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447 results

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Page 1
Molecular docking and structure-based drug design strategies.
Ferreira LG, Dos Santos RN, Oliva G, Andricopulo AD. Ferreira LG, et al. Molecules. 2015 Jul 22;20(7):13384-421. doi: 10.3390/molecules200713384. Molecules. 2015. PMID: 26205061 Free PMC article. Review.
The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the bindin …
The integration of computational and experimental strategies has been of great value in the identification and development of novel promisin …
Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors.
Boby ML, Fearon D, Ferla M, Filep M, Koekemoer L, Robinson MC; COVID Moonshot Consortium‡; Chodera JD, Lee AA, London N, von Delft A, von Delft F, Achdout H, Aimon A, Alonzi DS, Arbon R, Aschenbrenner JC, Balcomb BH, Bar-David E, Barr H, Ben-Shmuel A, Bennett J, Bilenko VA, Borden B, Boulet P, Bowman GR, Brewitz L, Brun J, Bvnbs S, Calmiano M, Carbery A, Carney DW, Cattermole E, Chang E, Chernyshenko E, Clyde A, Coffland JE, Cohen G, Cole JC, Contini A, Cox L, Croll TI, Cvitkovic M, De Jonghe S, Dias A, Donckers K, Dotson DL, Douangamath A, Duberstein S, Dudgeon T, Dunnett LE, Eastman P, Erez N, Eyermann CJ, Fairhead M, Fate G, Fedorov O, Fernandes RS, Ferrins L, Foster R, Foster H, Fraisse L, Gabizon R, García-Sastre A, Gawriljuk VO, Gehrtz P, Gileadi C, Giroud C, Glass WG, Glen RC, Glinert I, Godoy AS, Gorichko M, Gorrie-Stone T, Griffen EJ, Haneef A, Hassell Hart S, Heer J, Henry M, Hill M, Horrell S, Huang QYJ, Huliak VD, Hurley MFD, Israely T, Jajack A, Jansen J, Jnoff E, Jochmans D, John T, Kaminow B, Kang L, Kantsadi AL, Kenny PW, Kiappes JL, Kinakh SO, Kovar B, Krojer T, La VNT, Laghnimi-Hahn S, Lefker BA, Levy H, Lithgo RM, Logvinenko IG, Lukacik P, Macdonald HB, MacLean … See abstract for full author list ➔ Boby ML, et al. Science. 2023 Nov 10;382(6671):eabo7201. doi: 10.1126/science.abo7201. Epub 2023 Nov 10. Science. 2023. PMID: 37943932 Free PMC article.
Key Topics in Molecular Docking for Drug Design.
Torres PHM, Sodero ACR, Jofily P, Silva-Jr FP. Torres PHM, et al. Int J Mol Sci. 2019 Sep 15;20(18):4574. doi: 10.3390/ijms20184574. Int J Mol Sci. 2019. PMID: 31540192 Free PMC article. Review.
Molecular docking has been widely employed as a fast and inexpensive technique in the past decades, both in academic and industrial settings. ...In this review, we present an overview of the method and attempt to summarise recent developments regarding four main aspects of …
Molecular docking has been widely employed as a fast and inexpensive technique in the past decades, both in academic and industrial s …
Discovering small-molecule senolytics with deep neural networks.
Wong F, Omori S, Donghia NM, Zheng EJ, Collins JJ. Wong F, et al. Nat Aging. 2023 Jun;3(6):734-750. doi: 10.1038/s43587-023-00415-z. Epub 2023 May 4. Nat Aging. 2023. PMID: 37142829
Our approach enriched for structurally diverse compounds with senolytic activity; of these, three drug-like compounds selectively target senescent cells across different senescence models, with more favorable medicinal chemistry properties than, and selectivity comparable to, tho …
Our approach enriched for structurally diverse compounds with senolytic activity; of these, three drug-like compounds selectively target sen …
A Mammalian Target of Rapamycin-Perilipin 3 (mTORC1-Plin3) Pathway is essential to Activate Lipophagy and Protects Against Hepatosteatosis.
Garcia-Macia M, Santos-Ledo A, Leslie J, Paish HL, Collins AL, Scott RS, Watson A, Burgoyne RA, White S, French J, Hammond J, Borthwick LA, Mann J, Bolaños JP, Korolchuk VI, Oakley F, Mann DA. Garcia-Macia M, et al. Hepatology. 2021 Dec;74(6):3441-3459. doi: 10.1002/hep.32048. Epub 2021 Sep 21. Hepatology. 2021. PMID: 34233024 Free article.
Furthermore, Plin3 directly interacted with the autophagy proteins focal adhesion interaction protein 200 KDa and autophagy-related 16L, suggesting that Plin3 functions as a docking protein or is involved in autophagosome formation to activate lipophagy. ...
Furthermore, Plin3 directly interacted with the autophagy proteins focal adhesion interaction protein 200 KDa and autophagy-related 16L, sug …
Ligand- and receptor-based docking with LiBELa.
dos Santos Muniz H, Nascimento AS. dos Santos Muniz H, et al. J Comput Aided Mol Des. 2015 Aug;29(8):713-23. doi: 10.1007/s10822-015-9856-1. Epub 2015 Jul 4. J Comput Aided Mol Des. 2015. PMID: 26141308
In pursuit of an advance in current methods we developed a mixed docking approach combining ligand- and receptor-based strategies in a docking engine, where tridimensional descriptors for shape and charge distribution of a reference ligand guide the initial placemen …
In pursuit of an advance in current methods we developed a mixed docking approach combining ligand- and receptor-based strategies in …
Sugarcane cystatins: From discovery to biotechnological applications.
Shibao PYT, Santos-Júnior CD, Santiago AC, Mohan C, Miguel MC, Toyama D, Vieira MAS, Narayanan S, Figueira A, Carmona AK, Schiermeyer A, Soares-Costa A, Henrique-Silva F. Shibao PYT, et al. Int J Biol Macromol. 2021 Jan 15;167:676-686. doi: 10.1016/j.ijbiomac.2020.11.185. Epub 2020 Dec 4. Int J Biol Macromol. 2021. PMID: 33285201 Review.
In this review, we summarize a comprehensive history of all sugarcane cystatins, presenting an updated phylogenetic analysis; chromosomal localization, and genomic organization. We also present protein docking of CaneCPI-5 in the active site of human cathepsin B, insights …
In this review, we summarize a comprehensive history of all sugarcane cystatins, presenting an updated phylogenetic analysis; chromosomal lo …
Improving Blind Docking in DOCK6 through an Automated Preliminary Fragment Probing Strategy.
Jofily P, Pascutti PG, Torres PHM. Jofily P, et al. Molecules. 2021 Feb 25;26(5):1224. doi: 10.3390/molecules26051224. Molecules. 2021. PMID: 33668914 Free PMC article.
Probing protein surfaces to accurately predict the binding site and conformation of a small molecule is a challenge currently addressed through mainly two different approaches: blind docking and cavity detection-guided docking. Although cavity detection-guided blind …
Probing protein surfaces to accurately predict the binding site and conformation of a small molecule is a challenge currently addressed thro …
Practices in Molecular Docking and Structure-Based Virtual Screening.
Dos Santos RN, Ferreira LG, Andricopulo AD. Dos Santos RN, et al. Methods Mol Biol. 2018;1762:31-50. doi: 10.1007/978-1-4939-7756-7_3. Methods Mol Biol. 2018. PMID: 29594766
In this context, the integration of experimental techniques, such as X-ray crystallography, and computational methods, such as molecular docking, has promoted the emergence of several areas in drug discovery, such as structure-based drug design (SBDD). ...A detailed descri …
In this context, the integration of experimental techniques, such as X-ray crystallography, and computational methods, such as molecular …
447 results