![Structural Bioinformatics DBs
• Databases storing 3D structural information obtained
from experimental techniques (Crystallography, NMR,
Electron microscopy) of proteins, DNA, RNA, viruses,
carbohydrates, lipids and others.
• Protein DataBank [PDB]
– (premier macromolecular structure DB; www.rcsb.org)
• PDBsum (www.ebi.ac.uk/thornton-srv/databases/pdbsum)
• Structural Classification of Proteins [SCOP]
– (scop.mrc-lmb.cam.ac.uk/scop)
• CATH database (www.cathdb.info/index.html)
• Cambridg Structural DB [CSD at the CCDC]
– (contains 3D structural information of small molecules; www.ccdc.cam.ac.uk)](https://image.slidesharecdn.com/bioinformatics-lecturexxiii-160805074435/85/Bioinformatics-lecture-xxiii-4-320.jpg)
Bioinformatics lecture xxiii
- 1. Dr. M. Kamran Azim H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi Chem-727 (Bioinformatics) Lecture-23 Structural Bioinformatics Resources
- 2. 2 What is Structural Bioinformatics? • Structural bioinformatics refers to the analysis of macromolecular structure particularly proteins, using computational tools and theoretical frameworks. • The process of predicting the 3D structures of proteins from comparison of sequence alignments, secondary and tertiary structure prediction, experimental structural biology data.
- 3. 3 Techniques in Structural Bioinformatics • Structural Bioinformatics DBs (PDB, SCOP, CATH) • Molecular visualization (RasMol, SwissPDB viewer) • Protein structure prediction Secondary structure prediction (PHD, PSIPRED) Tertiary structure prediction Homology modeling (Modeller, Composer) Fold Recognition (Genthreader, TOP) Ab initio structure Prediction (Robetta) • Protein-protein Interaction prediction (Rosetta) • Protein structure comparison (DALI) • Protein structure classification (SCOP, CATH) • Molecular docking (Dock, FlexX)
- 4. Structural Bioinformatics DBs • Databases storing 3D structural information obtained from experimental techniques (Crystallography, NMR, Electron microscopy) of proteins, DNA, RNA, viruses, carbohydrates, lipids and others. • Protein DataBank [PDB] – (premier macromolecular structure DB; www.rcsb.org) • PDBsum (www.ebi.ac.uk/thornton-srv/databases/pdbsum) • Structural Classification of Proteins [SCOP] – (scop.mrc-lmb.cam.ac.uk/scop) • CATH database (www.cathdb.info/index.html) • Cambridg Structural DB [CSD at the CCDC] – (contains 3D structural information of small molecules; www.ccdc.cam.ac.uk)
- 5. Techniques for Molecular Structural Determinations Macromolecular Crystallography
- 7. Electron density maps→atomic coordinates sets atomic coordinates sets (x,y,z coordinates of every atom of molecule) in text file.
- 8. PDB • A repository for the 3-D structural data of large biological macro-molecules, such as proteins, nucleic acids and viruses. • The data obtained by X-ray crystallography or NMR spectroscopy and submitted to PDB by scientists from around the world, and can be accessed at no charge on the internet. • Each structure submitted to PDB receives a four-character alphanumeric identifier, its PDB-ID; e.g. 1ACE, 1M43 • The file formats used by the PDB; – The PDB file format (file extension pdb or ent). This format has 80 characters per line. – The "macromolecular Crystallographic Information file" format, mmCIF. – An XML version of this format, called PDBML, was described in 2005. – The structure files can be downloaded in any of these three formats.
- 9. PDB holdings list (March 2009; update weekly)
- 10. The Cambridge Structural Database The world repository of small molecule crystal structures • The CSD records bibliographic, chemical and crystallographic information for organic molecules and metal-organic compounds; – whose 3D structures have been determined using X-ray diffraction and neutron diffraction. • The CSD records results of: single crystal studies and powder diffraction studies – which yield 3D atomic coordinate data for at least all non-H atoms. • The CSD includes crystal structure data arising from publications in the open literature and private Communications to the CSD (via direct data deposition).