The document discusses various databases and resources for analyzing proteins and chemical compounds. It describes the Conserved Domain Database, which contains models of conserved protein domains and alignments. It also mentions CD tree, which allows viewing conserved domains. Other resources discussed include protein clusters, which group related protein sequences, and biosystems, which describe interacting biological components like genes and proteins. The document also provides information about PubChem, including the Compound, Substance, and BioAssay databases that contain chemical structures, sample descriptions, and biological screening results.

2. TYPE YOUR DESIRED PROTEIN
e
Ex.collagen

3. Will get a option like “Conserved domain “ about that Protein .

4. Conserved Domain
The Conserved Domain Database (CDD) is a database of well-
annotated
multiple sequence alignment models and derived database search
models,
for ancient domains and full-length proteins.

5. select

7. CD tree

8. CD tree is a helper application to view and examine conserved domains
Curated at NCBI .
CD tree works with Cn3D as its alignment viewer/editor ,and its used for
both classification and research tool for functional annotation .
Sequence alignment is used to identify the similarity between consequence of
Functional ,structural , or evolutionary relationship sequences

15. Protein Clusters :
Is a collection of related protein seq’ consist of protein derived from
The annotation of whole genomes , organelles and plasmids.
It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses

18. Protein Structure

21. CHEMICALS

22. BIO SYSTEM

23. Is a group of molecules that intract new biological system
It provides links One type of biosystem is a biological pathway, which can consist
of interacting genes, proteins, and small molecules.
Another type of biosystem is a disease, which can involve components such as
genes, biomarkers, and drugs.

26. The Compound-centric BioActivity service reports the available biological screening
results for a single or a set of chemical samples. This service provide means for one
to examine and compare biological outcomes across multiple biological tests. Please
specify compounds using the given input methods. To retrieve specific test results,
please specify bioassays.

29. Pub chem Compound
The PubChem Compound Database contains validated chemical depiction
information provided to describe substances in PubChem Substance. Structures
stored within PubChem Compounds are pre-clustered and cross-referenced by
identity and similarity groups

30. Links from PubChem's chemical structure records to other Entrez databases provide
information on biological properties. These include links to PubMed scientific literature
and NCBI's protein 3D structure resource. Links to PubChem's bioassay database
present the results of biological screening. Links to depositor web sites provide further
information. A PubChem FTP site, Download Facility, Power User
Gateway(PUG),Standardization Service, Score Matrix Service, Structure Clustering,
and Deposition Gateway are also available.
PubChem provides tips and example code to allow users to add PubChem search
tool (free) in their sites. A PubChem publication site provides links to published articles

31. The PubChem Substance Database contains descriptions of
samples, from a variety of sources, and links to biological
screening results that are available in PubChem BioAssay.
If the chemical contents of a sample are known, the
description includes links to PubChem Compound.