Review of ring perception algorithms for chemical graphs

Downs, Geoffrey M.; Gillet, Valerie J.; Holliday, John D.; Lynch, Michael

doi:10.1021/ci00063a007

Cited by 112 publications

(100 citation statements)

References 54 publications

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“…(Berger et al, 2004;May and Steinbeck, 2014). In this work, we use the smallest set of smallest rings (SSSR) (Downs et al, 1989) as defined by OpenBabel and many chemoinformatic software packages to enumerate the number of aromatic rings in this work. Ring enumeration is the only task specific to the software implementation, but otherwise the patterns specified can be ported to other software packages.…”

Section: Pattern Specification For Matching Substructuresmentioning

confidence: 99%

Technical Note: Development of chemoinformatic tools to enumerate functional groups in molecules for organic aerosol characterization

Ruggeri

Takahama

2016

Atmos. Chem. Phys.

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Abstract. Functional groups (FGs) can be used as a reduced representation of organic aerosol composition in both ambient and controlled chamber studies, as they retain a certain chemical specificity. Furthermore, FG composition has been informative for source apportionment, and various models based on a group contribution framework have been developed to calculate physicochemical properties of organic compounds. In this work, we provide a set of validated chemoinformatic patterns that correspond to (1) a complete set of functional groups that can entirely describe the molecules comprised in the α-pinene and 1,3,5-trimethylbenzene MCMv3.2 oxidation schemes, (2) FGs that are measurable by Fourier transform infrared spectroscopy (FTIR), (3) groups incorporated in the SIMPOL.1 vapor pressure estimation model, and (4) bonds necessary for the calculation of carbon oxidation state. We also provide example applications for this set of patterns. We compare available aerosol composition reported by chemical speciation measurements and FTIR for different emission sources, and calculate the FG contribution to the O : C ratio of simulated gasphase composition generated from α-pinene photooxidation (using the MCMv3.2 oxidation scheme).

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Section: Pattern Specification For Matching Substructuresmentioning

confidence: 99%

Technical Note: Development of chemoinformatic tools to enumerate functional groups in molecules for organic aerosol characterization

Ruggeri

Takahama

2016

Atmos. Chem. Phys.

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“…With this information, we developed a robust ring perception method with dramatically reduced computing time. This method may have considerable influence on various fields of science and engineering, including electrical circuit testing (23,24), periodic timetable planning (25), dealing with rigidity of framework structure (26), chemical ring perception (9), and in network analysis of complicated biological pathways with thousands of nodes.…”

Section: Resultsmentioning

confidence: 99%

“…Some theoretical aspects are summarized by Downs et al (9). Although various methods to find SSSRs have been developed using algorithms based on both methods, none are robust (10).…”

Section: Figmentioning

confidence: 99%

“…Because large-membered rings may contain smaller rings and are not members of {C SSSR }, ring identification starts from the smallest ring (e.g., a three-membered ring) and repeated with increasing numbers of ring members until the total number of SSSRs reaches the theoretical number of smallest rings, n SSSR (nullity, cyclomatic number), as defined by the Euler rule (9).…”

Section: Figmentioning

confidence: 99%

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A robust method for searching the smallest set of smallest rings with a path-included distance matrix

Lee

Kang

Cho

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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The perception of rings in graphs is widely used in many fields of science and engineering. Algorithms developed in the chemistry community, called smallest set of smallest rings (SSSR), applicable only for simple graphs or chemical structures. In contrast, algorithms developed by the computer science community, called minimum cycle basis (MCB) are identical to SSSR yet exhibit greater robustness. MCB-based algorithms can correctly reveal all rings in any complex graph. However, they are slow when applied to large complex graphs due to the inherent limitations of the algorithms used. Here, we suggest a heuristic method called RP-Path. This method is a robust, simple, and fast search method with O ( n 3 ) runtime algorithm that correctly identifies the SSSR of all of the test case of complex graphs by using approach different from the MCB-based method. Both the robustness and improvement in speed are achieved by using a path-included distance matrix and describing the characteristic features of rings in the matrix. This method is accurate and faster than any other methods and may find many application in various fields of science and engineering that use complicated graphs with thousands of nodes.

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“…The important role played by ring systems in drug discovery has meant that much effort has been devoted over very many years to the development of automated methods for their identification, representation and searching (see, e.g., [1][2][3][4][5][6][7][8][9]). Recent developments in combinatorial chemistry mean that it is now possible to synthesise large libraries of compounds, consisting of a central ring system to which are attached a range of different substituents [10].…”

Section: Introductionmentioning

confidence: 99%

Scaffold Searching: Automated Identification of Similar Ring Systems for the Design of Combinatorial Libraries

Bohl¹,

Dunbar

Gifford

et al. 2002

Quant. Struct.‐Act. Relat.

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Rigid ring systems can be used to position receptor-binding functional groups in 3D space and they thus play an increasingly important role in the design of combinatorial libraries. This paper discusses the use of shape-similarity methods to identify ring systems that are structurally similar to, and aligned with, a user-defined target ring system. These systems can be used as alternative scaffolds for the construction of a combinatorial library.

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Review of ring perception algorithms for chemical graphs

Cited by 112 publications

References 54 publications

Technical Note: Development of chemoinformatic tools to enumerate functional groups in molecules for organic aerosol characterization

Technical Note: Development of chemoinformatic tools to enumerate functional groups in molecules for organic aerosol characterization

A robust method for searching the smallest set of smallest rings with a path-included distance matrix

Scaffold Searching: Automated Identification of Similar Ring Systems for the Design of Combinatorial Libraries

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