DG-AMMOS: A New tool to generate 3D conformation of small molecules using D istance G eometry and A utomated M olecular M echanics O ptimization for in silico S creening
| العنوان: | DG-AMMOS: A New tool to generate 3D conformation of small molecules using D istance G eometry and A utomated M olecular M echanics O ptimization for in silico S creening |
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| المؤلفون: | Tania Pencheva, Bruno O. Villoutreix, David Lagorce, Maria A. Miteva |
| المساهمون: | Molécules Thérapeutiques in silico (MTI), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre of Biomedical Engineering, Bulgarian Academy of Sciences (BAS), We would like to thank the Inserm institute, Paris Descartes University and Paris Diderot University for supports. TP thanks the 'Mairie de Paris' fellowship and the National Science Fund of Bulgaria, BMC, Ed. |
| المصدر: | BMC Chemical Biology BMC Chemical Biology, BioMed Central, 2009, 9 (1), pp.6. ⟨10.1186/1472-6769-9-6⟩ BMC Chemical Biology, Vol 9, Iss 1, p 6 (2009) |
| بيانات النشر: | Springer Science and Business Media LLC, 2009. |
| سنة النشر: | 2009 |
| مصطلحات موضوعية: | Computer science, In silico, Nanotechnology, Energy minimization, 01 natural sciences, Molecular mechanics, Computational science, lcsh:Biochemistry, 03 medical and health sciences, Drug Discovery, lcsh:QD415-436, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 030304 developmental biology, 0303 health sciences, Virtual screening, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Drug discovery, Process (computing), [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Small molecule, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 0104 chemical sciences, 010404 medicinal & biomolecular chemistry, Molecular Medicine, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Software, Generator (mathematics) |
| الوصف: | Background Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Results Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. Conclusion DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods. |
| وصف الملف: | application/pdf |
| تدمد: | 1472-6769 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fa10968df03b3c22dbaed8f0f5dc908dTest https://doi.org/10.1186/1472-6769-9-6Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....fa10968df03b3c22dbaed8f0f5dc908d |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14726769 |
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