Abasyn University Peshawar

Name: Ihsan Ullah

Depart: BS Medical lab technology
Protein Databank (PDB):

PDB is a primary protein structure database. It is a

crystallographic database for the three-dimensional structure
of large biological molecules, such as proteins.

The database holds data derived from mainly three sources:

Structure determined by X-ray crystallography, NMR
(Nuclear magnetic resonance spectroscopy) experiments, and
molecular modeling
Protein Sequence Databases

The most comprehensive source of information on

proteins is found in protein sequence databases, of which
there are two types:

universal databases whose aim is to collect bio-logical

information on the most varied amount of species .

 specialized databases that cater (supply) for specific

groups or families of proteins or specific organisms .
SEQUENCE REPOSITORIES
 Several protein sequence databases act as repositories
(storage) of protein sequences.
These databases add little on no additional information to
the sequence records they contain
 e.g: GenPept, NCBI's entrez Protein, e Reference
Sequence
SWISS-PROT
 SWISS-PROT is a universal protein sequence database
established in 1986 and maintained collaboratively, since
1987 by the Department of Medical Biochemistry of the
University of Geneva and the EMBL Data Library
 The leading universal Curated protein sequence data base
is SWISS Prot, which contained 140000 Curated sequence
entries from over 8300 different species as on November
2003.
PROTEIN STRUCTURE DATABASE
SCOP:A Structural Classification of Proteins database
 Class Architecture Topology Homologous (CATH):-
SCOP :The classification of the proteins is on
hierarchical levels:
Family
Super family
 Common fold
 Class
CATH
The CATH database is a classification of protein domains
based not only on sequence information, but also on
structural and functional properties
The first CATH release from 1997 contained only 8,078
domains.
 In addition to the four main levels, CATH comprises five
more layers, called S, O, L, I and D.
The first four layers group domains according to
increasing sequence overlap and similarity whereas the D-
level assigns a unique identifier to every domain.