Representation of the Molecular Topology of Cyclical Structures by Means of Cycle Graphs. 2. Application to Clustering of Chemical Databases

Abstract

The great size of chemical databases and the high computational cost required in the atom-atom comparison of molecular structures for the calculation of the similarity between two chemical compounds necessitate the proposal of new clustering models with the aim of reducing the time of recovery of a set of molecules from a database that satisfies a range of similarities with regard to a given molecule pattern. In this paper we make use of the information corresponding to the cycles existing in the structure of molecules as an approach for the classification of chemical databases. The clustering method here proposed is based on the representation of the topological structure of molecules stored in chemical databases through its corresponding cycle graph. This method presents a more appropriate behavior for others described in the bibliography in which the information corresponding to the cyclicity of the molecules is also used.

Representation of the Molecular Topology of Cyclical Structures by Means of Cycle Graphs. 3. Hierarchical Model of Screening of Chemical Databases

“…(1) the cycle level represents CG graphs, graphs whose nodes represent cycles of the molecule and whose edges represent the common nodes among the cycles. , …”

“…The cycle graphs (CG) and cycle and chain graphs (CCG) , (molecular graphs based on the cyclicity of the structure) represent a clear example. These graphs have demonstrated their utility for extraction of topological invariants contributing measures of complexity, cyclicity, and symmetry of the molecular structures and in the clustering of chemical databases.…”

“…In this paper an abstract model of screening is described that considers the hierarchical paradigm of classification of databases based on the cycle and chain graphs. , The screening model is based on consideration of the structural entitiescycles and acyclic chainspresent in the molecular graphs and in representation, at different levels of abstraction, of the molecular shape using these structural entities by means of an easy and simple graphic notation.…”

“…The graph of equivalent cycles ECG is built, , a homomorphic graph to the GC graph, in the following way.…”

Algorithm for Exhaustive and Nonredundant Organic Stereoisomer Generation

“…Computer-assisted exhaustive generation of stereoisomers is an important contribution to structure elucidation − and molecular design. − At present, areas such as drug or material design are relevant and also require this type of computer system and software. In that context computational generator systems − are an important complement for systems such as similarity searching, − database systems, − descriptor calculators of different types, − and many others − that could became part of a virtual high throughput screening system oriented in a predictive way as a useful making decision tool.…”