Basic Applied Bioinformatics

CHAPTER 31Prediction of Tertiary Structure of Protein: Ab Initio Approach

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

31.1 INTRODUCTION

Protein folding is dictated by the physical forces acting on the atoms of the protein. In general, the most accurate way of formulating the protein‐folding or structure prediction problem is in terms of an all‐atom model subject to the physical forces. Energy functions compatible with the protein representation are considered during the ab initio approach. Faster algorithms are developed to search the best‐fitting formation, in order to minimize the energy function while predicting the tertiary structure ab initio.

31.1.1 Principle

To predict the protein structure based on physical principles (rather than comparative homology using the previously reported structures). The structural conformations that minimize the energy function are evaluated for the structures that the protein is likely to adopt under native conditions.

31.2 OBJECTIVE

To predict the tertiary structure of a peptide using an ab initio approach with the online tool RaptorX.

31.3 PROCEDURE (RAPTORX)

1. Suppose we need to predict the structure of the given protein sequence (Bubaline Dicer I; NCBI Protein Accession Number BAP00765.1): >BAP00765|Bbu_Dicer1

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