There are 2037 published reports of membrane protein structures in this database.
Figure 1 shows the total number of membrane protein structures deposited in PDB as of August 2020 and this data was derived from the mpstruc database. The surface of membrane proteins is also comparatively hydrophobic and can only be extracted from the cell membrane with detergents which cause challenges at many levels, including expression, solubilization, purification, crystallization, data collection and structure solution. One such family of protein that poses a great challenge to study is membrane proteins due to their partially flexibility and lack of stability. This undeniable truth led to the famous outbreak of using homology modeling to determine the three dimensional structure of proteins whose structures were otherwise difficult to solve. This template-based modeling technique became a plausible computational technique because of the fact that evolutionary related proteins share a similar structure. 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. 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. Owing to their pharmaceutical significance, structural analysis of various GPCR proteins using techniques like homology modeling is of utmost importance. 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. We get profound insights on structurally unsolved, yet clinically important drug targeting proteins through single or multiple template modeling.
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. Homology modeling is one of the key discoveries that led to a rapid paradigm shift in the field of computational biology.
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