Supplementary Files for 'An Extended In silico Modeling Method' Integrating Homology, Threading and Dynamics to Devise Quality Protein Structures

A combination of homology modeling, threading and molecular dynamics was employed to predict the BAG3 protein structure. Unavailability of suitable templates to model the entire structure evoked us to model it using a novel extended modeling method. The 3-D structure prediction was primarily performed with I-TASSER and RaptorX servers using their default parameters. The best models were chosen from the server outputs based on integrated C-scores, B-factors, and low Root Mean Square (RMSD) values. These models were then used as templates to model the final structure of BAG3 using standalone python-based software MODELLER 10.0. This model-building procedure is identical to NMR spectroscopy-based structure elucidation. The modeled BAG3 was further refined through the GalaxyRefine server that improved the clash scores, poor rotamers, percentage Ramachandran outliers, and percentage bad side-chain rotamers. Finally, 2000 steps each of the steepest descent and conjugate gradient were performed in Swiss PDB viewer (SPDBV) using GROMOS96 force-field in-vacuo to optimise the modeled structure.