Edgar E. Daza

Graph Theoretical Similarity Approach To Compare Molecular Electrostatic Potentials

In this work we introduce a graph theoretical method to compare MEPs, which is independent of molecular alignment. It is based on the edit distance of weighted rooted trees, which encode the geometrical and topological information of Negative Molecular Isopotential Surfaces. A meaningful chemical classification of a set of 46 molecules with different functional groups was achieved. Structure--activity relationships for the corticosteroid binding affinity (CBG) of 31 steroids by means of hierarchical clustering resulted in a clear partitioning in high, intermediate, and low activity groups, whereas the results from quantitative structure--activity relationships, obtained from a partial least-squares analysis, showed comparable or better cross-validated correlation coefficients than the ones reported for previous methods based solely in the MEP.

Metabolic networks: beyond the graph.

Drugs are devised to enter into the metabolism of an organism in order to produce a desired effect. From the chemical point of view, cellular metabolism is constituted by a complex network of reactions transforming metabolites one in each other. Knowledge on the structure of this network could help to develop novel methods for drug design, and to comprehend the root of known unexpected side effects. Many large-scale studies on the structure of metabolic networks have been developed following models based on different kinds of graphs as the fundamental image of the reaction network. Graphs models, however, comport wrong assumptions regarding the structure of reaction networks that may lead into wrong conclusions if they are not taken into account. In this article we critically review some graph-theoretical approaches to the analysis of centrality, vulnerability and modularity of metabolic networks, analyzing their limitations in estimating these key network properties, consider some proposals explicit or implicitly based on directed hypergraphs regarding their ability to overcome these issues, and review some recent implementation improvements that make the application of these models in increasingly large networks a viable option.

Polynomial expressions for rydberg-klein-rees curves of diatomic covalent molecules

Abstract The ground-state potential-energy curves for 17 diatomic covalent molecules were calculated using a recent version of the functional method. We consider a point at infinity to improve the long-range potential behaviour. For all these molecules the results obtained are satisfactory.

Molecular Electrostatic Potential as a Graph

We present several procedures to represent molecular electrostatic potential as a graph, based on the pattern of critical points and their neighborhood relations. This representation is used for the molecular electrostatic comparison, which is reduced to a comparison of tree-type graphs. Several methods to compare trees are also presented. The applications of this algorithm to compare and classify molecules through their electrostatic potential are illustrated.

On Molecular Graph Comparison

Since the last half of the nineteenth century, molecular graphs have been present in several branches of chemistry. When used for molecular structure representation, they have been compared after mapping the corresponding graphs into mathematical objects. However, direct molecular comparison of molecular graphs is a research field less explored. The goal of this mini-review is to show some distance and similarity coefficients which were proposed to directly compare molecular graphs or which could be useful to do so.