The current experiment is designed to investigate the structure of proteins using on-line tools for protein classification viz. CATH and SCOP.

REQUIREMENTS :

Unix (including Linux) workstation (e.g., Sun, Alpha, Silicon Graphics, PC), PC with MS Windows (preferably with a 64-bit processor, 2GB RAM), or Power Macintosh, internet connection etc.

PROCEDURE :

Part A : Using CATH to study hierarchical classification of protein-domain structures.

a. Searching domains in the CATH database:

1. Point the browser to http://www.cathdb.info/.

2. The CATH database can be browsed, searched and downloaded using the links present in the "Links for Researchers section".

3. To search the CATH database use "Search CATH by ID/sequence/text" link.

4. Search by id can be done using "CATH domain id", "CATH chain id" or "PDB id" whereas text search can be performed using-structural or functional term like "chaperone" or "helix". Search by sequence can be performed by pasting protein sequences in FASTA format.

5. Search by ID displays "domain id, structure, CATH code, the different chains present, PDB code and functional annotation if known". To identify homologous domains, click in the "CATH code". The classification, architecture, topology, homologous superfamily, sequence and structural information related to the domain can be obtained by clicking on the "Domain ID"; Search using keyword displays the PDB files and CATH classification code and name that contain the search term. More information on the domain can be obtained by clicking the "CATH code" of the classification entries.

6. Search by "sequence" blasts against sequences derived from structural domains present in CATH database and displays domains with similar sequences present in CATH with their "Domain ID" and "CATH code". More information on the domains can be obtained using the "Domain Id" and "CATH code" link.

b. Performing structural and functional analysis of proteins in CATH :

1. Retrieve the PDB id for the protein of interest.

2. Paste the "PDB id" or upload a "PDB file", check the "PDB versus CATH CATHEDRAL Scan" and click on "Continue".

3. CATHEDRAL Server identifies the domains present in the protein.

4. Structural and Topological information on the domains present in the protein of interest can be obtained using "Domain ID" and "Topology ID". Functional information, taxonomic distributions, multi-domain architectures and protein-protein interaction data can be obtained using the Geno3D Server link.

Part B : Using SCOP to study structural classification of proteins :

1. Point your browser to http://scop.mrc-lmb.cam.ac.uk/scop/.

2. Data in SCOP can be browsed using "Enter SCOP at the top of the hierarchy" or searched using the "Keyword search of SCOP entries".

3. Search in SCOP can be performed using the "sunid: a unique identifier for all entries in the SCOP hierarchy; for e.g. search using "57942" displays results for the coiled coil proteins", "sees: an identifier for class (alphabetical), fold, superfamily, family (all numerical); for e.g. to search for truncated haemoglobin family the sees is "a.1.1.1" where "a" is the class code and the remaining numericals refer to the fold, superfamily, family code respectively" and "keyword search".

4. Multiple keywords can be given by combining the keywords with "+' or operator; for e.g. to search for "hemoglobin in pig only", the search would be represented as "hemoglobin +pig" whereas to search for "all haemoglobin entries except those present in human" the search keyword would be "hemoglobin -human". Search for new families, superfamilies, folds or classes is possible using keywords like "newfa", "newsf, "newcf, "newel" respectively.

5. Search using "MSDIite" searches text fields in PDB and returns links to the corresponding CATH entry.

6. Identify the class and describe the fold of the protein. Using the superfamily link find the functional annotation given to the protein.

7. The 3-D structures of the domains can be studied by clicking on the Rasmol or chime link Identify the secondary structures elements present in the structures. Other domain related information can be obtained with link option.