Scribd
Upload
41 views23 pages

05 Structural Databases

The document provides an overview of various structural databases used for protein and nucleic acid research, including the Protein Data Bank (PDB), Nucleic Acid Database (NDB), and Molecular Modeling Database (MMDB). It details how to search for structures using identification codes, keywords, and advanced search options, as well as how to access structural information and download files. Additionally, it mentions related databases like CATH and SCOP for further classification and analysis of structures.

Uploaded by

anshulnitnaware53777
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
41 views23 pages

05 Structural Databases

The document provides an overview of various structural databases used for protein and nucleic acid research, including the Protein Data Bank (PDB), Nucleic Acid Database (NDB), and Molecular Modeling Database (MMDB). It details how to search for structures using identification codes, keywords, and advanced search options, as well as how to access structural information and download files. Additionally, it mentions related databases like CATH and SCOP for further classification and analysis of structures.

Uploaded by

anshulnitnaware53777
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
You are on page 1/ 23

Structural

Databases
1. PDB
2. CATH
3. NDB
4. SCOP
5. MMDB
Protein Data Bank (PDB)
PDB
• PDB identification code

4-character identifier also called PDB ID

• [0—9][A—Z or 0—9] [A—Z or 0—9] [A—Z or 0—9].

e.g., 1LYZ (hen’s egg-white lysozyme)

• Enter the identification code into the PDB ID box and hit the Explore button.
• The Structure Explore page for this entry is returned.

• If the PDB ID is not known, clicking Search Lite opens the query page.

• Enter the keyword (name of ligand/biomacromolecule or author) and


click the Search button.
• In the advanced search, clicking Search Field opens the
query form (Figure ).

• Construct combination of your query options including


• PDB ID,
• citation author,
• chain type (for protein, enzyme, carbohydrate, DNA or RNA),
• Compound information,
• PDB header, and
• experimental technique used.
• Clicking the Search button returns you to the search page with a list of
hits from which you select the desired entry to access the Summary
information of the selected molecule.
• From the Summary information, the user can choose one of many
options including
• View Structure,
• Download/Display File,
• Structural Neighbors (links to CATH, CE, PSSP, SCOP and VAST),
• Geometry, or
• equence Details.

• Select Download/Display File, then choose PDB text and PDB non
compression format to retrieve the pdb file in text format.

• To view the structure online, select View Structure followed by


choosing one of the 3D display options.

• The display can be saved as image.jpg/image.gif.


• The Structure Neighbors provide links to
• CATH (fold classification by domain),
• CE (representative structure comparison, structure alignments,
structure superposition tool),
• FSSP (fold tree, domain dictionary, sequence neighbors,
structure superposition),
• SCOP (Class, fold, superfamily, and family classification), and
• VAST (representative structure comparison, structure
alignments, structure superposition tool).
• The Geometry option provides tables of
• Dihedral angles,
• bond angles, and
• bond lengths.
Nucleic Acid Database (NDB)
• The structural information about nucleic acids can be obtained from PDB or Nucleic Acid
Database (NDB) at http://ndbserver.rutgers.edu/NDB/ndb.html.

• On the NDB home page, choose Search Nucleic acid database search Quick search to open the
search form for the database (Figure 12.4).

• Activate Classification list box (listing of the database by classes: DNA, DNA/RNA, Peptide
nucleic acid, Peptide nucleic acid/DNA, Protein/DNA, Protein/RNA, Ribosome, Ribozyme, RNA,
and tRNA).

• Highlight the desired class, and click the Execute Selection button to open a list of database for
the class.

• Highlight an entry and click the Display Selection button.

• An information page providing NDB ID, Compound name, Sequence, Citation, Crystal
information, Coordinates, and Views is returned.

• Click the link, coordinates for the asymmetric unit to open the coordinate file and save it as
nuclacid.pdb.
Molecular modeling database
(MMDB)
• Molecular modelling database (MMDB) of Entrez is a subset of 3D structures from
PDB recorded in asn.1 format (Wang et. al., 2002).

• The database that provides the link between 3D structures and sequences can be
accessed at http:// www.ncbi.nlm.nih.gov/Entrez/structure.html.

• Enter author’s last name or text words/ keywords (e.g., zinc finger, DNA protein
complex, or topoisomerase) or PDB ID (if it is known) and click the Search or Go
button.

• A list of hits is returned.

• Select the desired entries and then click the PDB ID to receive the MMDB Structure
summary (Figure 12.3).

• Choose options (radios) to view or save the structure file as structure.

• cgi (Cn3D), structure. In (KineMage), or structure.pdb (RasMol).


• Sequence similarities or structure similarities can be
viewed/saved by clicking the respective chain designation
of Sequence neighbours or Structure neighbours.

• This returns the sequence display summary or VAST


structure neighbours, respectively.
CATH
SCOP

You might also like