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BIRLA INSTITUTE OF SCIENTIFIC RESEARCH, JAIPUR

Summer Training Exercises



Day5

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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: Chemical Sketching - Molinspiration

Introduction

Biologically active compound act as a drug.these software is helpful for sketching molecule. Smiles file format is The Simplified Molecular Input Line Entry Specification (SMILES) a line notation for molecules. SMILES strings include connectivity but do not include 2D or 3D coordinates.

Hydrogen atoms are not represented. Other atoms are represented by their element symbols B, C, N, O, F, P, S, Cl, Br, and I. The symbol "=" represents double bonds and "#" represents triple bonds. Branching is indicated by (). Rings are indicated by pairs of digits.

Name      Formula      SMILES String
Methane      CH4        C
Ethanol      C2H6O        CCO
Benzene      C6H6        C1=CC=CC=C1 or c1ccccc1
Ethylene      C2H4        C=C

STEPS:

  • Open the site
    http://www.molinspiration.com

  • click on free on-line cheminformatics services

  • Use the icon | for single carbon || for double bond

  • Red cross is eraser

  • Sketch molecule aspirin.

  • For it Open site
    http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound

  • search for aspirin

  • For smiles format take it from pubchem canonical smiles

  • paste smiles format CC(=O)OC1=CC=CC=C1C(=O)O in paste smiles here.

  • click on calculate properties and predict bioactivity

  • You will get output predict bioactivity

  • GPCR ligand -0.66
    Ion channel modulator -0.91
    Kinase inhibitor -0.49
    Nuclear receptor ligand -1.23

  • You will get output for calculate properties.


  • miLogP 1.434
    TPSA 63.604
    natoms 13
    MW 180.159
    nON 4
    nOHNH 1
    nviolations 0
    nrotb 3
    volume 155.574

Section - 3: 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




  4. Press the button 'build model'.


  5. you can see result after a while





  6. Swissmodel provide 3 best results according to their score


    It provide- Sequence identity, Alignment and Structure


  7. We can also download the detailed results

    Section - 4: 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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    Section - 5: Homology Modeling using Chimera

    1. Open target sequence into chimera
      (File -> Open -> (select target file from file browser)
      or can download target sequence online by-
      File -> Fetch by ID (provide ID related to given databases)
      This step opens target protein sequence into 'sequence viewer'.
    2. To view secondary structures in this target sequence
      go to (in 'sequence viewer')
      Structure -> Secondary Structure -> Show Actual/ Show Predicted

    3. show/hide these structures in 'sequence viewer'
      go to (in 'sequence viewer')
      Info -> Region Browser

    4. Template Sequence Search
      To model structure of this target protein firstly a known structure protein sequence is searched which is much similar to this target sequence. For this Blast is performed and target sequence is aligned with PDB database's protein structures. We take a much similar sequence (with having low resolution parameter) known as 'Template Sequence'.

      Following process is followed for the same-

      go to (in 'sequence viewer')
      • a) Info -> Blast Protein

      • b) select target protein and click OK

      • c) Select program 'blast' and database 'pdb' ( can enter desired E-value and Matrix used for BLAST ) and click OK

      This opens results of BLAST search. Click on 'Columns' buttons to view desired parameters in results by selecting the options. Check 'Resolution' to view resolution of proteins given.

    5. View alignment of target sequence to blast results

      For this, select a protein from results and click on 'Show in MAV'.
      (MAV stands for MultAlign Viewer)

    6. Loading Template Structure into 'Chimera'
      Select a best hit template protein from above results and click on 'Load Structure'.

    7. Modelling Structure of template sequence

      go to (in 'MultAlign Viewer')
      • a) Structure -> Modeller(homology)

      • b) Choose target sequence

      • c) Choose template sequence

      • d) Enter valid key of MODELLER (to run modeller via web service[MODELIRANJE]) or Run Modeller locally

      • e) Can set 'Advance Option'

      • f) Click OK


      It will take some time to model structure of target protein on template.

    8. 'Modeller Result' box is opened when models are build. We can check our model by selecting each models.

    9. To show/hide Template and models from viewer
      go to (in 'Chimera Viewer')
      Favorites -> Model Panel
      (On/ Off checkbox to given Name to show/hide structures)

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