Transputer implementations of chemical substructure searching algorithms

Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2

Background

Searching for substructures in molecules belongs to the most elementary tasks in cheminformatics and is nowadays part of virtually every cheminformatics software. The underlying algorithms, used over several decades, are designed for the application to general graphs. Applied on molecular graphs, little effort has been spend on characterizing their performance. Therefore, it is not clear how current substructure search algorithms behave on such special graphs. One of the main reasons why such an evaluation was not performed in the past was the absence of appropriate data sets.

Results

In this paper, we present a systematic evaluation of Ullmann’s and the VF2 subgraph isomorphism algorithms on molecular data. The benchmark set consists of a collection of 1235 SMARTS substructure expressions and selected molecules from the ZINC database. The benchmark evaluates substructures search times for complete database scans as well as individual substructure-molecule pairs. In detail, we focus on the influence of substructure formulation and size, the impact of molecule size, and the ability of both algorithms to be used on multiple cores.

Conclusions

The results show a clear superiority of the VF2 algorithm in all test scenarios. In general, both algorithms solve most instances in less than one millisecond, which we consider to be acceptable. Still, in direct comparison, the VF2 is most often several folds faster than Ullmann’s algorithm. Additionally, Ullmann’s algorithm shows a surprising number of run time outliers.

On enumeration of congeners of common persistent organic pollutants

Congeners are molecules based on the same carbon skeleton but different by the number of substituents and/or a substitution pattern. Various Persistent Organic Pollutants (POPs) exist in the environment as families of halogen substituted congeners and/or their hydroxyl and methoxy substituted derivatives. Numbers of possible congeners resulting from substitution of a parent POP molecule with only one type of chemical group are generally available. At the same time, numbers of mixed-substituent congeners have not been counted and presented yet, although there is an increasing interest in such as is the increasing number of research articles presenting results on already identified Cl-/Br-mixed type congeners and/or their HO-/CH(3)O-mixed metabolites. We have enumerated and counted possible mixed-substituent congeners of common POPs. This article presents the obtained numbers for congener families of benzene, naphthalene, biphenyl, diphenyl ether, dibenzo-p-dioxin, dibenzofuran, anthracene, pyrene and others and obtained by substitution of up to five chemical group types.

From chemical documentation to chemoinformatics: 50 years of chemical information science

This paper summarizes the historical development of the discipline that is now called `chemoinformatics'. It shows how this has evolved, principally as a result of technological developments in chemistry and biology during the past decade, from long-established techniques for the modelling and searching of chemical molecules. A total of 30 papers, the earliest dating back to 1957, are briefly summarized to highlight some of the key publications and to show the development of the discipline.

Chemoinformatics: Past, Present, and Future†

The history of chemoinformatics is reviewed in a decade-by-decade manner from the 1940s to the present. The focus is placed on four traditional research areas: chemical database systems, computer-assisted structure elucidation systems, computer-assisted synthesis design systems, and 3D structure builders. Considering the fact that computer technology has been one of the major driving forces of the development of chemoinformatics, each section will start from a brief description of the new advances in computer technology of each decade. The summary and future prospects are given in the last section.

Searching for pharmacophoric patterns in databases of three-dimensional chemical structures

This paper provides an overview of the research that has been carried out in Sheffield over the last decade into searching techniques for databases of three-dimensional (3D) chemical structures. A 3D structure or query pattern is represented by a labelled graph, in which the nodes and the edges of the graph are used to represent atoms and the associated inter-atomic distances, respectively. The presence of a pharmacophore in each of the structures in a database can then be tested by means of a subgraph isomorphism algorithm, the computational requirements of which are minimized by the use of an initial screening procedure that eliminates the majority of the structures from the subgraph-isomorphism search. Analogous graph-based representation and searching methods can also be used with flexible 3D structures: in this case, the edges of the graphs represent inter-atomic distance ranges and a final conformational search needs to be carried out for those molecules that match the query pharmacophore in the subgraph-isomorphism search. The paper also reviews related work on the automatic identification of pharmacophoric patterns and on 3D similarity searching.