Structural databases provide the structural information of various proteins and RNAs.

(a) Protein Structural Databases

The list of various protein structural databases is as following:

 

Database

Description

Url

PDB

(Protein Data Bank)

The Protein Data Bank is a repository of the 3-D structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography or NMR spectroscopy

http://www.rcsb.org/pdb/home/home.do

DALI

The Dali server is used for the comparison of 3D protein structures in the Protein Data Bank (PDB)

http://ekhidna.biocenter.helsinki.fi/dali_server

CATH

 

CATH classifies the protein domain structures and a hierarchical clustering by grouping the protein domain with sequence and structure similarity.

http://www.cathdb.info/

SCOP

(Structural Classification of Proteins)

SCOP classifies protein on the basis of their structures. The classi?cation of protein structures in the database is based on evolutionary relationships and

on the principles that govern their three-dimensional structure.

http://scop.berkeley.edu/

Relibase

Relibase is a web-based database that provides tools for the investigation and analysis of protein-ligand complexes

http://relibase.ccdc.cam.ac.uk/account_utilities/login_form.php

BIND

( Biomolecular Interaction Network Database)

The BIND database provides with the full descriptions of interactions of various protein, molecular complexes and pathways.

http://bond.unleashedinformatics.com/Action

DIP

(Database of Interacting Proteins)

DIP contains the experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.

http://dip.doembi.ucla.edu/dip/Main.cgi

MINT

(Molecular INTeraction database)

MINT provides with the experimentally verifiedprotein-protein interactions

http://mint.bio.uniroma2.it/mint/Welcome.do

BioGRID

BioGRID is the database which gives the protein and genomic interactions

http://thebiogrid.org

PPI

PPI database is a repository of protein protein interactions and Protein Interaction Domains

http://ppi.fli-leibniz.de

IntAct

This database gives the details of various protein- protein interactions as well other molecular interactions

http://www.ebi.ac.uk/intact/main.xhtml

HPRD

(Human Protein Reference Database)

This repository contains information on human protein functions including protein-protein interaction, post-trans- lational modifications, enzyme-substrate relationships and disease associations.

http://www.hprd.org/

PDBTM

(Protein Data Bank of Transmembrane Proteins)

PDBTM is a database which provides with the information of various Trans membrane proteins.

http://pdbtm.enzim.hu/

ModBase

It is comprehensive database of Comparative Protein Structure Models

http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi

HCA

(Hydrophobic cluster database)

HCA database classifies proteins on the bases of structure.

http://www2.ufp.pt/~pedros/HCA_db/

HSSP

 

The HSSP database is a database of homology-derived secondary structure. Ii is a derived database which merges information from three-dimensional structures and one-dimensional sequ- ences of proteins.

http://swift.cmbi.kun.nl/swift/hssp/

CCDC

( Cambridge Crystallographic  Data Centre)

CCDC database provides the crystal structure of various proteins

http://www.ccdc.cam.ac.uk/

MPDB

It is a collection of various peptides, proteins and protein families

http://www.mpdb.tcd.ie/

 

(b) RNA Structural Databases

Some of the RNA structural databases is as following:

Database

Description

Url

SCOR

(Structural Classification of   RNA)

The Structural Classification of RNA (SCOR) is a database designed to provide a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships

http://scor.berkeley.edu/

RNA STRAND

It is a comprehensive collection of RNA secondary structures, and provide the ways of analysing, searching and updating the proposed database.

http://www.rnasoft.ca/strand/

FSDB

The frameshift database is a comprehensive compilation of experimentally known or computationally predicted data about programmed ribosomal frameshifting. The database provides the graphical view of the frameshift cassettes and the genes utilizing frameshifting for their expression.

http://wilab.inha.ac.kr/fsdb/

RAG

It classifies RNAs according to their topological characteristics and provides the RNA designs and Structures

http://www.biomath.nyu.edu:80/rna/rna.php

Viral RNA Structure Database

It provides with the information of RNA structure of various viruses.

http://rna.tbi.univie.ac.at:80/cgi-bin/virusdb.cgi