O'Reilly logo

Computational Intelligence and Pattern Analysis in Biological Informatics by Jason T. Wang, Sanghamitra Bandyopadhyay, Ujjwal Maulik

Stay ahead with the world's most comprehensive technology and business learning platform.

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, tutorials, and more.

Start Free Trial

No credit card required

CHAPTER 8

CHARACTERIZATION OF CONFORMATIONAL PATTERNS IN ACTIVE AND INACTIVE FORMS OF KINASES USING PROTEIN BLOCKS APPROACH

G. AGARWAL, D. C. DINESH, N. SRINIVASAN, AND ALEXANDRE G. DE BREVERN

8.1 INTRODUCTION

The three-dimensional (3D) structure, which is critical for the function of a protein is usually conserved during evolution. It holds a wealth of information that can be harnessed to understand various aspects of proteins including sequence–structure–function–evolutionary relationships. The understanding of these complex relationships is facilitated by a simplistic one-dimensional (1D) representation of the tertiary structure like a string of letters.

The advantage is an easier visualization without losing much of the vital information due to dimension reduction. Using various methodologies, local structural patterns that can be combined to generate the desired backbone conformation have been identified that use atomic coordinates characterising 3D structures of proteins. Protein blocks (PBs) is a set of 16 such local structural descriptors, denoted by letters ap that have been derived using unsupervised machine learning algorithms and can approximate the 3D space of proteins. Each letter corresponds to a pentapeptide with distinct values of eight dihedral angles (Φ,Ψ).

We demonstrate the use of PBs to characterize structural variations in enzymes using kinases as the case study. A protein kinase undergoes structural alterations as it switches to its active conformation ...

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, interactive tutorials, and more.

Start Free Trial

No credit card required