3decision
| File:3decision logo.svg | |
| Developer(s) | Discngine discngine |
|---|---|
| Initial release | 2015 |
| Engine | |
| Available in | English |
| Website | 3decision |
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3decision ([1]site) is a Discngine software for structure-based drug design and discovery.[1]
It is a fully annotated and searchable biomolecular structural database that stores, centralizes, visualizes and analyzes internal and external experimental protein structures and models. The collaborative web-based interface of 3decision gives experts in Molecular modelling, Medicinal chemistry, Structural biology, but also in Protein engineering and Computational toxicology, a common ground for ideation and decision-making in structure-based drug discovery (similar platforms already exist in other scientific areas).[2]
The main applications of 3decision in drug discovery are: structure-based design, target validation, pocket detection[3][4] and druggability assessment[5][6], off-target analysis, protein-ligand interaction analysis, selectivity analysis, compound design validation with docking (R-dock[7]), sequence and structure annotation analysis[8], medicinal chemistry applications and biologics applications. It is available as Software-as-a-Service (SaaS) subscription and through AWS cloudformation templates.
Data integrated in the 3decision software are from Protein Data Bank[9], UniProt[10], ChEMBL[11] and more. With 3decision's public REST API the software can be integrated into other drug discovery software and internal workflows (e.g. Virtual Reality software Nanome ([2]site).
Gallery
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3decision interface - 3D Viewer
See also
References
- ↑ Yu W, MacKerell AD Jr. Computer-Aided Drug Design Methods. Methods Mol Biol. 2017;1520:85-106. https://link.springer.com/protocol/10.1007/978-1-4939-6634-9_5
- ↑ Rahman, M. H., Schimpf, C., Xie, C., and Sha, Z. (October 1, 2019). "A Computer-Aided Design Based Research Platform for Design Thinking Studies." ASME. J. Mech. Des. December 2019; 141(12): 121102. https://doi.org/10.1115/1.4044395
- ↑ Le Guilloux, V., Schmidtke, P. & Tuffery, P. Fpocket: An open source platform for ligand pocket detection. BMC Bioinformatics 10, 168 (2009) https://doi.org/10.1186/1471-2105-10-168.
- ↑ Peter Schmidtke, Axel Bidon-Chanal, F. Javier Luque, Xavier Barril, MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories, Bioinformatics, Volume 27, Issue 23, 1 December 2011, Pages 3276–3285, https://doi.org/10.1093/bioinformatics/btr550.
- ↑ Eric B Fauman, Brajesh K Rai, Enoch S Huang, Structure-based druggability assessment—identifying suitable targets for small molecule therapeutics, Current Opinion in Chemical Biology,Volume 15, Issue 4,2011,Pages 463-468,ISSN 1367-5931,https://doi.org/10.1016/j.cbpa.2011.05.020.
- ↑ Soga S, Shirai H, Kobori M, Hirayama N. Use of amino acid composition to predict ligand-binding sites. J Chem Inf Model. 2007 Mar-Apr;47(2):400-6. doi: https://pubs.acs.org/doi/10.1021/ci6002202. Epub 2007 Jan 23. PMID: 17243757.
- ↑ Ruiz-Carmona S, Alvarez-Garcia D, Foloppe N, Garmendia-Doval AB, Juhos S, Schmidtke P, et al. (2014) rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids. PLoS Comput Biol 10(4): e1003571. https://doi.org/10.1371/journal.pcbi.1003571
- ↑ Isberg V, de Graaf C, Bortolato A, Cherezov V, Katritch V, Marshall FH, Mordalski S, Pin JP, Stevens RC, Vriend G, Gloriam DE. Generic GPCR residue numbers - aligning topology maps while minding the gaps. Trends Pharmacol Sci. 2015 Jan;36(1):22-31. Epub 2014 Dec 22. PMID: 25541108; PMCID: PMC4408928.1 DOI:https://doi.org/10.1016/j.tips.2014.11.001
- ↑ H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne. (2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242.
- ↑ Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100
- ↑ Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibrián-Uhalte E, Davies M, Dedman N, Karlsson A, Magariños MP, Overington JP, Papadatos G, Smit I, Leach AR. (2017) The ChEMBL database in 2017. Nucleic Acids Res., 45(D1) D945-D954. https://doi.org/10.1093/nar/gkw1074
External links
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