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R. P. Mondaini

Publications and source records attributed to R. P. Mondaini.

6 recordsLinked to original sources
arXiv2018

The Protein Family Classification in Protein Databases via Entropy Measures

In the present work, we review the fundamental methods which have been developed in the last few years for classifying into families and clans the distribution of amino acids in protein databases. This is done through functions of random variables, the Entropy Measures of probabilities of occurrence of the amino acids. An intensive study of the Pfam databases is presented with restrictions to families which could be represented by rectangular arrays of amino acids with m rows (protein domains) and n columns (amino acids). This work is also an invitation to scientific research groups worldwide to undertake the statistical analysis with different numbers of rows and columns since we believe in the mathematical characterization of the distribution of amino acids as a fundamental insight on the determination of protein structure and evolution.

q-bio.BM↗
arXiv2005

A New Approach to the Study of the Smith + Smith Conjecture

The search for a point set configurations of the R^3 space which contains the smallest value of the Euclidean Steiner Ratio is almost finished. In the present work we introduce some analytical methods which aim to support a famous conjecture of Discrete Mathematics literature. The relations of this problem with that of molecular architecture in terms of motivation as well as application of the formulae obtained is also emphasized.

math-ph↗
arXiv2005

Modelling the Biomacromolecular Structure with Selected Combinatorial Optimization Techniques

Modern approaches to the search of Relative and Global minima of potential energy function of Biomacromolecular structures include techniques of combinatorial optimization like the study of Steiner Points and Steiner Trees. These methods have been successfully applied to the problem of modelling the configurations of the average atomic positions when they are disposed in the usual sequence of evenly spaced points along right circular helices. In the present contribution, we intend to show how these methods can be adapted for explaining the advantages of introducing the concept of a Steiner Ratio Function (SRF). We also show how this new concept is adequate for fitting the results obtained by computing experiments and for providing an improvement to these results if we use the restriction of working with Full Steiner Trees.

math-ph↗