Computational Molecular Biology

Molecular Biology Databases

Doug Brutlag

October 1, 2009

• Homework # 2 Due October 8, 2009
• Slides (HTML)
• Slides (PDF)

Software

• Chime Plugin
• Cn3D
• PyMol
• RasMol
• Swiss-PDB Viewer

National Center for Biotechnology Information

• National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/
• Entrez Databases http://www.ncbi.nlm.nih.gov/Entrez/
• NCBI Handbook http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook
• NCBI Nucleotide Sequence Database http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide
• NCBI Protein Sequence Database http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein
• Online Mendelian Inheritance in Man http://www.ncbi.nlm.nih.gov/omim/
• Entrez Structure Database http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Structure

   

PDB Protein Structure Database

• Protein Data Bank (Structures) http://www.pdb.org/
• Protein Structure Initiative http://www.nigms.nih.gov/Initiatives/PSI.htm

European Bioinformatics Institute

• European Bioinformatics Institute http://www.ebi.ac.uk/
• EMBL Nucleotide Sequence Database http://www.ebi.ac.uk/embl/
• Universal Protein Resource http://www.ebi.ac.uk/uniprot/
• Searching UniProt with Text http://www.ebi.uniprot.org/uniprot-srv/uniProtPowerSearch.do
• Search UniProt with BLAST http://www.ebi.ac.uk/blast2/index.html?UniProt

Protein Identification Resource

• Protein Identification Resource - PIR http://pir.georgetown.edu/
• PIR SF Protein Clustering project http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml
• PIR IProClass access to UniProt http://pir.georgetown.edu/pirwww/dbinfo/iproclass.shtml
• PIR iProLink Literature and Knowledge Links http://pir.georgetown.edu/pirwww/iprolink

Expasy Proteomics Server

• ExPASy Proteomics Server http://www.expasy.ch/
• SwissProt & TREMBL http://www.expasy.ch/sprot/
• Growth of Swiss-Prot http://www.expasy.ch/sprot/
• Sequence Retrieval System http://www.expasy.ch/srs5/
• Swiss Model: Comparative Modeling Server http://swissmodel.expasy.org/
• ExPASy Proteomic Tools http://www.expasy.org/tools/
• PROSITE Database http://www.expasy.ch/prosite/
• Swiss 2D Page http://www.expasy.org/ch2d/

Other Internet Resources

PMGM SeqWeb Interface
CMGM Web Pointers
A description of the currently available databases on PMGM
GenBank Feature Table
Amos's WWW Links
Entrez Searches
PDB
NCBI News Letter

Molecular Dat abases on the Web

NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION	EXPASY MOLECULAR BIOLOGY SERVER	EUROPEAN BIOINFORMATICS INSTITUTE
THE INSTITUTE FOR GENOME RESEARCH	DOE HUMAN GENOME PROGRAM	DNA DATABASE OF JAPAN
THE NATIONAL HUMAN GENOME RESEARCH INSTITUTE	THE PDB PROTEIN STRUCTURE DATABASE	EUROPEAN MOLECULAR BIOLOGY LABORATORY

Molecular Biology Bookmarks

PMGM WEB POINTERS

ExPASy Life Science Directory

Back to Biochem 218 Syllabus