Atom-by-atom searching using massive parallelism. Implementation of the Ullmann subgraph isomorphism algorithm on the distributed array processor

Willett, Peter; Wilson, Terence; Reddaway, S.F.

doi:10.1021/ci00002a008

Cited by 12 publications

(6 citation statements)

References 10 publications

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“…Several papers have been written espousing various published subgraph isomorphism/chemical substructure searching algorithms, 15,17,21,[68][69][70][71][72][73][74][75] but there is a general consensus that the Ullman algorithm 76 is the most appropriate for geometric chemical substructure searching. 16,[65][66][67][68][77][78][79][80][81][82][83][84][85][86][87][88][89][90] For this application, a dynamic implementation of the Ullman algorithm was employed. The Ullman algorithm is composed of a depthfirst search (DFS) and an intermittent relaxation procedure.…”

Section: Mosdap Modular Operationsmentioning

confidence: 99%

“…For the development of MOSDAP, a literature search was performed in an attempt to discern the most efficient algorithm applicable to chemical substructure searching. Several papers have been written espousing various published subgraph isomorphism/chemical substructure searching algorithms, ,,,− but there is a general consensus that the Ullman algorithm is the most appropriate for geometric chemical substructure searching. ,− ,− For this application, a dynamic implementation of the Ullman algorithm was employed. The Ullman algorithm is composed of a depth-first search (DFS) and an intermittent relaxation procedure.…”

Section: Mosdap Modular Operationsmentioning

confidence: 99%

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Molecular Structure Disassembly Program (MOSDAP): A Chemical Information Model To Automate Structure-Based Physical Property Estimation

Raymond

Rogers

1999

J. Chem. Inf. Comput. Sci.

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Chemical information theory and molecular structure searching have long been used as computational aids to researchers in the pharmaceutical field to estimate molecular structure−property relationships and to assist in drug design. Tailored to these and other specific applications, such endeavors have been expensive to develop and typically are very specialized. Often, they are not readily available and are not a part of the open literature. Because the number of chemicals in commercial use is growing daily (with over 18 million molecular species now catalogued by Chemical Abstract Services), there is a need among engineers in the chemical process industries for predictive structure−property algorithms. The most common and useful methods are those based on group contribution that require only the chemical structure of interest. Unfortunately, each group contribution method typically has its own fragment library and specialized rules, making such models difficult to automate for general use by the engineering community. This work, which has culminated in the creation of the Molecular Structure Disassembly Program (MOSDAP) software, is focused on combining and improving upon the best published methods in four areas: (1) lexicographical entry of structures, (2) prescreening methods, (3) abstract representation of molecular structures, and (4) structure manipulation routines. Additional features, such as a custom modification of the published Ullman substructure search algorithm specific to molecular graphs and an exact cover procedure to elucidate structural ambiguities, have been added by us to address specific problems encountered in group contribution methods. At present, most of the popular published group contribution methods can be automated using MOSDAP as a general engine for converting formula line notation (e.g., SMILES strings) into corresponding sets of functional groups and/or features.

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Section: Mosdap Modular Operationsmentioning

confidence: 99%

Section: Mosdap Modular Operationsmentioning

confidence: 99%

Molecular Structure Disassembly Program (MOSDAP): A Chemical Information Model To Automate Structure-Based Physical Property Estimation

Raymond

Rogers

1999

J. Chem. Inf. Comput. Sci.

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“…Furthermore, graphs allow the substructure search problem to be solved by graph isomorphism techniques, i.e., searching molecules for substructures is equivalent to testing two labeled graphs for subgraph isomorphism. The subgraph isomorphism problem is well studied [15-17] and one of the oldest and most applied algorithms [18-22] was introduced by Ullmann in 1976 [7]. Over the years that followed, only a few subgraph isomorphism methods were introduced [11,16,23], the most recent being the VF2 algorithm [12].…”

Section: Introductionmentioning

confidence: 99%

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

Ehrlich

Rarey

2012

J Cheminform

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BackgroundSearching 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.ResultsIn 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.ConclusionsThe 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.

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“…The Ullman algorithm, is used here. It has been extensively evaluated and developed by Willett et al . − for the detection of subgraph isomorphism with a wide variety of types of graphs. The Ullman algorithm has been shown to be highly efficient, and special requirements need to be met here, not least the need to identify all isomorphisms or partial isomorphisms between query and database structure graphs.…”

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confidence: 99%

The Sheffield Generic Structures Projecta Retrospective Review

Lynch

Holliday

1996

J. Chem. Inf. Comput. Sci.

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The problems posed by the requirements for storage and manipulation of generic chemical structure definitions in patents are reviewed. Chemists and patents agents have developed an armory of linguistic devices over many decades so that a generic structure description can describe large and often unlimited numbers of substances as a result of the combinatorial opportunities provided. The nature of these linguistic devices is defined, and the theoretical foundations devised during the Sheffield project for the successful solution of the problems in order to provide the desired retrieval facilities are reviewed. Progress toward the practical implementation of a system based on these solutions is evaluated. The relevance of the data structures and algorithms devised in this work to the issues raised by developments in combinatorial libraries is also reviewed.

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Atom-by-atom searching using massive parallelism. Implementation of the Ullmann subgraph isomorphism algorithm on the distributed array processor

Cited by 12 publications

References 10 publications

Molecular Structure Disassembly Program (MOSDAP): A Chemical Information Model To Automate Structure-Based Physical Property Estimation

Molecular Structure Disassembly Program (MOSDAP): A Chemical Information Model To Automate Structure-Based Physical Property Estimation

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

The Sheffield Generic Structures Projecta Retrospective Review

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