ncbi cn3d4 1 mmdb structure tools
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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

NCBI Cn3D4.1MMDB Structure Tools

Introduction to Bioinformatics

NSF – UC Davis

ncbi cn3d4 1
NCBI Cn3D4.1
  • MMDB
  • NCBI Cn3D4.1
  • VAST
  • Structure viewing
  • Structure alignments
  • Comparing proteins
slide3
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
retrieve a pdb structure
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)
links to explore
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/
viewing 3d structures
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
3d structure viewers
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
ncbi cn3d viewer
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
mage viewer
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
rasmol structure viewer
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
pdb protein data bank
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
cn3d tutorial
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
manipulation of the image
Manipulation of the Image
  • From the image window, explore the menu headings (and take your time!)
    • File
    • View
    • Show / hide
    • Style
    • Window
    • Help
manipulating the structure
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
sequence alignment viewer
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
importing structures
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.)
viewing aligned sequences
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
problem posing
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.
summary
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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