Summer Training MAY-JULY, 2016


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Section - 1: Protein Structure Prediction: Homology Modeling

Lab 1: Homology Modeling using Swissmodel


  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

  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

    The Structure Analysis and Verification Server version 4

    This metaserver runs 6 programs for checking and validating protein structures during and after model refinement.

    PROCHECK : Checks the stereochemical quality of a protein structure by analyzing residue-by-residue geometry and overall structure geometry. [Reference]

    WHAT_CHECK : Derived from a subset of protein verification tools from the WHATIF program (Vriend, 1990), this does extensive checking of many sterochemical parameters of the residues in the model. [Reference]

    ERRAT : Analyzes the statistics of non-bonded interactions between different atom types and plots the value of the error function versus position of a 9-residue sliding window, calculated by a comparison with statistics from highly refined structures. [Reference]

    VERIFY_3D : Determines the compatibility of an atomic model (3D) with its own amino acid sequence (1D) by assigning a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar etc) and comparing the results to good structures. References: [Bowie et al., 1991; Luethy et al., 1992].

    PROVE : Calculates the volumes of atoms in macromolecules using an algorithm which treats the atoms like hard spheres and calculates a statistical Z-score deviation for the model from highly resolved (2.0 Å or better) and refined (R-factor of 0.2 or better) PDB-deposited structures. [PUBMED Reference].

    CRYST1 record matches : We take the CRYST1 record and search the entire PDB for matches and report these as possibly similar structures.

    Ramachandran Plot : We produce an interactive Ramachandran plot. Also a standalone server linked above.

    WedMol Viewer : We provide a structure viewer in the web page, although not all browsers support it. We are working to pvoride a more robust viewer

  8. Steps:

    1. Open SAVES SERVER webpage:

    2. Upload the PDB file.

    3. RUN all programs