Bhageerath: A web-enabled high performance computing software suite for predicting the tertiary structures of small globular proteins using all atom energy based ab initio methods

摘要

Protein folding considered as the holy grail of molecular biology continues to remain elusive even after six decades of the discovery of secondary structures. While significant advances have been made in tertiary structure prediction via knowledge-base driven Bioinformatics methodologies, all atom models, which promise a physicochemical understanding of the folding and detection of new folds, have yet to mature to be predictive. We describe here an energy based software suite for narrowing down the conformational search space of globular proteins. The protocol comprises eight different computational modules that form an automated pipeline and which is optimized to run on a cluster. The software suite initially predicts the secondary structure starting from the sequence and generates multiple trial structures by sampling the conformational space of the loop residues. It combines physics based potentials with biophysical filters and empirical energy functions to finally arrive at five plausible candidate structures for the native.