Incorporating Protein Sequence and Evolutionary Information in a Structural Pattern Matching Approach for Contact Maps

Content Provider	CiteSeerX
Author	Radwan, Hazem Ahmed, A. Glasgow, Janice I.
Abstract	Abstract — Protein structure prediction from the primary sequence remains a major challenging problem in bioinformatics. The main issue here is that it is computationally complex to reliably predict the full three-dimensional structure of a protein from its one-dimensional sequence. A two-dimensional contact map has, therefore, been used as an intermediate step in this problem. A contact map is a simpler, yet representative, alternative for the three-dimensional protein structure. In this paper, we propose a pattern matching approach to locate similar substructural patterns between protein contact map pairs using protein sequence information. These substructural patterns are of particular interest to our research, because they could ultimately be used as building blocks for a bottom-up approach to protein structure prediction from contact maps. We further demonstrate how to improve the performance of identifying these patterns by incorporating both protein sequence and evolutionary information. The results are benchmarked using a large standard protein dataset. We performed statistical analyses (e.g., Harrell-Davis Quantiles and Bagplots) that show sequence information is more helpful in locating short-range contacts than long-range contacts. Moreover, incorporating evolutionary information has remarkably improved the performance of locating similar short-range contacts between contact map pairs. Keywords-protein structure prediction; protien contact maps; structural pattern matching; evolutionary information; harrell-davis quantiles. I.
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Subject Keyword	Evolutionary Information Contact Map Protein Sequence Structural Pattern Matching Approach Harrell-davis Quantiles Bottom-up Approach Similar Substructural Pattern Long-range Contact Protein Contact Map Pair Structure Prediction Primary Sequence Statistical Analysis Building Block Intermediate Step Short-range Contact Similar Short-range Contact Abstract Protein Structure Prediction Three-dimensional Protein Structure Large Standard Protein Dataset Main Issue Substructural Pattern Full Three-dimensional Structure Contact Map Pair Sequence Information Protein Sequence Information Particular Interest Keywords-protein Structure Prediction One-dimensional Sequence Structural Pattern Matching Major Challenging Problem Two-dimensional Contact Map
Content Type	Text