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

Abstract

Abstract. Proteins are macromolecules that facilitate virtually every biological process. Information on functional and structural characteristics of proteins is invaluable in life sciences, but remain difficult to obtain, both computationally and experimentally.In recent work, we have introduced a novel method for functional characterization, which we refer to as protein energy profiling. The eProS (energy profile suite) is an online knowledgebase, toolbox and database that provides a webspace for protein energy profile analyses to the scientific community. The objective of eProS is to offer a free-for-all repository of energy profile data, annotations, visualizations, as well as tools that can aid in deducing relations complementing and supporting findings made by traditional bioinformatics methods.In this paper, we discuss the underlying biological and theoretical backgrounds used by implemented methods and tools, and also introduce recent enhancements and developments. eProS is available at http://bioservices.hs-mittweida.de/Epros.

Pyridine Nucleotide Coenzyme Specificity of p-Hydroxybenzoate Hydroxylase and Related Flavoprotein Monooxygenases

“…In the first step of energy profile analyses, energy profile distance trees were generated. As shown recently (Heinke and Labudde, 2013; Heinke et al, 2015) such distance trees can indicate functional and structural relations and, in case of PHBHs, can support the proposed molecular evolution. To obtain such distance trees, pairwise energy profile alignments were computed as elucidated and, for each energy profile alignment, the corresponding dScore was derived, leading to an energy profile distance matrix.…”

“…The phylogenetic analysis and its outcome is of major relevance for the identification of the pyridine nucleotide coenzyme binding sites. The above described methods were validated by the herein described protein energy profiling, which allows for drawing sequence—structure relations (Heinke et al, 2015).…”

“…The sequence of residue energy potentials ( E 1 ,…, E i ,…, E n ) corresponds to the protein's energy profile (Dressel et al, 2007; Heinke and Labudde, 2012, 2013; Heinke et al, 2015). In addition, an algorithm for aligning two energy profiles has been adapted from Mrozek et al (2007) which, besides detecting similarities and differences of residue energy potentials, can also give a distance scoring function (referred to as dScore) as a measure of global energy profile similarity of two energy profiles P 1 and P 2 (Heinke and Labudde, 2013; Heinke et al, 2015): eqnarrayright center leftdScorefalse(P1,P2false)=-logtrue(xr-xtrue¯PxOpt-xtrue¯Ptrue),…”