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NCBI Cn3D4.1 MMDB Structure Tools

NCBI Cn3D4.1 MMDB Structure Tools . Introduction to Bioinformatics NSF – UC Davis. NCBI Cn3D4.1. MMDB NCBI Cn3D4.1 VAST Structure viewing Structure alignments Comparing proteins. MMDB. Access amino acid and nucleic acid sequences, and protein structures .pdb, .val, .mage

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NCBI Cn3D4.1 MMDB Structure Tools

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  1. NCBI Cn3D4.1MMDB Structure Tools Introduction to Bioinformatics NSF – UC Davis

  2. NCBI Cn3D4.1 • MMDB • NCBI Cn3D4.1 • VAST • Structure viewing • Structure alignments • Comparing proteins

  3. MMDB • Access amino acid and nucleic acid sequences, and protein structures • .pdb, .val, .mage • Retrieve PubMed documents • Get taxonomy information • View sequence neighbors • View structure neighbors

  4. Retrieve a PDB Structure • Go to the MMDB page at: http://www.ncbi.nlm.nih.gov/Structure/ • In the upper right search field enter a PDB/MMDB-Id: (1VID for example) • If you don’t know a PDB accession ID, search NCBI structure using the gene and or protein name (e.g. COMT)

  5. Links to Explore • Click the blue protein tab to see the PDB entry in GenPept. Scan the file contents • Click the blue CDs entry to see the Pfam entry in the Conserved Domain Database • Click the chain to see VAST structure neighbors (and import them into VAST) • Click the methyltransf_3 tab to see ‘query’ sequence alignment against CDD neighbors • Follow PDB link to http://www.rcsb.org/pdb/

  6. Viewing 3D Structures • Now choose the gray box – View 3D structure – and select best model, then: • Mage • RasMol • Cn3D • You’ll need to have each of these apps. properly installed on your local computer

  7. 3D Structure Viewers • Download and install MAGE • http://kinemage.biochem.duke.edu/kinemage/kinemage.php • Download and install RasMol • http://www.rasmol.org • Download and install NCBI Cn3D4.1 • http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

  8. NCBI Cn3D Viewer • Roughly 2.5 Mbyte download from NCBI • Easy to install and very stable • Launches from MMDB (if selected) • The Cn3D tutorial is cumbersome, and the instructions for VAST alignment in particular • http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dtut.shtml

  9. MAGE Viewer • Lightweight, easy to install • Can view small molecules well • Good in organic chemistry classes • Libraries aren’t easy to find though • Think about using Chime for molecules • MMDB will export MAGE files • Resolution isn’t very good by comparison

  10. RasMol Structure Viewer • Views .pdb files • Very lightweight and powerful • Has a help file to download • Coloring chains / bonds is easy • Easy to export into image files

  11. PDB - Protein Data Bank • http://www.rcsb.org/pdb/ • Database of over 35,000 structures • Look up a structure by ID, or search • Download raw .pdb formats, or .jpeg images of structures to include in reports • “Molecule of the Month” and links to SCOP and CATH are key site features

  12. Cn3D Tutorial • You can launch Cn3D directly from the Windows or Mac OS, or from a .val file • With Cn3D open, chose file, open, and then locate a file with a .val extension • Or, from MMDB entry, choose view 3D structure, best model, with Cn3D display • The file will download to your computer • Select open from the dialog window

  13. Manipulation of the Image • From the image window, explore the menu headings (and take your time!) • File • View • Show / hide • Style • Window • Help

  14. Manipulating the Structure • You can view the structure in a number of formats. Try animation, and spin! • Okay – now go to view, animation, stop! • Use show hide, and pick structures, residues, aligned residues, everything • You’ll need to go to the Sequence / Alignment Viewer, and select residues

  15. Sequence Alignment Viewer • Take some time to browse the menus, as these will become very important later • View • Edit (grayed until import) • Mouse mode • Unaligned justification (grayed until import) • Imports • Now go to imports, show imports

  16. Importing Structures • This section gets tough. Open tutorial! • If you are working with a theme, have those structures and sequences ready. • Go to Import Viewer, then choose edit, import structures, or import sequences • Hint – import the larger sequence from the smaller sequence if you have more than one identical chains (dimers etc.)

  17. Viewing Aligned Sequences • Cn3D4.1 will do an automatic alignment of sequences - not stated in the tutorial! • Choose merge alignments, merge all • You now have a merged sequence • Go back to sequence / alignment viewer • Aligned residues are in UPPERCASE! • Now go to Show / Hide aligned residues

  18. Problem Posing • Compare proteins from different sources, but same conserved domain (use CDD) • HIV/SIV and HTLV/STLV (1ENV protein) • Hemoglobin / Myoglobin (2HHD / 1M6C) • Sequence alignment is a good approach to phylogenetics exercises, esp. mutation • Use NCBI genome to locate proteins for HIV, SIV, HTLV, STLV, Prion, SARS, etc.

  19. Summary • Protein structure visualization tools can be fun to use, but require lots of practice • Start with NCBI Structure and MMDB • Locate the .pdb and .val structure files • Open them in RasMol, MAGE, and Cn3D • Try doing sequence alignments in Cn3D, using a biological problem (like HIV etc.)

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