A Comparative Study of Homology Modeling Algorithms for NPTX2 Structure Prediction

Alzheimer’s Disease (AD) is a very prevalent neurological disorder that results in loss of memory due to the
weakening of synapses. Down-regulation of neuronal Pentraxin (NPTX2), a secretory protein is one of the causes
for AD. The structure of a protein is very important to predict the protein’s function. The experimental structure
of NTPX2 is not available yet. Hence in this study, three structures for NPTX2 were generated using Geno3D,
Modeller9.20 and Swiss Model. The quality of the protein was validated using PROCHECK and ERRAT. The
PROCHECK results for the structures modeled using Geno3D, Modeller, and Swiss Model showed 63%, 87.3%
and 88.2% residues in the most favoured regions and 2.5%, 0.0%, 0.00% residues in disallowed regions
respectively. The ERRAT results showed an overall quality factor of 90.27, 60.476, 77.54 respectively. The
model generated from Swiss Model can be considered as best model because in PROCHECK the model showed
high number of residues in the most favoured region and no residues were in the disallowed region. The ERRAT
result also showed an overall quality factor greater than 75. Though Geno3D showed a good overall quality
factor, it showed about 2.5% residues in the disallowed region. Structure Modeled using Modeller showed good
results for Ramachandran plot with no residues in the disallowed region. However, its overall quality factor was
only 60.476. These structures predicted can lay a foundation for discovering new drugs for the treatment of AD