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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


  • 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:

  • 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

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


  • Download and install RasMol


  • Download and install NCBI Cn3D4.1


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


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


  • 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.


  • 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.)