integratedgenomics.com/GOLD/
- http://www.tigr.org/tdb/mdb/mdbinprogress.html
- Ensembl genome download (mainly Eukaryotes)
- Complete Published Genome Projects: 524
Web servers
- World Index of BioMolecular Visualization Resources
- PDBSiteScan
- Catalytic Site Atlas (CSA) — a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
- SiteEngine — Functional Sites Structural Search Engine; Recognizes regions on the surface of one protein that resemble a specific binding site of another.
- SuMo
- ASTRAL — The ASTRAL Compendium for Sequence and Structure Analysis.
- MolMovDB — Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis.
- SCOP: Structural Classification of Proteins
- Dali Fold Classification — based on exhaustive, all-against-all 3D structure comparison of protein structures in the Protein Data Bank
- PDBsum — provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank
- BLOCKS — a service for biological sequence analysis
- Searching for 3D functional sites in a protein structure
- wikipedia:Structural genomics
Data acquisition (search engines)
Keyword
- SRS (tutorials can be found at http://www.icgeb.trieste.it/~netsrv/courses/RH/srs/ or http://www.no.embnet.org/Programs/DB/srs_tut.php3)
- Entrez (tutorial can be fond at http://www.ncbi.nlm.nih.gov:80/Database/tut1.html)
Similarity
Multiple sequence alignment
- ClustalX (ftp) (tutorial can be found at http://www.bioinf.org/molsys/ClustalX_tutorial.html)
- BioEdit
- BCM search launcher
- GCG
- Lists
- STRAP — Multiple Sequence Alignment
Prediction
- NNPREDICT — Protein Secondary Structure Prediction
- Pattern and profile searches Pattern and profile searches
Phylogenetic analysis
- PAUPp (tutorial can be found at http://paup.csit.fsu.edu/Quick_start_v1.pdf)
- Mega2
- PHYLIP
- Treeview
- List
Taxonomy
- Species 2000
- uBio — uses names and taxonomic intelligence to manage information about organisms
- BioLib — an international encyclopaedia of plants, fungi, and animals.
- Forestry Images
- The 2006 IUCN Red List of Threatened Species
Software
Other
- Bioinform — bioinformatics news service.
- Bioinformatics.ca — curated web directory of molecular biology and bioinformatics resources
- Bioinformatik — categorical web directory for bioinformatics theory - from the Univ. of Düsseldorf. Mathematics and Computer-based.
- Bioplanet Jobs — bioinformatics jobs, education resources, bulletin board, CV posting.
- Canadian Bioinformatics Resource — dedicated to providing researchers with convenient, effective access to high-quality bioinformatics tools and databases.
- CMS Molecular Biology Resources — a compendium of tools for molecular biology, biotechnology, molecular evolution, biochemistry and biomolecular modeling.
- DNA and Protein Analysis Toolkit — compendium of bioinformatics computing services from The Rockefeller University. Many different ways to analyse biomolecules.
- Genome Programs — links to online genomics resources - including the individual projects.
- Molecular Biological Sites — includes sequence search windows, as well as databases and tools related with proteomics and structural bioscience.
- Snowdeal.org — a weblog that provides daily updates and links to news items and stories of interest to bioinformatics community.
- UBC Bioinformatics Centre Resource Directory — currated and categorized database of links to the top bioinformatics and molecular biology resources on the web.
- The OpenScience Project
- Quick guide to characteristics of metal sites in proteins
- sfcheck — a program for assessing the agreement between the atomic model and X-ray data or EM map.
- OmicsWorld
- OMICS: A Journal of Integrative Biology
- ZINC — a free database of commercially-available compounds for virtual screening.
- BIO.SK - Directory
- Wikiomics.org — (User:Christoph)
- Omics.org — an openfree wiki site for -omes and -omics in Biotechnology and Bioscience.
- OpenWetWare.org
- AAA Wiki — considers sequenced Drosophila genomes.
- openfree BioDomain.org — a list of biological domains.
- wikipedia:Bioinformatics
- wikibooks:Computational Biology (aka Bioinformatics)
