C C D C & DSSP(Bioinformatics)

1. Seminar
On
CCDC &DSSP
Submitted by-
R.P. MAURYA
M.Sc.Ag.2nd sem.
Department of genetics and plant breeding
Submitted to-
DR; RITU BATRA
Department of genetics and plant breeding

2. CONTENT
1. What is Biological Databases
2. Types of Biological Databases
3. What is Crystal structure & Crystallography.
4. CCDC (Cambridge Crystallographic Data Centre)
5. Cambridge Structural Database
6. CSD-Community
7. Dictionary of protein secondary structure (DSSP)

3. A database is a computerized archive used to store and
organize data in such a way that information can be retrieved
easily via a variety of search criteria. Databases are composed
of computer hardware and software for data management.
.
What is Biological Databases:-

4. Types of Biological Databases:-
Nucleotide database
 GenBank (more...)
 EMBL: European Molecular Biology Laboratory
 DDBJ: DNA Data Bank of Japan
Protein database
 Swiss-Prot
 PIR-International: Protein Information Resource
 Uni prot
Sequence cluster database
 ProDom.
 Cluster
 SYSTERS
 Prptomap

5. Structure Database :-
In biology, a protein structure database is a
database that is modeled around the various experimentally determined
protein structures. The aim of most protein structure databases is to
organize and annotate the protein structures, providing the biological
community access to the experimental data in a useful way.
 CCDC :-(Cambridge Crystallographic Data Centre)
 DSSP : -(Dictionary of protein secondary structure)
 SCOP
 CATH

6.  Crystal structure:-
crystal structure is a description of the
ordered arrangement of atoms,ions or molecules in a
crystalline material.
Crystallography:-The word "crystallography" derives
from the Greek words crystallon "cold drop, frozen
drop", with its meaning extending to all solids with
some degree of transparency, and graphein "to write".

7.  Crystallography is the experimental science of
determining the arrangement of atoms in the
crystalline solids (see crystal structure).

8. CCDC (Cambridge Crystallographic Data Centre):-
 The Cambridge Crystallographic Data Centre (CCDC) is the home of
small molecule crystallography data and is a leader in software for
pharmaceutical discovery, materials development, research and
education.
 It is a Originating in the Department of Chemistry at the University of
Cambridge.
 It is a non-profit organization whose primary role is the compilation and
maintenance of the Cambridge Structural Database.
 They also perform analysis on the database for the benefit of the
scientific community,

9. History :-
 The CCDC grew out of the activities of the crystallography group led by Dr.
Olga Kennard OBE FRS in the Department of Organic, Inorganic and
Theoretical Chemistry of the University of Cambridge.
 From 1965, the group began to collect published bibliographic, chemical
and crystal structure data for all small molecules studied by X-ray or neutron
diffraction.
 the rapid developments in computing taking place at this time, this
collection was encoded in electronic form and became known as the
Cambridge Structural Database (CSD).
 The first releases of the CSD System to the USA, Italy and Japan occurred in
the early 1970s.
 The CCDC established US applications and support operations in the USA in
October 2013 at Rutgers, the State University of New Jersey, where we are
co-located with the RCSB Protein Data Bank

10. Objectives:-
 Advancement and promotion of the science of chemistry and
Crystallography for the public benefits.
 Complies the Cambridge Structural Database
 Maxemises worldwide accessibility to C S D
 CCDC URL –http://www.ccdc.com.ac.uk

11. Cambridge Structural Database :-
 The Cambridge Structural Database (CSD) is both a repository and a
validated and curated resource for the three-dimensional structural data
of molecules or crystal structure hosted by C C D C.
 It is stores bibliographic, chemical, Crystallography information for :-
 organic molecule and metal-organic and organometallic molecules
 •The specific entries are complementary to the other crystallographic
databases such as the Protein Data Bank (PDB), Inorganic Crystal Structure
Database and International Centre for Diffraction Data
 •The data, typically obtained by X-ray crystallography and less frequently by
neutron diffraction

12. Contents:-
The CSD is updated with about 50,000 new structures
each year,and with improvements to existing entries.
Entries (structures) in the repository are released
for public access shortly after the corresponding entry
has appeared in the peer-reviewed scientific literature.

14. CSD-Community:-
 The CCDC offers a selection of products and services free of charge for
the benefit of the scientific community.
 The services detailed below cover a wide range of crystallographic tools -
from data collection, validation and visualisation to teaching, research
and analysis.

15. EnCIFer:-
 “Safely check and edit crystallographic information files (CIFs) without
compromising the syntax
 The Crystallographic Information File (CIF) is the internationally agreed
standard file format for information exchange in crystallography

16. Relibase:-
“ Relibase is a web-based system for searching and
analysing protein-ligand structures in the Protein Data
Bank (PDB).”
CSDSymmetry:-
“CSDSymmetry is the most complete collation of
observed molecular and crystallographic symmetry
properties to date.”

17. Deposit Structures
 CIF deposition and validation service

18. Mercury:-
 “Crystal Structure Visualisation, Exploration and Analysis Made Easy”
 Mercury offers a comprehensive range of tools for 3D structure
visualization and the exploration of crystal packing. With a long pedigree
and over 10,000 downloads.

19. CSD Teaching Database:-
 “The CSD Teaching Database is a 700+ structure subset carefully selected
to enhance chemistry learning”
 These include compounds used to illustrate fundamental concepts of
bonding and structure, conformational analysis, stereochemistry and
reaction mechanisms.
 Examples of all major chemical functional groups as well as a wide range
of broader chemical classes, including carbohydrates, nucleotides, amino
acids, steroids, porphyrins, alkaloids, catena structures, and high
polymers.

20. Access Structures:-
 View and retrieve structures in the Cambridge Structural Database
 Viewing the data:- The structure files may be viewed using one of several
open source computer programs such as Jmol and MDL Chime, Pymol, UCSF
Chimera, Rasmol, WINGX,[8
 the CCDC and Discovery Studio provides a free version of its molecule
visualization program Mercury.

21. Dictionary of protein secondary
structure (DSSP):-
 The DSSP program was designed by Wolfgang Kabsch and Chris Sander
to standardize secondary structure assignment.
 DSSP is a database of secondary structure assignments (and much more)
for all protein entries in the Protein Data Bank (PDB)
 DSSP is also the program that calculates DSSP entries from PDB entries
 Users can also upload the modeled/predicted tertiary structure file (in
PDB format) for assignment of secondary structures.

22. Theory:-
 The DSSP program works by calculating the most likely secondary
structure assignment given the 3D structure of a protein.
 It does this by reading the position of the atoms in a protein (the ATOM
records in a PDB file) followed by calculation of the H-bond energy
between all atoms.
 The best two H-bonds for each atom are then used to determine the
most likely class of secondary structure for each residue in the protein
 This means you do need to have a full and valid 3D structure for a
protein to be able to calculate the secondary structure.

23. Databank:-
 The DSSP as a databank is maintained by the CMBI.
 You can access individual files using our search system MRS at
http://mrs.cmbi.ru.nl. If you want to download all the DSSP files your best
choice is to use rsync.
 To download all the DSSP files to the local directory /data/dssp you
would use the command: rsync -a rsync://rsync.cmbi.ru.nl/dssp
/data/dssp
 Web server & service :- We've created a web server to calculate DSSP
files from PDB files. You can find the server at http://www.cmbi.ru.nl/xssp/
 Application:- The current version of DSSP is available as a prebuilt binary
for Windows and for Linux. You can download the binaries from
ftp://ftp.cmbi.ru.nl/pub/software/dssp/

25. DSSP File Format:-
 Input form:-
The header part of each DSSP file is self explaining, it contains
some of the information copied over from the PDB file and there are some
statistics gathered while calculating the secondary structure.

26.  The second half of the file contains the calculated secondary structure
information per residue. What follows is a brief explanation for each
column.

27. Output Page:-