STRUCTURE AND CHEMICAL DB, RETRIVAL OF PROTEIN 3D STRUCTURE

Question 1

Protein data bank(PDB)

Answer 1

• to find the 3D structure and sequence info of protein (aim)

-it is an archive of experimentally determined 3d structure of protein and other macromolecules

-operated by- Rutgers, the state uni of New Jersey
-san Diego supercomputer center at uni of California, San Diego
-RCSB- research collaboration for structural bioinformatics

-funds from NIH and dep of energy and national science foundation

-https://www.rcsb.org

Question 2

CATH

Answer 2

-class, architecture, topology, homology
-the cath data are obtained from pdb files from pdb
-class- the broadest level of classification, dividing proteins into major categories based on their overall structural features.

-architecture- within each class, protein divided into diff architural motifis based on secondary structures (alpha helices, beta sheets)

-topology- this analyses the spacial arrangement of secondary structures

-homology- evolutionary relationships of proteins, check if they are from same ancestor and are homologous proteins.

-https://www.cathdb.info

Question 3

SCOP

Answer 3

• structural classification of proteins
  -https://scop2.mrc-lmb.cam.ac.uk

-FOLD- based on their overall structural similarity.
-common arrangement of secondary structural elements

• SUPERFAMILY- within the same fold,
  based on similarities in their overall structures and functions.
  -typically share a common evolutionary origin.

-FAMILY- further structural and functional similarity
- have significant homologous character

-DOMAIN- provides information at the domain level, identifying compact structural units