Chemoinformatics: a view of the field and current trends in method development.

https://www.cs.ucr.edu/~stelo/cpm/cpm05/cpm05_9_2_Fukagawa.pdf

Inferring a graph from path frequency

In this paper, we enumerate enumeration problems and algorithms. This survey is under construction. If you know some results not in this survey or there is anything wrong, please let me know.

Enumeration of Enumeration Algorithms.

Chemical compounds are usually represented as graph structured data in computers. In this review article, we overview several graph classes relevant to chemical compounds and the computational complexities of several fundamental problems for these graph classes. In particular, we consider the following problems: determining whether two chemical graphs are identical, determining whether one input chemical graph is a part of the other input chemical graph, finding a maximum common part of two input graphs, finding a reaction atom mapping, enumerating possible chemical graphs, and enumerating stereoisomers. We also discuss the relationship between the fifth problem and kernel functions for chemical compounds.

http://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/172449/1/csbj.201302004.pdf

Comparison and enumeration of chemical graphs

Inverse-QSPR/QSAR aims to solve the inverse problem of chemical structure generation based on QSPR/QSAR models, once the properties or activities are specified. To efficiently solve this problem, an exhaustive ring-system-based structure generation methodology was developed. The concept of the applicability domain (AD) is automatically acknowledged within the proposed strategy. The local AD is considered by introducing the probability distribution of a given data set, and the universal AD is considered using ring-system-based fragments in the training data set. Structures with desired properties or activities are enumerated by assembling fragments, including atomic elements, in a tree-like way. The usefulness of the proposed method is demonstrated through a case study of ligand design for the human alpha 2A adrenergic receptor (ADR2A_HUMAN). We succeeded in generating structures focusing only on a pre-defined region in chemical space, resulting in structures whose desired activity has a high likelihood being efficiently generated. In addition, the limitations of our proposed method and future challenges are discussed.

Ring-System-Based Exhaustive Structure Generation for Inverse-QSPR/QSAR.

Computational methods of enumerating chemical graphs have attained great importance in chemoinformatics since they lead to a variety of useful applications including structure determination of nove...

Branch-and-bound algorithms for enumerating treelike chemical graphs with given path frequency using detachment-cut.

This paper considers the problem of enumerating all non-isomorphic tree-like chemical graphs with given path frequency, where "tree-like" means that the graph can be viewed as a tree if multiple edges (i.e., edges with the same end points) and a benzene ring are treated as one edge and one vertex, respectively, and "path frequency" is a vector of the numbers of specified vertex-labeled paths that must be realized in every output. This and related problems have several potential applications such as classification of chemical compounds, structure determination using mass-spectrum and/or NMR and design of novel chemical compounds. For this problem, several studies have been done. Recently, Fujiwara et al. (2008) showed two formulations and for each of them, they gave a branch-and-bound algorithm, which combined efficient enumeration of non-isomorphic trees with bounding operations based on the path frequency and the atom-atom bonds to avoid the generation of invalid trees. In this paper, based on their work and a result of Nagamochi (2006), we introduce two new bounding operations, the detachment-cut and the H-cut, to further reduce the size of the search space. We performed computational experiments to compare our proposed algorithms with those of Fujiwara et al. (2008) using some chemical compound data obtained from the KEGG LIGAND database (http://www.genome.jp/kegg/ligand.html). The results show that our proposed algorithms are much faster than their algorithms.

Yusuke Ishida

Papers

Branch-and-bound algorithms for enumerating treelike chemical graphs with given path frequency using detachment-cut.

Improved algorithms for enumerating tree-like chemical graphs with given path frequency.

Improved algorithms for enumerating tree-like chemical graphs with given path frequency