ArticleJournal of cheminformatics2009
Small Molecule Subgraph Detector (SMSD) toolkit.
Article in Journal of cheminformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
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- Finding branched pathways in metabolic network via atom group tracking.PLoS computational biology · 2021Article
- MET: a Java package for fast molecule equivalence testing.Journal of cheminformatics · 2020Article
- Maximum common property: a new approach for molecular similarity.Journal of cheminformatics · 2020Article
- A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function.Database : the journal of biological databases and curation · 2020Article
- Augmenting Basin-Hopping With Techniques From Unsupervised Machine Learning: Applications in Spectroscopy and Ion Mobility.Frontiers in chemistry · 2019Review
- Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents.PLoS computational biology · 2018Article
- A systematic approach to identify therapeutic effects of natural products based on human metabolite information.BMC bioinformatics · 2018Article
- System Pharmacology-Based Strategy to Decode the Synergistic Mechanism of Zhi-zhu Wan for Functional Dyspepsia.Frontiers in pharmacology · 2018Article
- The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.Journal of cheminformatics · 2017Article
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- Discovery of Mycobacterium tuberculosis InhA Inhibitors by Binding Sites Comparison and Ligands Prediction.Journal of medicinal chemistry · 2016Article
- Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching.Nature chemical biology · 2016Article
- Hepatic Safety of Atypical Antipsychotics: Current Evidence and Future Directions.Drug safety · 2016Review
- Open source molecular modeling.Journal of molecular graphics & modelling · 2016Review
- Computational Biology in the 21st Century: Scaling with Compressive Algorithms.Communications of the ACM · 2016Article
- Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases.Journal of molecular biology · 2016Article
- Reaction Decoder Tool (RDT): extracting features from chemical reactions.Bioinformatics (Oxford, England) · 2016Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFinding one small molecule (query) in a large target library is a challenging task in computational chemistry. Although several heuristic approaches are available using fragment-based chemical similarity searches, they fail to identify exact atom-bond equivalence between the query and target molecules and thus cannot be applied to complex chemical similarity searches, such as searching a complete or partial metabolic pathway.In this paper we present a new Maximum Common Subgraph (MCS) tool: SMSD (Small Molecule Subgraph Detector) to overcome the issues with current heuristic approaches to small molecule similarity searches. The MCS search implemented in SMSD incorporates chemical knowledge (atom type match with bond sensitive and insensitive information) while searching molecular similarity. We also propose a novel method by which solutions obtained by each MCS run can be ranked using chemical filters such as stereochemistry, bond energy, etc.
resultsIn order to benchmark and test the tool, we performed a 50,000 pair-wise comparison between KEGG ligands and PDB HET Group atoms. In both cases the SMSD was shown to be more efficient than the widely used MCS module implemented in the Chemistry Development Kit (CDK) in generating MCS solutions from our test cases.
conclusionPresently this tool can be applied to various areas of bioinformatics and chemo-informatics for finding exhaustive MCS matches. For example, it can be used to analyse metabolic networks by mapping the atoms between reactants and products involved in reactions. It can also be used to detect the MCS/substructure searches in small molecules reported by metabolome experiments, as well as in the screening of drug-like compounds with similar substructures.Thus, we present a robust tool that can be used for multiple applications, including the discovery of new drug molecules. This tool is freely available on http://www.ebi.ac.uk/thornton-srv/software/SMSD/
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.