Breadth-First Search Approach to Enumeration of Tree-Like Chemical Compounds

Zhao, Yang; Hayashida, Morihiro; Jindalertudomdee, Jira; Nagamochi, Hiroshi; Akutsu, Tatsuya

doi:10.1142/s0219720013430075

Cited by 5 publications

(7 citation statements)

References 16 publications

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“…We propose an algorithm BfsBenNaphEnum for enumerating chemical compounds containing benzene rings and naphthalene rings as cyclic structures. BfsBenNaphEnum utilizes our previously developed algorithms BfsSimEnum, BfsMulEnum [ 18 ], and assigns carbon position lists.…”

Section: Methodsmentioning

confidence: 99%

“…It was reported that OMG is able to deal with different valences for a kind of atom, and was not efficient for several instances compared with MOLGEN. While the remaining ones, such as EnuMol [ 16 , 17 ] as well as BfsSimEnum and BfsMulEnum [ 18 ], have a limitation of the structure of enumerated compounds, such as acyclic compounds for BfsSimEnum and BfsMulEnum and compounds with no cycle except for benzene rings for EnuMol, the methods consume significantly less computational time. There are also related application softwares, e.g.…”

Section: Introductionmentioning

confidence: 99%

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Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order

et al. 2016

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BackgroundDrug discovery and design are important research fields in bioinformatics. Enumeration of chemical compounds is essential not only for the purpose, but also for analysis of chemical space and structure elucidation. In our previous study, we developed enumeration methods BfsSimEnum and BfsMulEnum for tree-like chemical compounds using a tree-structure to represent a chemical compound, which is limited to acyclic chemical compounds only.ResultsIn this paper, we extend the methods, and develop BfsBenNaphEnum that can enumerate tree-like chemical compounds containing benzene rings and naphthalene rings, which include benzene isomers and naphthalene isomers such as ortho, meta, and para, by treating a benzene ring as an atom with valence six, instead of a ring of six carbon atoms, and treating a naphthalene ring as two benzene rings having a special bond. We compare our method with MOLGEN 5.0, which is a well-known general purpose structure generator, to enumerate chemical structures from a set of chemical formulas in terms of the number of enumerated structures and the computational time. The result suggests that our proposed method can reduce the computational time efficiently.ConclusionsWe propose the enumeration method BfsBenNaphEnum for tree-like chemical compounds containing benzene rings and naphthalene rings as cyclic structures. BfsBenNaphEnum was from 50 times to 5,000,000 times faster than MOLGEN 5.0 for instances with 8 to 14 carbon atoms in our experiments.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order

et al. 2016

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“…In the previous study, to reduce the search space (i.e., the size of a family tree), we utilized two constraints for molecular trees, center-rooted , and left-heavy [6]. Bfs-SimEnum outputs only center-rooted and left-heavy molecular trees.…”

Section: Preliminariesmentioning

confidence: 99%

“…Finally, a generated molecular tree is discarded if it is not in normal form [6]. We say that a molecular tree T is in normal form if T is center-rooted and left-heavy, and the center of T is a single vertex, or the center is an edge ( r, v ) and T ( v ) ≥ m T v ( r ) holds, where r is the root of T , and T v ( r ) denotes the subtree rooted at r obtained by subtracting T ( v ) from T .…”

Section: Preliminariesmentioning

confidence: 99%

“…EnuMol enumerates tree-like chemical compounds, or molecular tree graphs, by depth-first search (DFS) order [3-5]. In our previous study, we developed efficient algorithms BfsSimEnum and BfsMulEnum for enumeration of tree-like chemical compounds by breadth-first search (BFS) order [6]. For many instances, execution times by BfsSimEnum and BfsMulEnum were shorter than or comparable to those by the DFS-type method.…”

Section: Introductionmentioning

confidence: 99%

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Parallelization of enumerating tree-like chemical compounds by breadth-first search order

et al. 2015

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Enumeration of chemical compounds greatly assists designing and finding new drugs, and determining chemical structures from mass spectrometry. In our previous study, we developed efficient algorithms, BfsSimEnum and BfsMulEnum for enumerating tree-like chemical compounds without and with multiple bonds, respectively. For many instances, our previously proposed algorithms were able to enumerate chemical structures faster than other existing methods.Latest processors consist of multiple processing cores, and are able to execute many tasks at the same time. In this paper, we develop three parallelized algorithms BfsEnumP1-3 by modifying BfsSimEnum in simple manners to further reduce execution time. BfsSimEnum constructs a family tree in which each vertex denotes a molecular tree. BfsEnumP1-3 divide a set of vertices with some given depth of the family tree into several subsets, each of which is assigned to each processor.For evaluation, we perform experiments for several instances with varying the division depth and the number of processors, and show that BfsEnumP1-3 are useful to reduce the execution time for enumeration of tree-like chemical compounds. In addition, we show that BfsEnumP3 achieves more than 80% parallelization efficiency using up to 11 processors, and reduce the execution time using 12 processors to about 1/10 of that by BfsSimEnum.

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Universally Exhaustive Generation of Molecular Structures and Prediction of Their Electronic States Using Machine Learning for N‐type Organic Transistor Materials

Ohno

Hanna

Iino

et al. 2023

Chemistry An Asian Journal

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We have proposed a new method for the exploration of organic functional molecules, using an exhaustive molecular generator combined without combinatorial explosion and electronic state predicted by machine learning and adapted for developing n‐type organic semiconductor molecules for field‐effect transistors. Our method first enumerates skeletal structures as much as possible and next generates fused ring structures using substitution operations for atomic nodes and bond edges. We have succeeded in generating more than 4.8 million molecules. We calculated the electron affinity (EA) of about 51 thousand molecules with DFT calculation and trained the graph neural networks to estimate EA values of generated molecules. Finally, we obtained the 727 thousand molecules as candidates that satisfy EA values over 3 eV. The number of these possible candidate molecules is far beyond what we have been able to propose based on our knowledge and experience in synthetic chemistry, indicating a wide diversity of organic molecules.

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Breadth-First Search Approach to Enumeration of Tree-Like Chemical Compounds

Cited by 5 publications

References 16 publications

Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order

Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order

Parallelization of enumerating tree-like chemical compounds by breadth-first search order

Universally Exhaustive Generation of Molecular Structures and Prediction of Their Electronic States Using Machine Learning for N‐type Organic Transistor Materials

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