{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T08:19:34Z","timestamp":1790669974845,"version":"4.1.0"},"reference-count":22,"publisher":"MDPI AG","issue":"14","license":[{"start":{"date-parts":[[2021,7,13]],"date-time":"2021-07-13T00:00:00Z","timestamp":1626134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"AgriWasteValue","award":["NWE 750"],"award-info":[{"award-number":["NWE 750"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Molecular docking is widely used in computed drug discovery and biological target identification, but getting fast results can be tedious and often requires supercomputing solutions. AMIDE stands for AutoMated Inverse Docking Engine. It was initially developed in 2014 to perform inverse docking on High Performance Computing. AMIDE version 2 brings substantial speed-up improvement by using AutoDock-GPU and by pulling a total revision of programming workflow, leading to better performances, easier use, bug corrections, parallelization improvements and PC\/HPC compatibility. In addition to inverse docking, AMIDE is now an optimized tool capable of high throughput inverse screening. For instance, AMIDE version 2 allows acceleration of the docking up to 12.4 times for 100 runs of AutoDock compared to version 1, without significant changes in docking poses. The reverse docking of a ligand on 87 proteins takes only 23 min on 1 GPU (Graphics Processing Unit), while version 1 required 300 cores to reach the same execution time. Moreover, we have shown an exponential acceleration of the computation time as a function of the number of GPUs used, allowing a significant reduction of the duration of the inverse docking process on large datasets.<\/jats:p>","DOI":"10.3390\/ijms22147489","type":"journal-article","created":{"date-parts":[[2021,7,13]],"date-time":"2021-07-13T22:25:31Z","timestamp":1626215131000},"page":"7489","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["AMIDE v2: High-Throughput Screening Based on AutoDock-GPU and Improved Workflow Leading to Better Performance and Reliability"],"prefix":"10.3390","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8980-8772","authenticated-orcid":false,"given":"Pierre","family":"Darme","sequence":"first","affiliation":[{"name":"Universit\u00e9 de Reims Champagne Ardenne, ESCAPE EA 7510, 51097 Reims, France"},{"name":"Universit\u00e9 de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6743-7915","authenticated-orcid":false,"given":"Manuel","family":"Dauchez","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Reims Champagne Ardenne, CNRS UMR 7369, MEDyC, 51097 Reims, France"},{"name":"Plateau de Mod\u00e9lisation Mol\u00e9culaire Multi-\u00e9chelle, URCA, 51097 Reims, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnaud","family":"Renard","sequence":"additional","affiliation":[{"name":"Plateau de Mod\u00e9lisation Mol\u00e9culaire Multi-\u00e9chelle, URCA, 51097 Reims, France"},{"name":"Universit\u00e9 de Reims Champagne Ardenne, LICIIS\u2013LRC CEA DIGIT, 51097 Reims, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7038-241X","authenticated-orcid":false,"given":"Laurence","family":"Voutquenne-Nazabadioko","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominique","family":"Aubert","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Reims Champagne Ardenne, ESCAPE EA 7510, 51097 Reims, France"},{"name":"Centre Nationale de R\u00e9f\u00e9rence de la Toxoplasmose, CHU Reims, 51092 Reims, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandie","family":"Escotte-Binet","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Reims Champagne Ardenne, ESCAPE EA 7510, 51097 Reims, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Hugues","family":"Renault","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabelle","family":"Villena","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Reims Champagne Ardenne, ESCAPE EA 7510, 51097 Reims, France"},{"name":"Centre Nationale de R\u00e9f\u00e9rence de la Toxoplasmose, CHU Reims, 51092 Reims, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3670-4088","authenticated-orcid":false,"given":"Luiz-Angelo","family":"Steffenel","sequence":"additional","affiliation":[{"name":"Plateau de Mod\u00e9lisation Mol\u00e9culaire Multi-\u00e9chelle, URCA, 51097 Reims, France"},{"name":"Universit\u00e9 de Reims Champagne Ardenne, LICIIS\u2013LRC CEA DIGIT, 51097 Reims, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4436-0652","authenticated-orcid":false,"given":"St\u00e9phanie","family":"Baud","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Reims Champagne Ardenne, CNRS UMR 7369, MEDyC, 51097 Reims, France"},{"name":"Plateau de Mod\u00e9lisation Mol\u00e9culaire Multi-\u00e9chelle, URCA, 51097 Reims, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,7,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1016\/S1367-5931(02)00339-3","article-title":"Lead discovery using molecular docking","volume":"6","author":"Shoichet","year":"2002","journal-title":"Curr. Opin. Chem. Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1517\/17460441.2010.484460","article-title":"Virtual screening with AutoDock: Theory and practice","volume":"5","author":"Cosconati","year":"2010","journal-title":"Expert Opin. Drug Discov."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1002\/1097-0134(20010501)43:2<217::AID-PROT1032>3.0.CO;2-G","article-title":"Ligand\u2013protein inverse docking and its potential use in the computer search of protein targets of a small molecule","volume":"43","author":"Chen","year":"2001","journal-title":"Proteins Struct. Funct. Bioinf."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1111\/j.1582-4934.2008.00665.x","article-title":"Docking, virtual high throughput screening and in silico fragment-based drug design","volume":"13","author":"Zoete","year":"2009","journal-title":"J. Cell. Mol. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/jcc.21256","article-title":"AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility","volume":"30","author":"Morris","year":"2009","journal-title":"J. Comput. Chem."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1002\/pro.3771","article-title":"Flexible docking of peptides to proteins using CABS-dock","volume":"29","author":"Kurcinski","year":"2020","journal-title":"Protein Sci."},{"key":"ref_7","unstructured":"(2021, April 02). FlexAID: Revisiting Docking on Non-Native-Complex Structures. J. Chem. Inf. Modeling, Available online: https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jcim.5b00078."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"6177","DOI":"10.1021\/jm051256o","article-title":"Extra Precision Glide:\u2009 Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein\u2212Ligand Complexes","volume":"49","author":"Friesner","year":"2006","journal-title":"J. Med. Chem."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1002\/prot.10465","article-title":"Improved protein\u2013ligand docking using GOLD","volume":"52","author":"Verdonk","year":"2003","journal-title":"Proteins Struct. Funct. Bioinform."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1007\/s10822-011-9533-y","article-title":"Surflex-Dock: Docking benchmarks and real-world application","volume":"26","author":"Spitzer","year":"2012","journal-title":"J. Comput. Aided Mol. Des."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1007\/s12551-016-0247-1","article-title":"Software for molecular docking: A review","volume":"9","author":"Pagadala","year":"2017","journal-title":"Biophys. Rev."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/s40484-019-0172-y","article-title":"Progress in molecular docking","volume":"7","author":"Fan","year":"2019","journal-title":"Quant. Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/1758-2946-1-15","article-title":"Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock","volume":"1","author":"Bikadi","year":"2009","journal-title":"J. Cheminformatics"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1038\/s41586-020-2117-z","article-title":"An open-source drug discovery platform enables ultra-large virtual screens","volume":"580","author":"Gorgulla","year":"2020","journal-title":"Nature"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1021\/acs.jctc.0c01006","article-title":"Accelerating AutoDock4 with GPUs and Gradient-Based Local Search","volume":"17","author":"Koch","year":"2021","journal-title":"J. Chem. Theory. Comput."},{"key":"ref_16","unstructured":"Vasseur, R., Baud, S., Steffenel, L.A., Vigouroux, X., Martiny, L., Krajecki, M., and Dauchez, M. (2014). A Framework for Inverse Virtual Screening. BIOTECHNO 2014: The Sixth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies, IARIA."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/j.asoc.2014.10.049","article-title":"Solving molecular flexible docking problems with metaheuristics: A comparative study","volume":"28","author":"Nebro","year":"2015","journal-title":"Appl. Soft Comput."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1002\/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B","article-title":"Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function","volume":"19","author":"Morris","year":"1998","journal-title":"J. Comput. Chem."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Spalenka, J., Escotte-Binet, S., Bakiri, A., Hubert, J., Renault, J.-H., Velard, F., Duchateau, S., Aubert, D., Huguenin, A., and Villena, I. (2018). Discovery of New Inhibitors of Toxoplasma gondii via the Pathogen Box. Antimicrob. Agents Chemother., 62.","DOI":"10.1128\/AAC.01640-17"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1287\/moor.6.1.19","article-title":"Minimization by Random Search Techniques","volume":"6","author":"Solis","year":"1981","journal-title":"Math. Oper. Res."},{"key":"ref_21","unstructured":"Nuzillard, J.-M., Leroy, R., and Kuhn, S. (2020). Predicted carbon-13 NMR data of Natural Products (PNMRNP). Zenodo."},{"key":"ref_22","unstructured":"(2020, November 03). Open Babel. Available online: http:\/\/openbabel.org\/."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/14\/7489\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T06:29:42Z","timestamp":1760164182000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/14\/7489"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,7,13]]},"references-count":22,"journal-issue":{"issue":"14","published-online":{"date-parts":[[2021,7]]}},"alternative-id":["ijms22147489"],"URL":"https:\/\/doi.org\/10.3390\/ijms22147489","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,7,13]]}}}