Remote homology detection of proteins using 3D models enriched with physicochemical properties

Abstract

In this paper, a new method for remote protein homology detection called remote-3DP, is presented. The remote-3DP method is based on both predicted 3D information and physiochemical properties of amino acids. The remote-3DP method considers only 10 structural models to represent a protein and to distinguish between remote homologues and non-remote homologues in 54 SCOP families. The low dimensionality of the protein representation allows us to use different classification techniques and discover which one works better for each SCOP family. In this paper, we show that including a physicochemical property along with predicted 3D information into a local structural element, actually improves the accuracy in remote homology detection. The highest ROC score for a set of models that includes 3D information and the Hydropathy index reaches 0.953 on the SCOP 1.53 dataset. In addition, a model that ensembles the outputs of 10 physicochemical properties is built to make a consensus decision. The consensus strategy reaches a ROC score of 0.963 on the SCOP 1.53 dataset, surpassing the current methods based on sequence composition which accuracy range from 0.87 to 0.92. is in crisis. The process consisted of a literature review on this issue and an analysis of the information submitted. According to the results of the analysis to the 23 works of the final sample, one of the major causes of this crisis is that there is an inadequate interpretation of engineering concept by industry, the state, academia and society. The industry has no clarity about the roles that can play the most engineers; the State does not exercise an adequate control, regulation or prospects for the need of the country in engineering issues; training processes in the academy not attend efficiently the needs of the sector and seem to be in the opposite direction to the development of the globalized world, and society unknown the profession and value more occupations such as music, television, modeling and sport.Keyword: Engineering, engineering crisis, training processes, training professorial.