Dataset Information

Efficient enumeration of monocyclic chemical graphs with given path frequencies.

ABSTRACT:

Background

The enumeration of chemical graphs (molecular graphs) satisfying given constraints is one of the fundamental problems in chemoinformatics and bioinformatics because it leads to a variety of useful applications including structure determination and development of novel chemical compounds.

Results

We consider the problem of enumerating chemical graphs with monocyclic structure (a graph structure that contains exactly one cycle) from a given set of feature vectors, where a feature vector represents the frequency of the prescribed paths in a chemical compound to be constructed and the set is specified by a pair of upper and lower feature vectors. To enumerate all tree-like (acyclic) chemical graphs from a given set of feature vectors, Shimizu et al. and Suzuki et al. proposed efficient branch-and-bound algorithms based on a fast tree enumeration algorithm. In this study, we devise a novel method for extending these algorithms to enumeration of chemical graphs with monocyclic structure by designing a fast algorithm for testing uniqueness. The results of computational experiments reveal that the computational efficiency of the new algorithm is as good as those for enumeration of tree-like chemical compounds.

Conclusions

We succeed in expanding the class of chemical graphs that are able to be enumerated efficiently.

SUBMITTER: Suzuki M

PROVIDER: S-EPMC4049473 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Publications

Efficient enumeration of monocyclic chemical graphs with given path frequencies.

Suzuki Masaki M Nagamochi Hiroshi H Akutsu Tatsuya T

Journal of cheminformatics 20140530

<h4>Background</h4>The enumeration of chemical graphs (molecular graphs) satisfying given constraints is one of the fundamental problems in chemoinformatics and bioinformatics because it leads to a variety of useful applications including structure determination and development of novel chemical compounds.<h4>Results</h4>We consider the problem of enumerating chemical graphs with monocyclic structure (a graph structure that contains exactly one cycle) from a given set of feature vectors, where a ...[more]

PMID: 24955135

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Project description:Design problems of finding efficient patterns, adaptation of complex molecules to external environments, affinity of molecules to specific targets, dynamic adaptive behavior of chemical systems, reconstruction of 3D structures from diffraction data are examples of difficult to solve optimal design or inverse search problems. Nature inspires evolution strategies to solve design problems that are based on selection of successful adaptations and heritable traits over generations. To exploit this strategy in the creation of new materials, a concept of adaptive chemistry was proposed to provide a route for synthesis of self-adapting molecules that can fit to their environment. We propose a computational method of an efficient exhaustive search exploiting massive parallelization on modern GPUs, which finds a solution for an inverse problem by solving repetitively a direct problem in the mean field approximation. One example is the search for a composition of a copolymer that allows the polymer to translocate through a lipid membrane at a minimal time. Another example is a search of a copolymer sequence that maximizes the polymer load in the micelle defined by the radial core-shell potentials. The length and the composition of the sequence are adjusted to fit into the restricted environment. Hydrogen bonding is another pathway of adaptation to the environment through reversible links. A linear polymer that interacts with water through hydrogen bonds adjusts the position of hydrogen bonds along the chain as a function of the concentration field around monomers. In the last example, branching of the molecules is adjusted to external fields, providing molecules with annealed topology, that can be flexibly changed by changing external conditions. The method can be generalized and applied to a broad spectrum of design problems in chemistry and physics, where adaptive behavior in multi-parameter space in response to environmental conditions lead to non-trivial patterns or molecule architectures and compositions. It can further be combined with machine learning or other optimization techniques to explore more efficiently the parameter space.

Dataset Information

Efficient enumeration of monocyclic chemical graphs with given path frequencies.

Background

Results

Conclusions

Publications

Efficient enumeration of monocyclic chemical graphs with given path frequencies.

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