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Section - 1

Databases and tools in CADD

Various Databases:

Protein Data Bank

Repository for 3D‐structural data of biological macromolecules.The structures can be obtained by different techniques, e.g. crystallography, electron microscopy, NMR.

Data is freely accessible on the internet, e.g. www.rcsb.org .

Key resource for structural biology – most journals require experimentally determined structures to be submitted to the PDB before publication.

Protein Data Bank (PDB)
http://www.rcsb.org/pdb/home/home.do

PubChem

PubChem, released in 2004, provides information on the biological activities of small molecules.

PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system.

These are PubChem Substance, PubChem Compound, and PubChem BioAssay.

PubChem also provides a fast chemical structure similarity search tool.

PubChem
https://pubchem.ncbi.nlm.nih.gov

DrugBank Version 5.0

PubChem, released in 2004, provides information on the biological activities of small molecules.

PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system.

These are PubChem Substance, PubChem Compound, and PubChem BioAssay.

PubChem also provides a fast chemical structure similarity search tool.

3.DrugBank Version 5.0
https://www.drugbank.ca/

Section - 2: Protein Structure Prediction: Homology Modeling

Homology Modeling using Swissmodel

Steps:

1. Take a protein sequence in FASTA format whose structure is to be modelled. This is our 'Target Sequence'.


2. Now go to the webpage http://swissmodel.expasy.org/
   
   
   
   






3. Paste target sequence into swiss model workspace in FASTA format
   
   (you can also upload target sequence )
   
   you can provide a Project title and email-id-
   
   You have 2 options now you can either search for templates or build models directly
   
   



Press the button 'build model'.



4. you can see result after a while
   
   
   



Swissmodel provide 3 best results according to their score


It provide- Sequence identity, Alignment and Structure



5. We can also download the detailed results
   

   Section - 3: Protein Structure Validation

   The Structure Analysis and Verification using SAVES Server

   

   Steps:

   1. Open SAVES SERVER webpage: http://services.mbi.ucla.edu/SAVES/
   
   
   2. Upload the PDB file.
   
   
   3. RUN all programs
   
   

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