Section 3 Research Chapters

**55**

**Chapter 4**

**Abstract**

GPCR-EXP, GPCRdb

**1. Introduction**

Importance of Homology

Structures of GPCRs

*and Diwakar Kumar*

*Ananthasri Sailapathi, Seshan Gunalan,* 

Modeling for Predicting the

*Kanagasabai Somarathinam, Gugan Kothandan* 

Homology modeling is one of the key discoveries that led to a rapid paradigm shift in the field of computational biology. Homology modeling obtains the three dimensional structure of a target protein based on the similarity between template and target sequences and this technique proves to be efficient when it comes to studying membrane proteins that are hard to crystallize like GPCR as it provides a higher degree of understanding of receptor-ligand interaction. We get profound insights on structurally unsolved, yet clinically important drug targeting proteins through single or multiple template modeling. The advantages of homology modeling studies are often used to overcome various problems in crystallizing GPCR proteins that are involved in major disease-related pathways, thus paving way to more structural insights via in silico models when there is a lack of experimentally solved structures. Owing to their pharmaceutical significance, structural analysis of various GPCR proteins using techniques like homology modeling is of utmost importance.

**Keywords:** membrane protein, bovine rhodopsin, template-based modeling,

structure of proteins whose structures were otherwise difficult to solve.

The comparative modeling of proteins, more popularly known as homology modeling among the research community, is a computational procedure that constructs three dimensional atomic resolution structure of a 'target' protein, the structure of it is unknown. A new structure for the target protein is modeled using its own amino acid sequence and a known experimental structure of a homologous protein as a template based upon which the model is constructed. This template-based modeling technique became a plausible computational technique because of the fact that evolutionary related proteins share a similar structure [1]. This undeniable truth led to the famous outbreak of using homology modeling to determine the three dimensional

One such family of protein that poses a great challenge to study is membrane

proteins due to their partially flexibility and lack of stability. The surface of membrane proteins is also comparatively hydrophobic and can only be extracted
