{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T10:16:30Z","timestamp":1772619390571,"version":"3.50.1"},"reference-count":50,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T00:00:00Z","timestamp":1719878400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T00:00:00Z","timestamp":1719878400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"Science and Technology Department of National Administration of Traditional Chinese Medicine & Zhejiang Provincial Administration of Traditional Chinese Medicine","award":["GZY-ZJ-KJ-23032"],"award-info":[{"award-number":["GZY-ZJ-KJ-23032"]}]},{"name":"ZheJiang Province Natural Science Funding of China","award":["LGF20B020001"],"award-info":[{"award-number":["LGF20B020001"]}]},{"name":"Research Initiation Project of the Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University","award":["KYQD20230901"],"award-info":[{"award-number":["KYQD20230901"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Divers"],"published-print":{"date-parts":[[2024,8]]},"DOI":"10.1007\/s11030-024-10916-7","type":"journal-article","created":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T14:03:38Z","timestamp":1719929018000},"page":"2245-2262","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Identification of potential PIM-2 inhibitors via ligand-based generative models, molecular docking and molecular dynamics simulations"],"prefix":"10.1007","volume":"28","author":[{"given":"Tianli","family":"Qin","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yijian","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Miaomiao","family":"Kong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongliang","family":"Zhong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tao","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zixuan","family":"Xi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhenyong","family":"Qian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ke","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuepiao","family":"Cai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianzhang","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wulan","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,7,2]]},"reference":[{"issue":"9","key":"10916_CR1","doi-asserted-by":"publisher","first-page":"2570","DOI":"10.7150\/jca.53134","volume":"12","author":"Y Wang","year":"2021","unstructured":"Wang Y, Xiu J, Ren C, Yu Z (2021) Protein kinase PIM2: a simple PIM family kinase with complex functions in cancer metabolism and therapeutics. J Cancer 12(9):2570\u20132581. https:\/\/doi.org\/10.7150\/jca.53134","journal-title":"J Cancer"},{"issue":"15","key":"10916_CR2","doi-asserted-by":"publisher","first-page":"2316","DOI":"10.1182\/blood.2021014011","volume":"139","author":"M Haas","year":"2022","unstructured":"Haas M, Caron G, Chatonnet F, Manenti S, Alaterre E, Devin J et al (2022) PIM2 kinase has a pivotal role in plasmablast generation and plasma cell survival, opening up novel treatment options in myeloma. Blood 139(15):2316\u20132337. https:\/\/doi.org\/10.1182\/blood.2021014011","journal-title":"Blood"},{"issue":"1","key":"10916_CR3","doi-asserted-by":"publisher","first-page":"67","DOI":"10.3390\/cancers15010067","volume":"15","author":"Z Liu","year":"2023","unstructured":"Liu Z, Guo Y, Liu X, Cao P, Liu H, Dong X et al (2023) Pim-2 Kinase regulates energy metabolism in multiple myeloma. Cancers 15(1):67","journal-title":"Cancers"},{"issue":"9","key":"10916_CR4","doi-asserted-by":"publisher","first-page":"1237","DOI":"10.1038\/aps.2016.60","volume":"37","author":"YQ Zhao","year":"2016","unstructured":"Zhao YQ, Yin YQ, Liu J, Wang GH, Huang J, Zhu LJ, Wang JH (2016) Characterization of HJ-PI01 as a novel Pim-2 inhibitor that induces apoptosis and autophagic cell death in triple-negative human breast cancer. Acta Pharmacol Sin 37(9):1237\u201350. https:\/\/doi.org\/10.1038\/aps.2016.60","journal-title":"Acta Pharmacol Sin"},{"key":"10916_CR5","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1016\/j.cellsig.2018.11.011","volume":"59","author":"W Han","year":"2019","unstructured":"Han W, Li N, Liu J, Sun Y, Yang X, Wang Y (2019) MicroRNA-26b-5p enhances T cell responses by targeting PIM-2 in hepatocellular carcinoma. Cellular Signal 59:182\u201390. https:\/\/doi.org\/10.1016\/j.cellsig.2018.11.011","journal-title":"Cellular Signal"},{"issue":"7","key":"10916_CR6","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1038\/s41419-020-2700-0","volume":"11","author":"X Tang","year":"2020","unstructured":"Tang X, Cao T, Zhu Y, Zhang L, Chen J, Liu T et al (2020) PIM2 promotes hepatocellular carcinoma tumorigenesis and progression through activating NF-\u03baB signaling pathway. Cell Death Dis 11(7):510. https:\/\/doi.org\/10.1038\/s41419-020-2700-0","journal-title":"Cell Death Dis"},{"issue":"1","key":"10916_CR7","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1007\/s12253-017-0353-9","volume":"25","author":"K Ren","year":"2019","unstructured":"Ren K, Gou X, Xiao M, He W, Kang J (2019) Pim-2 cooperates with downstream factor XIAP to inhibit apoptosis and intensify malignant grade in prostate cancer. Pathol Oncol Res 25(1):341\u2013348. https:\/\/doi.org\/10.1007\/s12253-017-0353-9","journal-title":"Pathol Oncol Res"},{"issue":"13","key":"10916_CR8","doi-asserted-by":"publisher","first-page":"1462","DOI":"10.1002\/pros.22693","volume":"73","author":"K Ren","year":"2013","unstructured":"Ren K, Gou X, Xiao M, Wang M, Liu C, Tang Z, He W (2013) The over-expression of Pim-2 promote the tumorigenesis of prostatic carcinoma through phosphorylating eIF4B. Prostate 73(13):1462\u20131469. https:\/\/doi.org\/10.1002\/pros.22693","journal-title":"Prostate"},{"issue":"38","key":"10916_CR9","doi-asserted-by":"publisher","first-page":"6537","DOI":"10.1038\/s41388-019-0898-z","volume":"38","author":"X Han","year":"2019","unstructured":"Han X, Ren C, Yang T, Qiao P, Wang L, Jiang A et al (2019) Negative regulation of AMPK\u03b11 by PIM2 promotes aerobic glycolysis and tumorigenesis in endometrial cancer. Oncogene 38(38):6537\u20136549. https:\/\/doi.org\/10.1038\/s41388-019-0898-z","journal-title":"Oncogene"},{"issue":"1","key":"10916_CR10","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.bbrc.2018.09.062","volume":"506","author":"H Xin","year":"2018","unstructured":"Xin H, Deng Y, Cao J (2018) Proviral insertion in murine lymphomas 2 promotes stomach cancer progression by regulating apoptosis via reactive oxygen species-triggered endoplasmic reticulum stress. Biochem Biophys Res Commun 506(1):145\u2013152. https:\/\/doi.org\/10.1016\/j.bbrc.2018.09.062","journal-title":"Biochem Biophys Res Commun"},{"issue":"4","key":"10916_CR11","doi-asserted-by":"publisher","first-page":"953","DOI":"10.1016\/j.bbrc.2016.03.160","volume":"473","author":"Z Yu","year":"2016","unstructured":"Yu Z, Huang L, Qiao P, Jiang A, Wang L, Yang T et al (2016) PKM2 Thr454 phosphorylation increases its nuclear translocation and promotes xenograft tumor growth in A549 human lung cancer cells. Biochem Biophys Res Commun 473(4):953\u2013958. https:\/\/doi.org\/10.1016\/j.bbrc.2016.03.160","journal-title":"Biochem Biophys Res Commun"},{"issue":"3","key":"10916_CR12","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1038\/leu.2017.284","volume":"32","author":"MA Hospital","year":"2018","unstructured":"Hospital MA, Jacquel A, Mazed F, Saland E, Larrue C, Mondesir J et al (2018) RSK2 is a new Pim2 target with pro-survival functions in FLT3-ITD-positive acute myeloid leukemia. Leukemia 32(3):597\u2013605. https:\/\/doi.org\/10.1038\/leu.2017.284","journal-title":"Leukemia"},{"issue":"9","key":"10916_CR13","doi-asserted-by":"publisher","first-page":"2140","DOI":"10.3109\/10428194.2015.1124991","volume":"57","author":"K Kapelko-Slowik","year":"2016","unstructured":"Kapelko-Slowik K, Owczarek TB, Grzymajlo K, Urbaniak-Kujda D, Jazwiec B, Slowik M et al (2016) Elevated PIM2 gene expression is associated with poor survival of patients with acute myeloid leukemia. Leuk Lymphoma 57(9):2140\u20132149. https:\/\/doi.org\/10.3109\/10428194.2015.1124991","journal-title":"Leuk Lymphoma"},{"issue":"21","key":"10916_CR14","doi-asserted-by":"publisher","first-page":"6436","DOI":"10.3390\/molecules26216436","volume":"26","author":"K Kaewchim","year":"2021","unstructured":"Kaewchim K, Glab-ampai K, Mahasongkram K, Chulanetra M, Seesuay W, Chaicumpa W, Sookrung N (2021) Engineered fully human single-chain monoclonal antibodies to PIM2 kinase. Molecules 26(21):6436","journal-title":"Molecules"},{"issue":"1","key":"10916_CR15","doi-asserted-by":"publisher","first-page":"1844","DOI":"10.1038\/s41467-019-09867-7","volume":"10","author":"K Miyakawa","year":"2019","unstructured":"Miyakawa K, Matsunaga S, Yokoyama M, Nomaguchi M, Kimura Y, Nishi M et al (2019) PIM kinases facilitate lentiviral evasion from SAMHD1 restriction via Vpx phosphorylation. Nat Commun 10(1):1844. https:\/\/doi.org\/10.1038\/s41467-019-09867-7","journal-title":"Nat Commun"},{"issue":"Supplement 1","key":"10916_CR16","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1182\/blood-2022-159086","volume":"140","author":"F El Chaer","year":"2022","unstructured":"El Chaer F, McCloskey J, Rein LAM, Brown RA, Green SD, Pu JJ et al (2022) Preliminary data from the phase I\/II study of TP-3654, a selective oral PIM1 kinase inhibitor, in patients with myelofibrosis previously treated with or ineligible for JAK inhibitor therapy. Blood 140(Supplement 1):594\u2013595. https:\/\/doi.org\/10.1182\/blood-2022-159086","journal-title":"Blood"},{"issue":"16","key":"10916_CR17","doi-asserted-by":"publisher","first-page":"8736","DOI":"10.1021\/jacs.2c13467","volume":"145","author":"DM Anstine","year":"2023","unstructured":"Anstine DM, Isayev O (2023) Generative models as an emerging paradigm in the chemical sciences. J Am Chem Soc 145(16):8736\u20138750. https:\/\/doi.org\/10.1021\/jacs.2c13467","journal-title":"J Am Chem Soc"},{"issue":"8","key":"10916_CR18","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1038\/nrd1799","volume":"4","author":"G Schneider","year":"2005","unstructured":"Schneider G, Fechner U (2005) Computer-based de novo design of drug-like molecules. Nat Rev Drug Discov 4(8):649\u2013663. https:\/\/doi.org\/10.1038\/nrd1799","journal-title":"Nat Rev Drug Discov"},{"issue":"1","key":"10916_CR19","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1021\/acscentsci.7b00512","volume":"4","author":"MHS Segler","year":"2018","unstructured":"Segler MHS, Kogej T, Tyrchan C, Waller MP (2018) Generating focused molecule libraries for drug discovery with recurrent neural networks. ACS Cent Sci 4(1):120\u2013131. https:\/\/doi.org\/10.1021\/acscentsci.7b00512","journal-title":"ACS Cent Sci"},{"issue":"2","key":"10916_CR20","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1021\/acscentsci.7b00572","volume":"4","author":"R G\u00f3mez-Bombarelli","year":"2018","unstructured":"G\u00f3mez-Bombarelli R, Wei JN, Duvenaud D, Hern\u00e1ndez-Lobato JM, S\u00e1nchez-Lengeling B, Sheberla D et al (2018) Automatic chemical design using a data-driven continuous representation of molecules. ACS Cent Sci 4(2):268\u2013276. https:\/\/doi.org\/10.1021\/acscentsci.7b00572","journal-title":"ACS Cent Sci"},{"issue":"9","key":"10916_CR21","doi-asserted-by":"publisher","first-page":"1038","DOI":"10.1038\/s41587-019-0224-x","volume":"37","author":"A Zhavoronkov","year":"2019","unstructured":"Zhavoronkov A, Ivanenkov YA, Aliper A, Veselov MS, Aladinskiy VA, Aladinskaya AV et al (2019) Deep learning enables rapid identification of potent DDR1 kinase inhibitors. Nat Biotechnol 37(9):1038\u20131040. https:\/\/doi.org\/10.1038\/s41587-019-0224-x","journal-title":"Nat Biotechnol"},{"issue":"15","key":"10916_CR22","doi-asserted-by":"publisher","first-page":"10808","DOI":"10.1021\/acs.jmedchem.3c01009","volume":"66","author":"J Jin","year":"2023","unstructured":"Jin J, Wang D, Shi G, Bao J, Wang J, Zhang H et al (2023) FFLOM: a flow-based autoregressive model for fragment-to-lead optimization. J Med Chem 66(15):10808\u201310823. https:\/\/doi.org\/10.1021\/acs.jmedchem.3c01009","journal-title":"J Med Chem"},{"issue":"1","key":"10916_CR23","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1021\/acs.jmedchem.1c01205","volume":"65","author":"X Tan","year":"2022","unstructured":"Tan X, Li C, Yang R, Zhao S, Li F, Li X et al (2022) Discovery of Pyrazolo[3,4-d]pyridazinone derivatives as selective DDR1 inhibitors via deep learning based design, synthesis, and biological evaluation. J Med Chem 65(1):103\u2013119. https:\/\/doi.org\/10.1021\/acs.jmedchem.1c01205","journal-title":"J Med Chem"},{"issue":"16","key":"10916_CR24","doi-asserted-by":"publisher","first-page":"8683","DOI":"10.1021\/acs.jmedchem.9b02147","volume":"63","author":"C Cai","year":"2020","unstructured":"Cai C, Wang S, Xu Y, Zhang W, Tang K, Ouyang Q et al (2020) Transfer learning for drug discovery. J Med Chem 63(16):8683\u20138694. https:\/\/doi.org\/10.1021\/acs.jmedchem.9b02147","journal-title":"J Med Chem"},{"issue":"3","key":"10916_CR25","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1038\/s42256-020-0160-y","volume":"2","author":"M Moret","year":"2020","unstructured":"Moret M, Friedrich L, Grisoni F, Merk D, Schneider G (2020) Generative molecular design in low data regimes. Nat Mach Intell 2(3):171\u2013180. https:\/\/doi.org\/10.1038\/s42256-020-0160-y","journal-title":"Nat Mach Intell"},{"issue":"3","key":"10916_CR26","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1007\/s00521-004-0411-6","volume":"13","author":"AK Seghouane","year":"2004","unstructured":"Seghouane AK, Moudden Y, Fleury G (2004) Regularizing the effect of input noise injection in feedforward neural networks training. Neural Comput Appl 13(3):248\u2013254. https:\/\/doi.org\/10.1007\/s00521-004-0411-6","journal-title":"Neural Comput Appl"},{"issue":"2","key":"10916_CR27","doi-asserted-by":"publisher","first-page":"824","DOI":"10.1021\/acs.iecr.9b05885","volume":"59","author":"SY Zhang","year":"2020","unstructured":"Zhang SY, Bi KX, Qiu T (2020) Bidirectional recurrent neural network-based chemical process fault diagnosis. Ind Eng Chem Res 59(2):824\u2013834. https:\/\/doi.org\/10.1021\/acs.iecr.9b05885","journal-title":"Ind Eng Chem Res"},{"issue":"3","key":"10916_CR28","doi-asserted-by":"publisher","first-page":"474","DOI":"10.1016\/j.bmcl.2014.12.041","volume":"25","author":"A Ishchenko","year":"2015","unstructured":"Ishchenko A, Zhang L, Le Brazidec JY, Fan J, Chong JH, Hingway A et al (2015) Structure-based design of low-nanomolar PIM kinase inhibitors. Bioorg Med Chem Lett 25(3):474\u201380. https:\/\/doi.org\/10.1016\/j.bmcl.2014.12.041","journal-title":"Bioorg Med Chem Lett"},{"issue":"1","key":"10916_CR29","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1038\/s41392-023-01381-z","volume":"8","author":"Z Yang","year":"2023","unstructured":"Yang Z, Zeng X, Zhao Y, Chen R (2023) AlphaFold2 and its applications in the fields of biology and medicine. Signal Transduct Target Ther 8(1):115. https:\/\/doi.org\/10.1038\/s41392-023-01381-z","journal-title":"Signal Transduct Target Ther"},{"issue":"7","key":"10916_CR30","doi-asserted-by":"publisher","first-page":"1757","DOI":"10.1021\/ci3001277","volume":"52","author":"JJ Irwin","year":"2012","unstructured":"Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG (2012) ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 52(7):1757\u20131768. https:\/\/doi.org\/10.1021\/ci3001277","journal-title":"J Chem Inf Model"},{"issue":"1","key":"10916_CR31","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1186\/s13321-018-0293-8","volume":"10","author":"VD H\u00e4hnke","year":"2018","unstructured":"H\u00e4hnke VD, Kim S, Bolton EE (2018) PubChem chemical structure standardization. J Cheminform 10(1):36. https:\/\/doi.org\/10.1186\/s13321-018-0293-8","journal-title":"J Cheminform"},{"issue":"2","key":"10916_CR32","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1002\/jcc.21334","volume":"31","author":"O Trott","year":"2010","unstructured":"Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31(2):455\u2013461. https:\/\/doi.org\/10.1002\/jcc.21334","journal-title":"J Comput Chem"},{"issue":"7","key":"10916_CR33","doi-asserted-by":"publisher","first-page":"1739","DOI":"10.1021\/jm0306430","volume":"47","author":"RA Friesner","year":"2004","unstructured":"Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT et al (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47(7):1739\u201349. https:\/\/doi.org\/10.1021\/jm0306430","journal-title":"J Med Chem"},{"key":"10916_CR34","unstructured":"Delano WL (2002) PyMOL: An Open-Source Molecular Graphics Tool"},{"issue":"W1","key":"10916_CR35","doi-asserted-by":"publisher","first-page":"W530","DOI":"10.1093\/nar\/gkab294","volume":"49","author":"MF Adasme","year":"2021","unstructured":"Adasme MF, Linnemann KL, Bolz SN, Kaiser F, Salentin S, Haupt VJ, Schroeder M (2021) PLIP 2021: expanding the scope of the protein\u2013ligand interaction profiler to DNA and RNA. Nucleic Acids Res 49(W1):W530\u2013W534. https:\/\/doi.org\/10.1093\/nar\/gkab294","journal-title":"Nucleic Acids Res"},{"key":"10916_CR36","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1007\/978-1-4939-9869-2_17","volume":"2073","author":"TA Collier","year":"2020","unstructured":"Collier TA, Piggot TJ, Allison JR (2020) Molecular dynamics simulation of proteins. Methods Mol Biol 2073:311\u2013327. https:\/\/doi.org\/10.1007\/978-1-4939-9869-2_17","journal-title":"Methods Mol Biol"},{"key":"10916_CR37","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","volume":"1","author":"MJMT Abraham","year":"2015","unstructured":"Abraham MJMT, Schulz R, P\u00e1ll S, Smith JC, Hess B et al (2015) GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1:19\u201325","journal-title":"SoftwareX"},{"issue":"7","key":"10916_CR38","doi-asserted-by":"publisher","first-page":"1951","DOI":"10.1021\/ci500020m","volume":"54","author":"R Kumari","year":"2014","unstructured":"Kumari R, Kumar R, Lynn A (2014) g_mmpbsa\u2014A GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model 54(7):1951\u20131962. https:\/\/doi.org\/10.1021\/ci500020m","journal-title":"J Chem Inf Model"},{"issue":"W1","key":"10916_CR39","doi-asserted-by":"publisher","first-page":"W5","DOI":"10.1093\/nar\/gkab255","volume":"49","author":"G Xiong","year":"2021","unstructured":"Xiong G, Wu Z, Yi J, Fu L, Yang Z, Hsieh C et al (2021) ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Res 49(W1):W5-w14. https:\/\/doi.org\/10.1093\/nar\/gkab255","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"10916_CR40","doi-asserted-by":"publisher","first-page":"1734","DOI":"10.1021\/ci600238j","volume":"47","author":"S Koichi","year":"2007","unstructured":"Koichi S, Iwata S, Uno T, Koshino H, Satoh H (2007) Algorithm for advanced canonical coding of planar chemical structures that considers stereochemical and symmetric information. J Chem Inf Model 47(5):1734\u20131746. https:\/\/doi.org\/10.1021\/ci600238j","journal-title":"J Chem Inf Model"},{"issue":"1","key":"10916_CR41","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/1758-2946-4-22","volume":"4","author":"NM O'Boyle","year":"2012","unstructured":"O\u2019Boyle NM (2012) Towards a Universal SMILES representation\u2014A standard method to generate canonical SMILES based on the InChI. J Cheminform 4(1):22. https:\/\/doi.org\/10.1186\/1758-2946-4-22","journal-title":"J Cheminform"},{"issue":"12","key":"10916_CR42","doi-asserted-by":"publisher","first-page":"1023","DOI":"10.1038\/s42256-021-00418-8","volume":"3","author":"K Atz","year":"2021","unstructured":"Atz K, Grisoni F, Schneider G (2021) Geometric deep learning on molecular representations. Nat Mach Intell 3(12):1023\u20131032. https:\/\/doi.org\/10.1038\/s42256-021-00418-8","journal-title":"Nat Mach Intell"},{"issue":"7","key":"10916_CR43","doi-asserted-by":"publisher","first-page":"1235","DOI":"10.1162\/neco_a_01199","volume":"31","author":"Y Yu","year":"2019","unstructured":"Yu Y, Si XS, Hu CH, Zhang JX (2019) A review of recurrent neural networks: LSTM cells and network architectures. Neural Comput 31(7):1235\u20131270. https:\/\/doi.org\/10.1162\/neco_a_01199","journal-title":"Neural Comput"},{"key":"10916_CR44","doi-asserted-by":"publisher","first-page":"861","DOI":"10.21105\/joss.00861","volume":"3","author":"L McInnes","year":"2018","unstructured":"McInnes L, Healy J, Saul N, Gro\u00dfberger L (2018) UMAP: uniform manifold approximation and projection. J Open Source Softw 3:861","journal-title":"J Open Source Softw"},{"issue":"7","key":"10916_CR45","doi-asserted-by":"publisher","first-page":"2719","DOI":"10.1021\/jm901137j","volume":"53","author":"JB Baell","year":"2010","unstructured":"Baell JB, Holloway GA (2010) New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem 53(7):2719\u20132740. https:\/\/doi.org\/10.1021\/jm901137j","journal-title":"J Med Chem"},{"issue":"1\u20133","key":"10916_CR46","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/s0169-409x(00)00129-0","volume":"46","author":"CA Lipinski","year":"2001","unstructured":"Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 46(1\u20133):3\u201326. https:\/\/doi.org\/10.1016\/s0169-409x(00)00129-0","journal-title":"Adv Drug Deliv Rev"},{"issue":"18","key":"10916_CR47","doi-asserted-by":"publisher","first-page":"12964","DOI":"10.1039\/c6cp01555g","volume":"18","author":"Z Wang","year":"2016","unstructured":"Wang Z, Sun H, Yao X, Li D, Xu L, Li Y et al (2016) Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power. Phys Chem Chem Phys 18(18):12964\u201312975. https:\/\/doi.org\/10.1039\/c6cp01555g","journal-title":"Phys Chem Chem Phys"},{"key":"10916_CR48","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-020-0416-x","author":"D Probst","year":"2020","unstructured":"Probst D, Reymond JL (2020) Visualization of very large high-dimensional data sets as minimum spanning trees. J Cheminform. https:\/\/doi.org\/10.1186\/s13321-020-0416-x","journal-title":"J Cheminform"},{"issue":"1","key":"10916_CR49","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.1747-0285.2010.00986.x","volume":"76","author":"RY Yang","year":"2010","unstructured":"Yang RY, Yang KS, Pike LJ, Marshall GR (2010) Targeting the dimerization of epidermal growth factor receptors with small-molecule inhibitors. Chem Biol Drug Des 76(1):1\u20139. https:\/\/doi.org\/10.1111\/j.1747-0285.2010.00986.x","journal-title":"Chem Biol Drug Des"},{"issue":"6","key":"10916_CR50","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1085\/jgp.200409111","volume":"124","author":"TW Allen","year":"2004","unstructured":"Allen TW, Andersen OS, Roux B (2004) On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation. J Gen Physiol 124(6):679\u2013690. https:\/\/doi.org\/10.1085\/jgp.200409111","journal-title":"J Gen Physiol"}],"container-title":["Molecular Diversity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11030-024-10916-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11030-024-10916-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11030-024-10916-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,4]],"date-time":"2024-10-04T04:10:21Z","timestamp":1728015021000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11030-024-10916-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,2]]},"references-count":50,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2024,8]]}},"alternative-id":["10916"],"URL":"https:\/\/doi.org\/10.1007\/s11030-024-10916-7","relation":{},"ISSN":["1381-1991","1573-501X"],"issn-type":[{"value":"1381-1991","type":"print"},{"value":"1573-501X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,2]]},"assertion":[{"value":"1 April 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 June 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 July 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 have no competing interests to declare that are relevant to the content of this article.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}]}}