{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T23:13:16Z","timestamp":1768259596283,"version":"3.49.0"},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,5,30]],"date-time":"2024-05-30T00:00:00Z","timestamp":1717027200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,5,30]],"date-time":"2024-05-30T00:00:00Z","timestamp":1717027200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100005711","name":"Universit\u00e4t Hamburg","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100005711","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2024,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>In this work, we present the frontend of GeoMine and showcase its application, focusing on the new features of its latest version. GeoMine is a search engine for ligand-bound and predicted empty binding sites in the Protein Data Bank. In addition to its basic text-based search functionalities, GeoMine offers a geometric query type for searching binding sites with a specific relative spatial arrangement of chemical features such as heavy atoms and intermolecular interactions. In contrast to a text search that requires simple and easy-to-formulate user input, a 3D input is more complex, and its specification can be challenging for users. GeoMine\u2019s new version aims to address this issue from the graphical user interface perspective by introducing an additional visualization concept and a new query template type. In its latest version, GeoMine extends its query-building capabilities primarily through input formulation in 2D. The 2D editor is fully synchronized with GeoMine\u2019s 3D editor and provides the same functionality. It enables template-free query generation and template-based query selection directly in 2D pose diagrams. In addition, the query generation with the 3D editor now supports predicted empty binding sites for AlphaFold structures as query templates. GeoMine is freely accessible on the Proteins<jats:italic>Plus<\/jats:italic> web server (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/proteins.plus\">https:\/\/proteins.plus<\/jats:ext-link>).<\/jats:p>","DOI":"10.1007\/s10822-024-00563-3","type":"journal-article","created":{"date-parts":[[2024,5,30]],"date-time":"2024-05-30T05:02:21Z","timestamp":1717045341000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["User-centric design of a 3D search interface for protein-ligand complexes"],"prefix":"10.1007","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8171-0888","authenticated-orcid":false,"given":"Konrad","family":"Diedrich","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1428-0042","authenticated-orcid":false,"given":"Christiane","family":"Ehrt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8327-4936","authenticated-orcid":false,"given":"Joel","family":"Graef","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8529-8376","authenticated-orcid":false,"given":"Martin","family":"Poppinga","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Norbert","family":"Ritter","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9553-6531","authenticated-orcid":false,"given":"Matthias","family":"Rarey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,5,30]]},"reference":[{"key":"563_CR1","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235\u2013242. https:\/\/doi.org\/10.1093\/nar\/28.1.235","journal-title":"Nucleic Acids Res"},{"key":"563_CR2","doi-asserted-by":"publisher","first-page":"10441","DOI":"10.1021\/acs.jmedchem.9b01545","volume":"62","author":"B Kuhn","year":"2019","unstructured":"Kuhn B, Gilberg E, Taylor R, Cole J, Korb O (2019) How significant are unusual protein\u2013ligand interactions? Insights from Database Mining. J Med Chem 62:10441\u201310455. https:\/\/doi.org\/10.1021\/acs.jmedchem.9b01545","journal-title":"J Med Chem"},{"key":"563_CR3","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1007\/978-1-4020-9058-5_8","volume-title":"From protein structure to function with Bioinformatics","author":"EC Meng","year":"2009","unstructured":"Meng EC, Polacco BJ, Babbitt PC (2009) 3D motifs. Rigden. D.J. (eds) From protein structure to function with Bioinformatics. Springer, Dordrecht, pp 187\u2013216. https:\/\/doi.org\/10.1007\/978-1-4020-9058-5_8"},{"key":"563_CR4","doi-asserted-by":"publisher","first-page":"4121","DOI":"10.1021\/acs.jmedchem.6b00078","volume":"59","author":"C Ehrt","year":"2016","unstructured":"Ehrt C, Brinkjost T, Koch O (2016) Impact of binding site comparisons on Medicinal Chemistry and Rational Molecular Design. J Med Chem 59:4121\u20134151. https:\/\/doi.org\/10.1021\/acs.jmedchem.6b00078","journal-title":"J Med Chem"},{"key":"563_CR5","doi-asserted-by":"publisher","first-page":"e1008502","DOI":"10.1371\/journal.pcbi.1008502","volume":"16","author":"S Bittrich","year":"2020","unstructured":"Bittrich S, Burley SK, Rose AS (2020) Real-time structural motif searching in proteins using an Inverted Index Strategy. PLoS Comput Biol 16:e1008502. https:\/\/doi.org\/10.1371\/journal.pcbi.1008502","journal-title":"PLoS Comput Biol"},{"key":"563_CR6","doi-asserted-by":"publisher","first-page":"4257","DOI":"10.1021\/acs.jmedchem.5b01756","volume":"59","author":"O Korb","year":"2016","unstructured":"Korb O, Kuhn B, Hert J, Taylor N, Cole J, Groom C, Stahl M (2016) Interactive and versatile Navigation of Structural databases. J Med Chem 59:4257\u20134266. https:\/\/doi.org\/10.1021\/acs.jmedchem.5b01756","journal-title":"J Med Chem"},{"key":"563_CR7","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1111\/j.1747-0285.2010.00994.x","volume":"76","author":"D Mobilio","year":"2010","unstructured":"Mobilio D, Walker G, Brooijmans N, Nilakantan R, Denny RA, DeJoannis J, Feyfant E, Kowticwar RK, Mankala J, Palli S, Punyamantula S, Tatipally M, John RK, Humblet C (2010) Protein relational database and protein family knowledge bases to facilitate structure-based design analyses. Chem Biol Drug Des 76:142\u2013153. https:\/\/doi.org\/10.1111\/j.1747-0285.2010.00994.x","journal-title":"Chem Biol Drug Des"},{"key":"563_CR8","doi-asserted-by":"publisher","first-page":"1450","DOI":"10.1021\/ci300034x","volume":"52","author":"M Weisel","year":"2012","unstructured":"Weisel M, Bitter HM, Diederich F, So WV, Kondru R (2012) PROLIX: Rapid Mining of protein\u2013ligand interactions in large crystal structure databases. J Chem Inf Model 52:1450\u20131461. https:\/\/doi.org\/10.1021\/ci300034x","journal-title":"J Chem Inf Model"},{"key":"563_CR9","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1016\/S0022-2836(02)01408-0","volume":"326","author":"M Hendlich","year":"2003","unstructured":"Hendlich M, Bergner A, G\u00fcnther J, Klebe G (2003) Relibase: design and development of a database for Comprehensive Analysis of protein\u2013ligand interactions. J Mol Biol 326:607\u2013620. https:\/\/doi.org\/10.1016\/S0022-2836(02)01408-0","journal-title":"J Mol Biol"},{"key":"563_CR10","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1186\/1471-2105-9-312","volume":"9","author":"A Golovin","year":"2008","unstructured":"Golovin A, Henrick K (2008) MSDmotif: exploring protein sites and motifs. BMC Bioinf 9:312. https:\/\/doi.org\/10.1186\/1471-2105-9-312","journal-title":"BMC Bioinf"},{"key":"563_CR11","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1021\/acs.jcim.6b00561","volume":"57","author":"T Inhester","year":"2017","unstructured":"Inhester T, Bietz S, Hilbig M, Schmidt R, Rarey M (2017) Index-based Searching of Interaction patterns in large collections of protein-ligand interfaces. J Chem Inf Model 57:148\u2013158. https:\/\/doi.org\/10.1021\/acs.jcim.6b00561","journal-title":"J Chem Inf Model"},{"key":"563_CR12","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1186\/s12859-020-3352-x","volume":"21","author":"R Angles","year":"2020","unstructured":"Angles R, Arenas-Salinas M, Garc\u00eda R, Reyes-Suarez JA, Pohl E (2020) GSP4PDB: a web Tool to visualize, search and explore protein-ligand structural patterns. BMC Bioinf 21:85. https:\/\/doi.org\/10.1186\/s12859-020-3352-x","journal-title":"BMC Bioinf"},{"key":"563_CR13","doi-asserted-by":"publisher","first-page":"1384","DOI":"10.1021\/acs.jmedchem.1c01046","volume":"65","author":"J Graef","year":"2022","unstructured":"Graef J, Ehrt C, Diedrich K, Poppinga M, Ritter N, Rarey M (2022) Searching geometric patterns in protein binding sites and their application to Data Mining in protein kinase structures. J Med Chem 65:1384\u20131395. https:\/\/doi.org\/10.1021\/acs.jmedchem.1c01046","journal-title":"J Med Chem"},{"key":"563_CR14","doi-asserted-by":"publisher","first-page":"424","DOI":"10.1093\/bioinformatics\/btaa693","volume":"37","author":"K Diedrich","year":"2021","unstructured":"Diedrich K, Graef J, Sch\u00f6ning-Stierand K, Rarey M (2021) GeoMine: interactive pattern mining of protein-ligand interfaces in the Protein Data Bank. Bioinformatics 37:424\u2013425. https:\/\/doi.org\/10.1093\/bioinformatics\/btaa693","journal-title":"Bioinformatics"},{"key":"563_CR15","doi-asserted-by":"publisher","first-page":"1317","DOI":"10.1109\/TCBB.2019.2892099","volume":"17","author":"AV Fassio","year":"2020","unstructured":"Fassio AV, Santos LH, Silveira SA, Ferreira RS, de Melo-Minardi RC (2020) nAPOLI: a graph-based strategy to detect and visualize conserved protein-ligand interactions in large-scale. TCBB 17:1317\u20131328. https:\/\/doi.org\/10.1109\/TCBB.2019.2892099","journal-title":"TCBB"},{"key":"563_CR16","unstructured":"Desert Scientific Software (DesertSci) Proasis4. https:\/\/desertsci.com. Accessed 7 May 2024"},{"key":"563_CR17","unstructured":"Discngine 3decision. https:\/\/3decision.discngine.com. Accessed 7 May 2024"},{"key":"563_CR18","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","volume":"596","author":"J Jumper","year":"2021","unstructured":"Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, \u017d\u00eddek A, Potapenko A, Bridgland A, Meyer C, Kohl SAA, Ballard AJ, Cowie A, Romera-Paredes B, Nikolov S, Jain R, Adler J, Back T, Petersen S, Reiman D, Clancy E, Zielinski M,\u00a0Steinegger M, Pacholska M, Berghammer T, Bodenstein S, Silver D, Vinyals O, Senior AW, Kavukcuoglu K, Kohli P, Hassabis D (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596:583\u2013589. https:\/\/doi.org\/10.1038\/s41586-021-03819-2","journal-title":"Nature"},{"key":"563_CR19","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1093\/nar\/gkac305","volume":"50","author":"K Sch\u00f6ning-Stierand","year":"2022","unstructured":"Sch\u00f6ning-Stierand K, Diedrich K, Ehrt C, Flachsenberg F, Graef J, Sieg J, Penner P, Poppinga M, Ungeth\u00fcm A, Rarey M (2022) ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. Nucleic Acids Res 50:611\u2013615. https:\/\/doi.org\/10.1093\/nar\/gkac305","journal-title":"Nucleic Acids Res"},{"key":"563_CR20","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1093\/nar\/gkaa235","volume":"48","author":"K Sch\u00f6ning-Stierand","year":"2020","unstructured":"Sch\u00f6ning-Stierand K, Diedrich K, F\u00e4hrrolfes R, Flachsenberg F, Meyder A, Nittinger E, Steinegger R, Rarey M (2020) ProteinsPlus: interactive analysis of protein\u2013ligand binding interfaces. Nucleic Acids Res 48:48\u201353. https:\/\/doi.org\/10.1093\/nar\/gkaa235","journal-title":"Nucleic Acids Res"},{"key":"563_CR21","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1093\/nar\/gkx333","volume":"45","author":"R F\u00e4hrrolfes","year":"2017","unstructured":"F\u00e4hrrolfes R, Bietz S, Flachsenberg F, Meyder A, Nittinger E, Otto T, Volkamer A, Rarey M (2017) ProteinsPlus: a web portal for structure analysis of macromolecules. Nucleic Acids Res 45:337\u2013343. https:\/\/doi.org\/10.1093\/nar\/gkx333","journal-title":"Nucleic Acids Res"},{"key":"563_CR22","doi-asserted-by":"publisher","first-page":"3128","DOI":"10.1021\/acs.jcim.3c00336","volume":"63","author":"J Graef","year":"2023","unstructured":"Graef J, Ehrt C, Rarey M (2023) Binding site detection remastered: enabling fast, robust, and Reliable binding site detection and descriptor calculation with DoGSite3. J Chem Inf Model 63:3128\u20133137. https:\/\/doi.org\/10.1021\/acs.jcim.3c00336","journal-title":"J Chem Inf Model"},{"key":"563_CR23","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/1758-2946-6-12","volume":"6","author":"S Bietz","year":"2014","unstructured":"Bietz S, Urbaczek S, Schulz B, Rarey M (2014) Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes. J Cheminform 6:12. https:\/\/doi.org\/10.1186\/1758-2946-6-12","journal-title":"J Cheminform"},{"key":"563_CR24","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1758-2946-1-13","volume":"1","author":"T Lippert","year":"2009","unstructured":"Lippert T, Rarey M (2009) Fast automated placement of polar hydrogen atoms in protein-ligand complexes. J Cheminform 1:13. https:\/\/doi.org\/10.1186\/1758-2946-1-13","journal-title":"J Cheminform"},{"key":"563_CR25","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1007\/s10822-023-00522-4","volume":"37","author":"K Diedrich","year":"2023","unstructured":"Diedrich K, Krause B, Berg O, Rarey M (2023) PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams. J Comput Aided Mol Des 37:491\u2013503. https:\/\/doi.org\/10.1007\/s10822-023-00522-4","journal-title":"J Comput Aided Mol Des"},{"key":"563_CR26","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1021\/ml100164p","volume":"1","author":"K Stierand","year":"2010","unstructured":"Stierand K, Rarey M (2010) Drawing the PDB - protein-ligand complexes in two dimensions. ACS Med Chem Lett 1:540\u2013545. https:\/\/doi.org\/10.1021\/ml100164p","journal-title":"ACS Med Chem Lett"},{"key":"563_CR27","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1002\/cmdc.200700010","volume":"2","author":"K Stierand","year":"2007","unstructured":"Stierand K, Rarey M (2007) From modeling to Medicinal Chemistry: Automatic Generation of two-Dimensional Complex diagrams. ChemMedChem 2:853\u2013860. https:\/\/doi.org\/10.1002\/cmdc.200700010","journal-title":"ChemMedChem"},{"key":"563_CR28","doi-asserted-by":"publisher","first-page":"1710","DOI":"10.1093\/bioinformatics\/btl150","volume":"22","author":"K Stierand","year":"2006","unstructured":"Stierand K, Maass PC, Rarey M (2006) Molecular complexes at a glance: automated generation of two-dimensional complex diagrams. Bioinformatics 22:1710\u20131716. https:\/\/doi.org\/10.1093\/bioinformatics\/btl150","journal-title":"Bioinformatics"},{"key":"563_CR29","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1038\/nsb842","volume":"9","author":"TG Davies","year":"2002","unstructured":"Davies TG, Bentley J, Arris CE, Boyle FT, Curtin NJ, Endicott JA, Gibson AE, Goldin BT, Griffin RJ, Hardcastle IR, Jewsbury P, Johnson LN, Mesguich V, Newell DR, Noble MEM, Tucker JA, Wang L, Whitfield HJ (2002) Structure-based design of a potent purine-based cyclin-dependent kinase inhibitor. Nat Struct Mol Biol 9:745\u2013749. https:\/\/doi.org\/10.1038\/nsb842","journal-title":"Nat Struct Mol Biol"},{"key":"563_CR30","doi-asserted-by":"publisher","first-page":"3755","DOI":"10.1093\/bioinformatics\/bty419","volume":"34","author":"AS Rose","year":"2018","unstructured":"Rose AS, Bradley AR, Valasatava Y, Duarte JM, Prli\u0107 A, Rose PW (2018) NGL viewer: web-based molecular graphics for large complexes. Bioinformatics 34:3755\u20133758. https:\/\/doi.org\/10.1093\/bioinformatics\/bty419","journal-title":"Bioinformatics"},{"key":"563_CR31","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1093\/nar\/gkv402","volume":"43","author":"AS Rose","year":"2015","unstructured":"Rose AS, Hildebrand PW (2015) NGL viewer: a web application for molecular visualization. Nucleic Acids Res 43:576\u2013579. https:\/\/doi.org\/10.1093\/nar\/gkv402","journal-title":"Nucleic Acids Res"},{"key":"563_CR32","doi-asserted-by":"publisher","first-page":"36","DOI":"10.3390\/tropicalmed2030036","volume":"2","author":"AK Mitra","year":"2017","unstructured":"Mitra AK, Mawson AR (2017) Neglected tropical diseases: epidemiology and global burden. Trop Med Infect Dis 2:36. https:\/\/doi.org\/10.3390\/tropicalmed2030036","journal-title":"Trop Med Infect Dis"},{"key":"563_CR33","doi-asserted-by":"publisher","first-page":"104440","DOI":"10.1016\/j.ebiom.2023.104440","volume":"87","author":"Editorial","year":"2023","unstructured":"Editorial (2023) Leishmania: an urgent need for new treatments. EBioMedicine 87:104440. https:\/\/doi.org\/10.1016\/j.ebiom.2023.104440","journal-title":"EBioMedicine"},{"key":"563_CR34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s12639-010-0006-3","volume":"34","author":"B Chawla","year":"2010","unstructured":"Chawla B, Madhubala R (2010) Drug targets in Leishmania. J Parasit Dis 34:1\u201313. https:\/\/doi.org\/10.1007\/s12639-010-0006-3","journal-title":"J Parasit Dis"},{"key":"563_CR35","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/S1388-1981(00)00138-4","volume":"1529","author":"WD Nes","year":"2000","unstructured":"Nes WD (2000) Sterol methyl transferase: enzymology and inhibition. Mol Cell Biol Lipids 1529:63\u201388. https:\/\/doi.org\/10.1016\/S1388-1981(00)00138-4","journal-title":"Mol Cell Biol Lipids"},{"key":"563_CR36","doi-asserted-by":"publisher","first-page":"2937","DOI":"10.1128\/aac.48.8.2937-2950.2004","volume":"48","author":"S Orenes Lorente","year":"2004","unstructured":"Orenes Lorente S, Rodrigues JCF, Jim\u00e9nez Jim\u00e9nez C, Joyce-Menekse M, Rodrigues C, Croft SL, Yardley V, de Luca-Fradley K, Ruiz-P\u00e9rez LM, Urbina J, de Souza W, Gonz\u00e1lez Pacanowska D, Gilbert IH (2004) Novel azasterols as potential agents for treatment of Leishmaniasis and Trypanosomiasis. Antimicrob Agents Chemother 48:2937\u20132950. https:\/\/doi.org\/10.1128\/aac.48.8.2937-2950.2004","journal-title":"Antimicrob Agents Chemother"},{"key":"563_CR37","doi-asserted-by":"publisher","first-page":"101162","DOI":"10.1016\/j.imu.2023.101162","volume":"37","author":"PO Sakyi","year":"2023","unstructured":"Sakyi PO, Broni E, Amewu RK, Miller WA, Wilson MD, Kwofie SK (2023) Targeting Leishmania Donovani sterol methyltransferase for leads using pharmacophore modeling and computational molecular mechanics studies. Inf Med Unlocked 37:101162. https:\/\/doi.org\/10.1016\/j.imu.2023.101162","journal-title":"Inf Med Unlocked"},{"key":"563_CR38","doi-asserted-by":"publisher","first-page":"6502","DOI":"10.1021\/acs.jcim.0c01095","volume":"60","author":"F Flachsenberg","year":"2020","unstructured":"Flachsenberg F, Meyder A, Sommer K, Penner P, Rarey M (2020) A consistent Scheme for gradient-based optimization of protein\u2013ligand poses. J Chem Inf Model 60:6502\u20136522. https:\/\/doi.org\/10.1021\/acs.jcim.0c01095","journal-title":"J Chem Inf Model"},{"key":"563_CR39","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1021\/acs.jcim.3c01573","volume":"64","author":"F Flachsenberg","year":"2024","unstructured":"Flachsenberg F, Ehrt C, Gutermuth T, Rarey M (2024) Redocking the PDB. J Chem Inf Model 64:219\u2013237. https:\/\/doi.org\/10.1021\/acs.jcim.3c01573","journal-title":"J Chem Inf Model"},{"key":"563_CR40","doi-asserted-by":"publisher","first-page":"e4530","DOI":"10.1002\/pro.4530","volume":"32","author":"M Holcomb","year":"2022","unstructured":"Holcomb M, Chang Y, Goodsell DS, Forli S (2022) Evaluation of AlphaFold2 structures as docking targets. Protein Sci 32:e4530. https:\/\/doi.org\/10.1002\/pro.4530","journal-title":"Protein Sci"},{"key":"563_CR41","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1134\/S002689332202011X","volume":"56","author":"AY Rudenko","year":"2022","unstructured":"Rudenko AY, Mariasina SS, Sergiev PV,\u00a0Polshakov VI (2022) Analogs of S-Adenosyl-L-Methionine in studies of Methyltransferases. Mol Biol 56:229\u2013250. https:\/\/doi.org\/10.1134\/S002689332202011X","journal-title":"Mol Biol"},{"key":"563_CR42","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/1472-6807-5-19","volume":"5","author":"PZ Kozbial","year":"2005","unstructured":"Kozbial PZ, Mushegian AR (2005) Natural history of S-adenosylmethionine-binding proteins. BMC Struct Biol 5:19. https:\/\/doi.org\/10.1186\/1472-6807-5-19","journal-title":"BMC Struct Biol"},{"key":"563_CR43","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1021\/acs.jcim.5b00588","volume":"56","author":"S Bietz","year":"2016","unstructured":"Bietz S, Rarey M (2016) SIENA: efficient compilation of selective protein binding site ensembles. J Chem Inf Model 56:248\u2013259. https:\/\/doi.org\/10.1021\/acs.jcim.5b00588","journal-title":"J Chem Inf Model"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-024-00563-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10822-024-00563-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-024-00563-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,26]],"date-time":"2024-11-26T12:16:42Z","timestamp":1732623402000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10822-024-00563-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,30]]},"references-count":43,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,12]]}},"alternative-id":["563"],"URL":"https:\/\/doi.org\/10.1007\/s10822-024-00563-3","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,30]]},"assertion":[{"value":"3 April 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 May 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 May 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare the following competing financial interest(s): Proteins<i>Plus<\/i> and the NAOMI ChemBioSuite use some methods that are jointly owned and\/or licensed to BioSolveIT GmbH, Germany, MR is a shareholder of BioSolveIT GmbH.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"The GeoMine application is available at . The code of the InteractionDrawer library used for the drawing of interactive 2D diagrams is available at .","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Software availability"}}],"article-number":"23"}}