This document discusses several important databases and tools for protein structure and molecular modeling. It describes the Protein Data Bank (PDB) as a repository for 3D structural data of proteins and nucleic acids. It also outlines the National Center for Biotechnology Information (NCBI) and its Molecular Modeling Database (MMDB), which contains experimentally resolved protein structures from PDB with additional features. Other databases and tools mentioned include UniProt, ExPASy, BLAST, and their uses in analyzing protein sequences, structures, functions, and evolutionary relationships.

1. Bioinformatics is about using mathematics,
statistics and information technology to extract
useful information from large and complex
biological datasets.
SUB-TOPIC:- PROTEIN STRUCTURE &
MOLECULAR MODELING DATABASE

2. PROTEIN STRUCTURE AND MOLECULAR
MODELING DATABASE

3. OUTLINE:-
 Protein structure (3D)
 NCBI
 MMDB
 EXPASY
 UNIPROT
 BLAST
 PDB

4. PROTEIN 3D STRUCTURE
http://ppopen.informatik.tu-muenchen.de/
http://www.rcsb.org/pdb/home/home.do

6. Levels of protein structure
 Primary structure-The primary structure of a protein refers to
the linear sequence of amino acids in the polypeptide chain.
The primary structure is held together by covalent bonds such
as peptide bonds, which are made during the process of protein
biosynthesis or translation.
 Secondary structure-Secondary structure refers to highly
regular local sub-structures.Two main types of secondary
structure, the alpha helix and the beta strand orbeta sheets
 Tertiary structure-Tertiary structure refers to the three-
dimensional structure of a single, double, or triple
bonded protein molecule.The alpha-helix and beta pleated-
sheets are folded into a compact globular structure.
 Quaternary structure-Quaternary structure is the three-
dimensional structure of a multi-subunit protein and how the
subunits fit together.

7. NATIONAL CENTER FOR
BIOTECHNOLOGY
INFORMATION(NCBI)
http://www.ncbi.nlm.nih.gov

8. NCBI & Entrez
 One the most usefull and comprehensive
database collection is the NCBI , Part of the
NATIONAL LIBRARY OF MEDICINE - Home to
Genbank, Pubmed & many other familiar
Databases
 NCBI provides interesting summaries, browsers
& search tools
 Entrez is their batabase search interface
http://www.ncbi.nlm.nih.gov/entrez
 Can search on gene names, chromosomal
locations, diseases, articles, keywords, etc.........

11. MOLECULAR MODELING
DATABASE(MMDB)
http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml

12. MMDB
 Experimentally resolved structures of proteins, RNA,
and DNA, derived from the Protein Data Bank
(PDB), with value-added features such as explicit
chemical graphs, computationally identified 3D
domains (compact substructures) that are used to
identify similar 3D structures, as well as links to
literature, similar sequences, information
about chemicals bound to the structures, and more.
These connections make it possible, for example,
to find 3D structures for homologs of a protein
sequence of interest, then interactively view
the sequence-structure relationships, active
sites, bound chemicals, journal articles, and more.

17. EXPASY(PROTPARAM TOOL)
http://www.expasy.org/

18. ExPASy(PROTPARAM)
 ProtParam (References / Documentation) is a
tool which allows the computation of various
physical and chemical parameters for a given
protein stored in Swiss-Prot orTrEMBL or for a
user entered sequence.
 The computed parameters include the molecular
weight, theoretical pI, amino acid composition,
atomic composition, extinction coefficient,
estimated half-life, instability index, aliphatic
index and grand average of hydropathicity

21. UNIPROT
http://www.uniprot.org/

22. Uniprot
 The mission of UniProt is to provide the
scientific community with a comprehensive,
high-quality and freely accessible resource of
protein sequence and functional information.

24. BASIC LOCAL ALIGNMENT
SEARCH TOOL(BLAST)http://blast.ncbi.nlm.nih.gov/Blast.cgi

25. Basic Local Alignment Search
Tool(blast)
 Finds regions of local similarity
between sequences.
 Compares nucleotide or protein
sequences to sequence databases.
 Calculates statistical significance from
matches.
 Can be used to infer functional and
evolutionary relationships between
sequences.
 It can also help in identifying members
of the gene family.

29. PROTEIN DATA BANK
http://www.rcsb.org/pdb/home/home.do

30. Protein data bank
 Protein Data Bank (PDB) is a repository for
the 3-D structural data of large biological
molecules, such as proteins and nucleic
acids.
 PDB is overseen by an organization called
theWorldwide Protein Data Bank, wwPDB.
 PDB is a key resource in areas of structural
biology, such as structural genomics.

34. Useful Features of the Molecular Modeling
Database
 Facilitate computation on 3D structure data
 Analysis of individual structures and relationships
among them
 biological and geometrical features within 3D
structures
 conserved protein domain annotations
 evolutionary relationships among 3D structures
 functional relationships among 3D structures
 Interactive views of sequence-structure relationships
 Connections between 3D structure records and
associated literature, molecular, and chemical data