Structural Bioinformatics...............

Structural Bioinformatics..

1. Structural bioinformatics of protein and RNA Course Instructor: Ayisha Aman Course: Bioinformatics Course# BTH-3051

2. What is structural bioinformatics? Structural bioinformatics is the branch of bioinformatics which is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structure such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, and binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models.

3. About DNA

4. About RNA

5. About Protein

6. Protein Motifs and Domains

7. Bioinformatics Tools for Macromolecules Structure Visualization PROWL , For the visualization of protein primary structure PROWL is available. PROWL gives information about protein primary structure. It provides knowledge about the properties of amino acid like different parameters including solubility, density and isoelectric point. It also gives information that is used to make predictions about protein structure based on primary amino acid sequence. It also provides a lot of information on amino acids. For Ramachandran plot summary, PROCHECK is available.

8. Protein Structure Databases Protein databank (PDB) The Protein Data Bank ( PDB ) is a crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. It is the platform for processing and distribution of 3D macromolecular structure data primarily determined experimentally. Here structures are deposited by using X ray crystallography and NMR. This database provides access to the structural data as well as methods to visualize the structure and to download structural information.

9. NCBI Structure (MMDB) NCBI structure database is called MMDB (Molecular Modeling Database). Entrez page provides you access to MMDB. This database contains macromolecular 3D structure , also contains tools for structure visualization. MMDB contains both protein and polynucleotide with 10,000 structure.

10. Protein Structure visualization databases and tools Cn3-D (See in 3D) is a structure and sequence alignment viewer for NCBI databases. It allows to view 3D structures. Rasmol , most popular tool (software) for protein structure visualization. It reads molecular structure from PDB. Other include Chemscape Chime & Protein Explorer . Swiss PDB Viewer , by this tool we can analyze several proteins simultaneously. Kinemages , in this , entire image can be rotated, parts can be turned on or off etc. PDBsum , it is the database that gives pictorial summary on each macromolecular structure from PDB.

11. Protein Structure Alignment and its databases VAST , (Vector Alignment Search Tool), by NCBI and is used to identify similar protein 3D structures. DALI server, protein structure alignment tool, used for comparing structures in 3D.

12. Domain Architecture Databases CDD, (Conserved Domain Database) CDART , (Conserved domain architecture retrieval tool) , is used to search for protein with similar domain architecture.

13. Protein Classification Approaches Family (Evolutionary relatedness) Superfamily (Probable common evolutionary origin) Fold (major structural similarity)

14. SCOP (Structural Classification of Protein) A structural classification of proteins provides detailed and comprehensive description of structural and evolutionary relationships between all proteins. The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins. Proteins with the same shapes but having little sequence or functional similarity are placed in different superfamilies , and are assumed to have only a very distant common ancestor. Proteins having the same shape and some similarity of sequence and/or function are placed in "families", and are assumed to have a closer common ancestor.

15. CATH (Class, Architecture, Topology & Homologous superfamily) It provides classification of protein domain structures. Class, similar secondary structure. Architecture (fold), major structural similarity. Topology (Superfamily), probable common ancestry Family , clear evolutionary relationships.