Structure Assessment Analysis of Core Domain of Seven Protein Data Bank Entries of HIV-1 Protease Using Different in-silico Techniques

Despite the explosion in structural biologythe multi-dimensional complexity of the structure determination process of biomolecules like proteins significantly poses hindrances to drug development and study of interaction of ligands to the target. Since virtual screening has come up as a potential tool in the process of drug discovery the availability of macromolecular structures has limitations. Moreover, when more than one 3D structure is available it becomes all the more important to select the right structure for the study as the protein stability plays an important role in structure based drug design (SBDD). This study was carried out to find the most stable structure among the seven (2NMZ, 3FX5, 3BVB, 3IXO, 1KZK, 1ODW and 3HBO) structures HIV-1 Protease available in the protein data bank. The structure analysis of chain A of these PDB entries using in-silico approaches such as ANOLEA assessment server; Ramachandran plot analysis and Swiss model structure assessment server were performed. The structure assessment analysis revealed that there is a major difference among these PDB entries based on their energy and structural analysis. The PDB ID 2NMZ with a resolution of 0.97Åwas found to be the most stable and reliable structure for structure based drug designing.