Journal of Proteomics & Bioinformatics
Open Access

Abstract

Comparative Investigation of Techniques Used for Mtr Homology Model Refinement

Vivek Kumar, Debra Meyer and Namrita Lall

Mtr homology model requires structural refinement to erroneous regions that are not aligned correctly to the template. In this study, refinement methods: LM, MDS, 3Drefine, GalaxyRefine and FG-MD were compared. Errat plot showed a gradual increase in the overall quality factor of ~96% using LM, while there was abrupt increment of >90% for MDS, GalaxyRefine and FG-MD. In the case of LM, structure compatibility decreased to ~53%, whereas it increased to >74% in case of MDS and GalaxyRefine. Ramachandran plot showed residues in favoured region mobilized to allowed and outlier regions in LM, which led to an increased in 3.5% outlier residues. Similarly, 3Drefine and FG-MD also showed increase in outlier residues. In contrast, % residues available in favoured and outlier regions are observed to mobilize into allowed region in case of MDS and GalaxyRefine leading to decreased outlier residues. In addition, similarity score like RMSD, TM-score, MaxSub score and GDT-TS score were observed better in case of 3Drefine, GalaxyRefine and FG-MD. ProSA z-score also showed about -8 and stability in protein folds for MDS, 3Drefine, GalaxyRefine and FG-MD. The current study is a prototype which depicts comparison of used methods emphasizing MD-based techniques should be used for structural refinement.