Introduction
Our commitment to constant improvement led us to the development of several useful tools. Our script and software are
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- PDB Cl.O.E. (PDB Cleaner of Original Elements, doi.org/10.1021/acs.jcim.9b00428), which removes unnecessary elements from a PDB structure. The structures deposited in the Protein Data Bank often contain solvent molecules, ions and other compounds that derive from the crystallization process and are not strictly related to the protein function. PDB Cl.O.E. analyzes the structure and the function of the target and removes all the elements that are not required for the protein to perform its biological actions. For more information:
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- MAEΔΔδ to assist the configurational assignment of stereoisomers by comparing computational and experimental data (doi.org/10.1021/acs.joc.9b03129). For more information:
Latest papers:
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Di Micco S.; Lauro G.; Bifulco G.; “Extensive molecular dynamics simulations disclosed the stability of mPGES-1 enzyme and the structural role of glutathione (GSH) cofactor”, Mol. Inform., 2022, 41, 2200140. https://doi.org/10.1002/minf.202200140 |
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Gazzillo E.; Terracciano S.; Ruggiero D.; Potenza M.; Chini M.G.; Lauro G.; Fischer K.; Hofstetter R.K.; Giordano A.; Werz O.; Bruno I.; Bifulco G.; “Repositioning of quinazolinedione-based compounds on soluble epoxide hydrolase (sEH) through 3D structure-based pharmacophore model-driven Iinvestigation.”, Molecules, 2022, 27, 3866. https://doi.org/10.3390/molecules27123866 |
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Pierri M.; Gazzillo E.; Chini M.G.; Ferraro M.G.; Piccolo M.; Maione F.; Irace C.; Bifulco G.; Bruno I.; Terracciano S.; Lauro G.; “Introducing structure-based three-dimensional pharmacophore models for accelerating the discovery of selective BRD9 binders.”, Bioorg. Chem., 2022, 118, 105480. https://doi.org/10.1016/j.bioorg.2021.105480 |
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Lauro G.; Das P.; Riccio R.; Reddy D. S.; Bifulc, G.; “DFT/NMR approach for the configuration assignment of groups of stereoisomers by the combination and comparison of experimental and predicted sets of data.”, J. Org. Chem., 2020, 85, 3297-3306. https://doi.org/10.1021/acs.joc.9b03129 |
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Lauro G.; Bifulco G.; “Elucidating the relative and absolute configuration of organic compounds by quantum mechanical approaches.”, Eur. J. Org. Chem., 2020, 2020, 3929-3941. https://doi.org/10.1002/ejoc.201901878 |
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De Vita S.; Chini M.G.; Lauro G.; Bifulco G.; “Accelerating the repurposing of FDA-approved drugs against coronavirus disease-19 (COVID-19).”, RSC Adv., 2020, 10, 40867-40875. https://doi.org/10.1039/d0ra09010g |
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Chini M.G.; Urbani D.; Dambruoso P.; Riccio R.; Bifulco G.; “Elucidating heteroatom influence on homonuclear 4J(H,H) coupling constants by DFT/NMR approach.” Magn. Reson. Chem., 2020, 58, 566-575. https://doi.org/10.1002/mrc.4983 |
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De Vita S.; Lauro G.; Ruggiero D.; Terracciano S.; Riccio R.; Bifulco G.; “Protein preparation sutomatic protocol for high-throughput Inverse Virtual Screening: Accelerating the target identification by computational methods.”, J. Chem. Inf. Model., 2019, 59, 4678-4690. https://doi.org/10.1021/acs.jcim.9b00428 |
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Lauro G.; Masullo M.; Piacente S.; Riccio R.; Bifulco G.; “Inverse Virtual Screening allows the discovery of the biological activity of natural compounds.”, Bioorg. Med. Chem., 2012, 20, 3596-3602. https://doi.org/10.1016/j.bmc.2012.03.072 |