Documentation of Chemical Reactions by Computer Analysis of Structural Changes

Armitage, Joseph; Crowe, Joyce; Evans, Paul; Lynch, Michael; McGuirk, J. A.

doi:10.1021/c160027a006

Cited by 19 publications

(7 citation statements)

References 7 publications

(7 reference statements)

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“…The scaffold of molecule groups is defined as a common sub-graph of the graphs of the molecule groups. Representatively, Maximum Common Substructure (MCS), Matched Molecular Pairs (MMP), and Bemis and Murko (BM) are the commonly used methods to produce molecular scaffolds [27][28][29][30][31]. The scaffold, as per the MMP method, is defined as the common part among molecules that have different molecular fragments at the same single specific site [28,29].…”

Section: Molecular Scaffolds In Nc-mfpmentioning

confidence: 99%

“…The scaffold, as per the MMP method, is defined as the common part among molecules that have different molecular fragments at the same single specific site [28,29]. MCS method defines a scaffold as the maximum common edge subgraph of the graphs of molecule groups [30]. Unlike the MMP and MCS methods, the scaffolds produced by the BM method reveal a hierarchical structure [31].…”

Section: Molecular Scaffolds In Nc-mfpmentioning

confidence: 99%

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Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

et al. 2020

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Computer-aided research on the relationship between molecular structures of natural compounds (NC) and their biological activities have been carried out extensively because the molecular structures of new drug candidates are usually analogous to or derived from the molecular structures of NC. In order to express the relationship physically realistically using a computer, it is essential to have a molecular descriptor set that can adequately represent the characteristics of the molecular structures belonging to the NC's chemical space. Although several topological descriptors have been developed to describe the physical, chemical, and biological properties of organic molecules, especially synthetic compounds, and have been widely used for drug discovery researches, these descriptors have limitations in expressing NC-specific molecular structures. To overcome this, we developed a novel molecular fingerprint, called Natural Compound Molecular Fingerprints (NC-MFP), for explaining NC structures related to biological activities and for applying the same for the natural product (NP)-based drug development. NC-MFP was developed to reflect the structural characteristics of NCs and the commonly used NP classification system. NC-MFP is a scaffold-based molecular fingerprint method comprising scaffolds, scaffold-fragment connection points (SFCP), and fragments. The scaffolds of the NC-MFP have a hierarchical structure. In this study, we introduce 16 structural classes of NPs in the Dictionary of Natural Product database (DNP), and the hierarchical scaffolds of each class were calculated using the Bemis and Murko (BM) method. The scaffold library in NC-MFP comprises 676 scaffolds. To compare how well the NC-MFP represents the structural features of NCs compared to the molecular fingerprints that have been widely used for organic molecular representation, two kinds of binary classification tasks were performed. Task I is a binary classification of the NCs in commercially available library DB into a NC or synthetic compound. Task II is classifying whether NCs with inhibitory activity in seven biological target proteins are active or inactive. Two tasks were developed with some molecular fingerprints, including NC-MFP, using the 1-nearest neighbor (1-NN) method. The performance of task I showed that NC-MFP is a practical molecular fingerprint to classify NC structures from the data set compared with other molecular fingerprints. Performance of task II with NC-MFP outperformed compared with other molecular fingerprints, suggesting that the NC-MFP is useful to explain NC structures related to biological activities. In conclusion, NC-MFP is a robust molecular fingerprint in classifying NC structures and explaining the biological activities of NC

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Section: Molecular Scaffolds In Nc-mfpmentioning

confidence: 99%

Section: Molecular Scaffolds In Nc-mfpmentioning

confidence: 99%

Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

et al. 2020

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“…The first approach that was tested involved a comparison of the sets of connection tables representing the reactant and product molecules to identify common linear chains of atoms; these chains were then assembled to create the unchanged parts of the reaction equation and hence, by difference, the reaction site where the change had occurred [15,16]. Although elegant in concept, the complexity of the programs and the low processing rates of the computers then available meant that this similarity procedure had to be dropped in favour of procedures for the direct identification of the differences.…”

Section: Automatic Indexing Of Chemical Reactionsmentioning

confidence: 99%

Information retrieval research in the Department of Information Studies, University of Sheffield: 1965-1985

Lynch

Willett

1987

Journal of Information Science

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This paper discusses research which was carried out at the Department of Information Studies, University of Sheffield in the period 1965 to 1985 into storage and retrieval techniques for databases of textual and chemical structure data. The research includes the development of methods for the automatic production of printed subject indexes and for the indexing and retrieval of chemical structures and chemical reactions, the variety generation method for the analysis, characterization and storage of data in a range of types of textual database, the prediction of biological activity in chemical compounds, and the design of document retrieval systems.the textual context [47]. In large part, these similarities of application arise from the frequency distributions underlying these two types of data, a factor which has become clear from the studies described in Sections 4 and 5 of tlus paper. This

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“…In the chemical literature, this is often referred to as the maximum common substructure problem and denotes the largest substructure common to the collection of graphs under consideration. The graph-based similarity between the graphs representing molecules plays an important role in many aspects of chemistry and, increasingly, biology: examples include protein-ligand docking [1], database searching [2,3], the prediction of biological activity [4], reaction site modeling [5][6][7][8], and the interpretation of molecular spectra [9,10].…”

Section: Introductionmentioning

confidence: 99%

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Raymond

Willett

2002

Journal of Computer-Aided Molecular Design

339

118

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The maximum common subgraph (MCS) problem has become increasingly important in those aspects of chemoinformatics that involve the matching of 2D or 3D chemical structures. This paper provides a classification and a review of the many MCS algorithms, both exact and approximate, that have been described in the literature, and makes recommendations regarding their applicability to typical chemoinformatics tasks.

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Documentation of Chemical Reactions by Computer Analysis of Structural Changes

Cited by 19 publications

References 7 publications

Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

Information retrieval research in the Department of Information Studies, University of Sheffield: 1965-1985

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