An optimal alignment of proteins energy characteristics with crisp and fuzzy similarity awards

Abstract

In the paper, we discuss the usage of constant and fuzzy similarity awards while establishing an optimal alignment between energy characteristics of two compared protein energy profiles. Single protein energy profile is a set of energy characteristics of various types of energy. The energy profile is determined for a given protein structure. We use these profiles to find protein molecules of the same structural protein family and inspect conformational modifications in their molecular structures as an effect of biochemical reactions or environmental influences. Energy profiles are received in the computational process based on the molecular mechanics theory. Afterwards, these profiles can be stored in the special purpose database (EDB) and used by the search engine to find similar fragments of protein structures on the energy level. To optimize the alignment path we use modified, energy-adapted Smith-Waterman method with one of the tested similarity awards.

eProS – A Bioinformatics Knowledgebase, Toolbox and Database for Characterizing Protein Function

“…Mrozek et al had introduced a dynamic programming approach for generating energy profile alignments [10,11]. Furthermore, they had shown that energy profile alignment analyses can be employed to investigate the changes of conformational energy distributions that can be caused by structural rearrangements as results of f.e.…”

“…Recent studies have demonstrated that sequences of energy values, referred to as energy profiles, obtained from protein structures using fine and coarse-grained energy models can be used to characterize protein functionality and structural features [10,11,7,9]. Mrozek et al had introduced a dynamic programming approach for generating energy profile alignments [10,11].…”

“…Furthermore, they had shown that energy profile alignment analyses can be employed to investigate the changes of conformational energy distributions that can be caused by structural rearrangements as results of f.e. protein-protein interactions or ligand binding [10]. Using fine-grained energy models based on all-atom energy breakdowns to obtain energy profiles, as proposed by Mrozek et al, considers a variety of physio-chemical information (van der Waals and electrostatic interactions as well as chemical bond potentials).…”

“…To implement an automated energy profile generation pipeline for large-scale analyses thus becomes challenging. However, such analyses can be of interest in structural biology, as entire protein folds and families can be investigated in the focus of characterizing and understanding the energetic features that determine protein structure, stability and function [10,11,7,9].…”

Alignment of protein structure energy patterns represented as sequences of Fuzzy Numbers

“…Certainly, increasing the value of the spread causes a danger of accidental alignments. In the paper [36] we presented results of the research carried for families of protein molecules. The research constitutes the statistical foundation for parameters of the previous versions of the EAST.…”