Using Machine Learning in Accuracy Assessment of Knowledge-Based Energy and Frequency Base Likelihood in Protein Structures

Many aspects of the study of protein folding and dynamics have been affected by the accumulation of data about native protein structures and recent advances in machine learning. Computational methods for predicting protein structures from their sequences are now heavily based on machine learning tools and on approaches that extract knowledge and rules from data using probabilistic models. Many of these methods use scoring functions to determine which structure best fits a native protein sequence. Using computational approaches, we obtained two scoring functions: knowledge-based energy and likelihood of base frequency, and we compared their accuracy in measuring the sequence structure fit. We compared the machine learning models’ accuracy of predictions for knowledge-based energy and likelihood values to validate our results, showing that likelihood is a more accurate scoring function than knowledge-based energy.