CHAPTER 32Validation of Predicted Tertiary Structure of Protein

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

32.1 INTRODUCTION

The tertiary structure of a protein can be experimentally determined by nuclear magnetic resonance and X‐ray crystallography, which are expensive and labor‐intensive. Biocomputationally predicted tertiary structures must be validated for the permissibility of dihedral angles.

32.2 OBJECTIVE

To validate the predicted tertiary structure of a protein using two online tools, namely the WHAT IF web interface and MOLprabity.

32.3 PROCEDURE (WHAT IF TOOL FOR VALIDATING THE 3D STRUCTURE PREDICTION RESULTS)

  1. Input file: download the .pdb file of the modeled structure: after completion of structure prediction.
  2. Open the WHAT IF home page to check the reliability of the predicted structure. URL: http://swift.cmbi.ru.nl/servers/html/index.html.
  3. Click on “Build/check/repair model” in the left‐hand pane (Figure 32.1).
  4. Click on “Protein Model Check” (again, 3rd third option in the main window); this will enable the user to run a set of the protein structure prediction model checking option.
  5. Click on “Browse” button to upload the predicted model file (*.pdb format).
  6. Click on “Send” button to submit the structure for analysis.
Homepage of WHAT IF web interface with the encircled Build/check/repair model link (left pane) to initiate validation of the predicted tertiary structure of the peptide and Protein Model Check (right pane).

FIGURE 32.1 Homepage of WHAT IF web interface; click on “Build/check/repair model” link (in the left‐hand ...

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