Utilization of AlphaFold models for drug discovery: Feasibility and challenges. Histone deacetylase 11 as a case study
Open accessPublished version of a preprint
Abstract
Histone deacetylase 11 (HDAC11), an enzyme that cleaves acyl groups from acylated lysine residues, is the sole member of class IV of HDAC family with no reported crystal structure so far. The catalytic domain of HDAC11 shares low sequence identity with other HDAC isoforms which complicates the conventional template-based homology modeling. AlphaFold is a neural network machine learning approach for predicting the 3D structures of proteins with atomic accuracy even in absence of similar structures. However, the structures predicted by AlphaFold are missing small molecules as ligands and cofactors. In our study, we first optimized the HDAC11 AlphaFold model by adding the catalytic zinc ion followed by assessment of the usability of the model by docking of the selective inhibitor FT895. Minimization of the optimized model in presence of transplanted inhibitors, which have been described as HDAC11 inhibitors, was performed. Four complexes were generated and proved to be stable using three replicas of 50 ns MD simulations and were successfully utilized for docking of the selective inhibitors FT895, MIR002 and SIS17. For SIS17, The most reasonable pose was selected based on structural comparison between HDAC6, HDAC8 and the HDAC11 optimized AlphaFold model. The manually optimized HDAC11 model is thus able to explain the binding behavior of known HDAC11 inhibitors and can be used for further structure-based optimization.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996) · Journal of the American Chemical Society · doi:10.1021/ja9621760 · Cited by 14,078 · see citing works
Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., et al. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm0306430 · Cited by 10,057 · see citing works
Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm051256o · Cited by 6,964 · see citing works
Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-013-9644-8 · Cited by 6,130 · see citing works
Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm030644s · Cited by 5,280 · see citing works
Jorgensen, W. L., & Tirado‐Rives, J. (1988) · Journal of the American Chemical Society · doi:10.1021/ja00214a001 · Cited by 5,018 · see citing works
OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.
Harder, E. D., Damm, W., Maple, J., Wu, C., Reboul, M., Xiang, J.-Y., Wang, L.-L., Lupyan, D., Dahlgren, M. K., Knight, J. L., et al. (2016) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b00864 · Cited by 2,826 · see citing works
A hierarchical approach to all‐atom protein loop prediction
Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T., Honig, B. H., Shaw, D. E., & Friesner, R. A. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10613 · Cited by 2,541 · see citing works
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters
Bowers, K. J., Chow, D. E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossváry, I., Moraes, M. A., Sacerdoti, F. D., et al. (2006) · ACM/IEEE Conference on Supercomputing (SC) · doi:10.1109/sc.2006.54 · Cited by 2,164 · see citing works
Shelley, J. C., Cholleti, A., Frye, L. L., Greenwood, J. R., Timlin, M. R., & Uchimaya, M. (2007) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-007-9133-z · Cited by 2,091 · see citing works
Shivakumar, D., Williams, J., Wu, Y., Damm, W., Shelley, J. C., & Sherman, W. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct900587b · Cited by 1,945 · see citing works
Identifying and Characterizing Binding Sites and Assessing Druggability
Halgren, T. A. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci800324m · Cited by 1,771 · see citing works
On the Role of the Crystal Environment in Determining Protein Side-chain Conformations
Jacobson, M. P., Friesner, R. A., Xiang, Z., & Honig, B. H. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00470-9 · Cited by 1,289 · see citing works
Greenwood, J. R., Calkins, D., Sullivan, A. P., & Shelley, J. C. (2010) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-010-9349-1 · Cited by 967 · see citing works
New Method for Fast and Accurate Binding‐site Identification and Analysis
Halgren, T. (2007) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2007.00483.x · Cited by 880 · see citing works
Gao, L., Cueto, M. A., Asselbergs, F., & Atadja, P. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m111871200 · Cited by 744 · see citing works
Structural Snapshots of Human HDAC8 Provide Insights into the Class I Histone Deacetylases
Somoza, J. R., Skene, R. J., Katz, B. A., Mol, C., Ho, J. D., Jennings, A. J., Luong, C., Arvai, A., Buggy, J. J., Chi, E., et al. (2004) · Structure · doi:10.1016/j.str.2004.04.012 · Cited by 710 · see citing works
Sabe, V. T., Ntombela, T., Jhamba, L. A., Maguire, G. E. M., Govender, T., Naicker, T., & Kruger, H. G. (2021) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2021.113705 · Cited by 631 · see citing works
Histone deacetylase 6 structure and molecular basis of catalysis and inhibition
Hai, Y., & Christianson, D. W. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2134 · Cited by 521 · see citing works
AlphaFill: enriching AlphaFold models with ligands and cofactors
Hekkelman, M. L., de Vries, I., Joosten, R. P., & Perrakis, A. (2023) · Nature Methods · doi:10.1038/s41592-022-01685-y · Cited by 511 · see citing works
The histone deacetylase HDAC11 regulates the expression of interleukin 10 and immune tolerance
Villagra, A., Cheng, F., Wang, H.-W., Suarez, I., Glozak, M., Maurin, M., Nguyen, D., Wright, K. L., Atadja, P. W., Bhalla, K., et al. (2009) · Nature Immunology · doi:10.1038/ni.1673 · Cited by 455 · see citing works
Molecular modeling in drug discovery
Adelusi, T. I., Oyedele, A.-Q. K., Boyenle, I. D., Ogunlana, A. T., Adeyemi, R. O., Divine, U. C., Idris, M. O., Olaoba, O. T., Adedotun, I. O., Oladipo, E. K., et al. (2022) · Informatics in Medicine Unlocked · doi:10.1016/j.imu.2022.100880 · Cited by 409 · see citing works
Ren, F., Ding, X., Zheng, M., Korzinkin, M., Cai, X., Zhu, W., Mantsyzov, A., Aliper, A., Aladinskiy, V., Cao, Z., et al. (2023) · Chemical Science · doi:10.1039/d2sc05709c · Cited by 365 · see citing works
The AlphaFold Database of Protein Structures: A Biologist’s Guide
David, A., Islam, S., Tankhilevich, E., & Sternberg, M. J. E. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167336 · Cited by 268 · see citing works
Arts, J., King, P., Marin, A., Floren, W., Belin, A., Janssen, L., Pilatte, I., Roux, B., Decrane, L., Gilissen, R., et al. (2009) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-09-0547 · Cited by 231 · see citing works
How good are AlphaFold models for docking-based virtual screening?
Scardino, V., Di Filippo, J. I., & Cavasotto, C. N. (2023) · iScience · doi:10.1016/j.isci.2022.105920 · Cited by 207 · see citing works
HDAC11 regulates type I interferon signaling through defatty-acylation of SHMT2
Cao, J., Sun, L., Aramsangtienchai, P., Spiegelman, N. A., Zhang, X., Huang, W., Seto, E., & Lin, H. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1815365116 · Cited by 189 · see citing works
Dysregulated Class I histone deacetylases are indicators of poor prognosis in multiple myeloma
Mithraprabhu, S., Kalff, A., Chow, A. L., Khong, T. T., & Spencer, A. G. (2014) · Epigenetics · doi:10.4161/15592294.2014.983367 · Cited by 176 · see citing works
Histone deacetylase 11 is a fatty-acid deacylase
Kutil, Z., Novakova, Z., Meleshin, M., Mikesova, J., Schutkowski, M., & Barinka, C. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.7b00942 · Cited by 174 · see citing works
Whitehead, L., Dobler, M. R., Radetich, B., Zhu, Y., Atadja, P. W., Claiborne, T., Grob, J. E., McRiner, A., Pancost, M. R., Patnaik, A., et al. (2011) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2011.06.030 · Cited by 164 · see citing works
Computational Drug Design Methods—Current and Future Perspectives
Prieto-Martínez, F. D., López‐López, E., Juárez‐Mercado, K. E., & Medina‐Franco, J. L. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-816125-8.00002-x · Cited by 152 · see citing works
Histone deacetylase 11 is an ε-N-Myristoyllysine hydrolase
Moreno-Yruela, C., Galleano, I., Madsen, A. S., & Olsen, C. A. (2018) · Cell Chemical Biology · doi:10.1016/j.chembiol.2018.04.007 · Cited by 149 · see citing works
Cheng, F., Lienlaf, M., Perez-Villarroel, P., Wang, H.-W., Lee, C., Woan, K., Woods, D., Knox, T., Bergman, J., Pinilla-Ibarz, J., et al. (2014) · Molecular Immunology · doi:10.1016/j.molimm.2014.02.019 · Cited by 140 · see citing works
Programming and regulation of metabolic homeostasis by HDAC11
Sun, L., Marin de Evsikova, C., Bian, K., Achille, A., Telles, E., Pei, H., & Seto, E. (2018) · EBioMedicine · doi:10.1016/j.ebiom.2018.06.025 · Cited by 125 · see citing works
Protein structure prediction has reached the single-structure frontier
Lane, T. J. (2023) · Nature Methods · doi:10.1038/s41592-022-01760-4 · Cited by 125 · see citing works
Freese, K., Seitz, T., Dietrich, P., Lee, S. M. L., Thasler, W. E., Bosserhoff, A., & Hellerbrand, C. (2019) · Cancers · doi:10.3390/cancers11101587 · Cited by 124 · see citing works
Marek, M., Shaik, T. B., Heimburg, T., Chakrabarti, A., Lancelot, J., Ramos-Morales, E., Da Veiga, C., Kalinin, D., Melesina, J., Robaa, D., et al. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b01087 · Cited by 123 · see citing works
Self-citationHDAC8 catalyzes the hydrolysis of long chain fatty acyl lysine
Aramsangtienchai, P., Spiegelman, N. A., He, B., Miller, S. P., Dai, L., Zhao, Y., & Lin, H. (2016) · ACS Chemical Biology · doi:10.1021/acschembio.6b00396 · Cited by 118 · see citing works
HDAC11: a rising star in epigenetics
Liu, S., Wu, F., Jin, Y., Weiqin, C., & Xu, T. (2020) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2020.110607 · Cited by 116 · see citing works
HDAC11 suppresses the thermogenic program of adipose tissue via BRD2
Bagchi, R. A., Ferguson, B. S., Stratton, M. S., Hu, T., Cavasin, M. A., Sun, L., Lin, Y.-H., Liu, D., Londono, P., Song, K., et al. (2018) · JCI Insight · doi:10.1172/jci.insight.120159 · Cited by 110 · see citing works
Evaluation of AlphaFold2 structures as docking targets
Holcomb, M., Chang, Y., Goodsell, D. S., & Forli, S. (2022) · Protein Science · doi:10.1002/pro.4530 · Cited by 109 · see citing works
Yu, C., Chang, P., Hsin, L., & Chern, J. (2013) · Journal of Medicinal Chemistry · doi:10.1021/jm400564j · Cited by 106 · see citing works
HDAC11 is a regulator of diverse immune functions
Yanginlar, C., & Logie, C. (2017) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2017.12.002 · Cited by 106 · see citing works
Activity-Guided Design of HDAC11-Specific Inhibitors
Son, S. I., Cao, J., Zhu, C., Miller, S. P., & Lin, H. (2019) · ACS Chemical Biology · doi:10.1021/acschembio.9b00292 · Cited by 85 · see citing works
Binding of the Microbial Cyclic Tetrapeptide Trapoxin A to the Class I Histone Deacetylase HDAC8
Porter, N. J., & Christianson, D. W. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.7b00330 · Cited by 73 · see citing works
Chen, Y. X., Wang, X., Xiang, W., He, L., Tang, M., Wang, F., Wang, T., Yang, Z., Yi, Y., Wang, H., et al. (2016) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6b00579 · Cited by 72 · see citing works
Lundh, M., Christensen, D. P., Rasmussen, D. N., Mascagni, P., Dinarello, C. A., Billestrup, N., Grunnet, L. G., & Mandrup-Poulsen, T. R. (2010) · Diabetologia · doi:10.1007/s00125-010-1892-8 · Cited by 71 · see citing works
Neuroblastoma cells depend on HDAC11 for mitotic cell cycle progression and survival
Thole, T. M., Lodrini, M., Fabian, J., Wuenschel, J., Pfeil, S., Hielscher, T., Kopp-Schneider, A., Heinicke, U., Fulda, S., Witt, O., et al. (2017) · Cell Death & Disease · doi:10.1038/cddis.2017.49 · Cited by 67 · see citing works
HDAC11 deficiency disrupts oncogene-induced hematopoiesis in myeloproliferative neoplasms
Yue, L., Sharma, V., Horvat, N. P., Akuffo, A. A., Beatty, M. S., Murdun, C., Colin, C., Billington, J. M. R., Goodheart, W. E., Sahakian, E., et al. (2020) · Blood · doi:10.1182/blood.2019895326 · Cited by 67 · see citing works
Martin, M. W., Lee, J. Y., Lancia, D. R., Ng, P. Y., Han, B., Thomason, J. R., Lynes, M. S., Marshall, C. G., Conti, C., Collis, A. J., et al. (2018) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2018.05.021 · Cited by 63 · see citing works
Liu, J., Yu, Y., Kelly, J., Sha, D., Alhassan, A.-B., Yu, W., Maletic, M. M., Duffy, J. L., Klein, D. J., Holloway, M. K., et al. (2020) · ACS Medicinal Chemistry Letters · doi:10.1021/acsmedchemlett.0c00462 · Cited by 57 · see citing works
Lai, L., Shin, G. Y., & Qiu, H. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21228504 · Cited by 53 · see citing works
Inhibition of histone deacetylase 11 promotes human liver cancer cell apoptosis.
Gong, D., Zeng, Z., Yi, F., & Wu, J. (2019) · Europe PMC (PubMed Central) · Cited by 47 · see citing works
Decroos, C., Christianson, N., Gullett, L. E., Bowman, C. M., Christianson, K. E., Deardorff, M. A., & Christianson, D. W. (2015) · Biochemistry · doi:10.1021/acs.biochem.5b00881 · Cited by 46 · see citing works
Wang, W., Ding, B., Lou, W., & Lin, S. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.00724 · Cited by 46 · see citing works
Histone deacetylase 11 suppresses p53 expression in pituitary tumor cells
Wang, W., Fu, L., Li, S., Xu, Z., & Li, X. (2017) · Cell Biology International · doi:10.1002/cbin.10834 · Cited by 41 · see citing works
Continuous Activity Assay for HDAC11 Enabling Reevaluation of HDAC Inhibitors
Kutil, Z., Mikešová, J., Zessin, M., Meleshin, M., Nováková, Z., Alquicer, G., Kozikowski, A. P., Sippl, W., Bařinka, C., & Schutkowski, M. (2019) · ACS Omega · doi:10.1021/acsomega.9b02808 · Cited by 40 · see citing works
Self-citationLong non‑coding RNA BCYRN1 promotes prostate cancer progression via elevation of HDAC11
Huo, W., Qi, F., & Wang, K. (2020) · Oncology Reports · doi:10.3892/or.2020.7680 · Cited by 35 · see citing works
Trapoxin A Analogue as a Selective Nanomolar Inhibitor of HDAC11
Ho, T. T., Peng, C., Seto, E., & Lin, H. (2023) · ACS Chemical Biology · doi:10.1021/acschembio.2c00840 · Cited by 29 · see citing works
Fei, Q., Song, F., Jiang, X., Hong, H., Xu, X., Jin, Z., Zhu, X., Dai, B., Yang, J., Sui, C., et al. (2020) · Cancer Cell International · doi:10.1186/s12935-020-01325-5 · Cited by 28 · see citing works
Biomolecular Simulations in Structure‐Based Drug Discovery
Gervasio, F. L., & Spiwok, V. (2018) · Methods and principles in medicinal chemistry · doi:10.1002/9783527806836 · Cited by 26 · see citing works
Bülbül, E. F., Melesina, J., Ibrahim, H. S., Abdelsalam, M. A. M., Vecchio, A., Robaa, D., Zessin, M., Schutkowski, M., & Sippl, W. (2022) · Molecules · doi:10.3390/molecules27082526 · Cited by 17 · see citing works
Self-citationAntitumor activity of novel POLA1-HDAC11 dual inhibitors
Dallavalle, S., Musso, L., Cincinelli, R., Darwiche, N., Gervasoni, S. I., Vistoli, G., Guglielmi, M. B., Porta, I. L., Pizzulo, M., Modica, E., et al. (2021) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2021.113971 · Cited by 17 · see citing works
He, F., Wang, X., Wu, Q., Liu, S.-Z., Cao, Y., Guo, X., Yin, S., Yin, N., Li, B., & Fang, M. (2023) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2023.106645 · Cited by 16 · see citing works
Promoter conservation in HDACs points to functional implications
Boltz, T. A., Khuri, S., & Wuchty, S. (2019) · BMC Genomics · doi:10.1186/s12864-019-5973-x · Cited by 14 · see citing works
Yang, H., Yang, J., Cheng, H., Cao, H., Tang, S., Wang, Q., Zhao, J., Li, B., Ding, Y., & Ma, C. (2019) · Scientific Reports · doi:10.1038/s41598-019-54558-4 · Cited by 14 · see citing works
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Cited by
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Baselious, F., Hilscher, S., Robaa, D., Barinka, C., Schutkowski, M., & Sippl, W. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25021358 · Cited by 32 · see citing works
Self-citationBiological function and small molecule inhibitors of histone deacetylase 11
Jia, G., Liu, J., Hou, X., Jiang, Y., & Li, X. (2024) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2024.116634 · Cited by 19 · see citing works
Khatun, S., Bhagat, R. P., Dutta, R., Datta, A., Jaiswal, A., Halder, S., Jha, T., Amin, S. A., & Gayen, S. (2024) · Biochemical Pharmacology · doi:10.1016/j.bcp.2024.116312 · Cited by 15 · see citing works
Baselious, F., Hilscher, S., Hagemann, S., Tripathee, S., Robaa, D., Barinka, C., Hüttelmaier, S., Schutkowski, M., & Sippl, W. (2024) · Archiv der Pharmazie · doi:10.1002/ardp.202400486 · Cited by 16 · see citing works
Self-citationBuccheri, R., Coco, A., Pasquinucci, L., Amata, E., Marrazzo, A., & Rescifina, A. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26020850 · Cited by 7 · see citing works
Bhagat, R. P., Jyotisha, Dasgupta, I., Amin, S. A., Jakkula, P., Bhattacharya, A., Qureshi, I. A., & Gayen, S. (2025) · Molecular Diversity · doi:10.1007/s11030-025-11217-3 · Cited by 6 · see citing works
Berluti, F., Baselious, F., Hagemann, S., Hilscher, S., Schmidt, M., Hüttelmaier, S., Schutkowski, M., Sippl, W., & Ibrahim, H. S. (2024) · Archiv der Pharmazie · doi:10.1002/ardp.202400437 · Cited by 5 · see citing works
Self-citationHilscher, S., Meleshin, M., Baselious, F., Bařinka, C., Sippl, W., Schutkowski, M., & Schiene‐Fischer, C. (2025) · ACS Omega · doi:10.1021/acsomega.5c08195 · Cited by 4 · see citing works
Self-citationDiscovery and Characterization of Novel Non-Hydroxamate HDAC11 Inhibitors
Kopranovic, A., & Meyer‐Almes, F. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26135950 · Cited by 3 · see citing works
Resurgence of magnetic resonance techniques in the era of AlphaFold
Skinner, C. E., Haynes, B. A., & Isaacson, R. L. (2025) · Biophysical Reviews · doi:10.1007/s12551-025-01329-3 · Cited by 2 · see citing works
da Silva, A. D., & de Azevedo, W. F. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4949-7_13 · Cited by 1 · see citing works
Nováková, Z., Bartošová‐Sojková, P., Kudlacova, J., Baselious, F., Kutil, Z., Jaklová, P., Meleshin, M., Motlova, L., Schenkmayerová, A., Vrkoslav, V., et al. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag150 · Cited by 1 · see citing works
Self-citationBaselious, F., Hilscher, S., Handke, L., Bařinka, C., Schutkowski, M., & Sippl, W. (2025) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2025.110695 · Cited by 1 · see citing works
Self-citationKhan, A., Mohammad, A., Alshabrmi, F. M., Alatawi, E. A., Junaid, M., & Agouni, A. (2025) · Virus Research · doi:10.1016/j.virusres.2025.199665
HDAC11 Deacetylates BRAF to Regulate Kinase Activity and Cell Proliferation
Madueke, C. A., Andrade, R. E., & Pflum, M. K. H. (2025) · ACS Chemical Biology · doi:10.1021/acschembio.5c00631
Innovative AI for Drug Manufacturing
Ayyaswamy, K., Gobinath, V. M., & Kathirvel, N. (2026) · IGI Global eBooks · doi:10.4018/979-8-3373-7478-9.ch004
Structural and Enzymatic Basis for Impaired Deacylation of N -Acyl- N -Methyl Lysine Residues
Hilscher, S., Böttcher, P. H., Friedrich, F., Pannek, M., Baselious, F., Meleshin, M., Einsle, O., Bařinka, C., Steegborn, C., Sippl, W., et al. (2026) · Biochemistry · doi:10.1021/acs.biochem.6c00508 · Cited by 1 · see citing works
Self-citationPatel, A. R., Ghoghari, R. N., Makwana, B. S., Patel, A., & Chikhalia, K. H. (2026) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2026.147718
BindingDB (2026) · UC San Diego · doi:10.7270/q2b85dzw
- Authors
- Baselious, F., Robaa, D., & Sippl, W.
- Affiliations
- Martin Luther University Halle-Wittenberg (DE)
- Corresponding author
- Sippl, Wolfgang
- Venue
- Computers in Biology and Medicine
- Publisher
- Elsevier BV
- Published
- 2023-12
- Volume
- 167
- Pages
- 107700
- ISSN
- 0010-4825 (ISSN-L)
- OpenAlex
- W4388576120
- Cited by
- 20
- References
- 75
- Citations by year
- 2026: 5 · 2025: 9 · 2024: 5 · 2023: 1
- FWCI
- 2.86
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Computers in Biology and Medicine (publishedVersion, cc-by-nc-nd)
- ChemRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Digitalen Hochschulbibliothek Sachsen-Anhalt (Universitäts- und Landesbibliothek Sachsen-Anhalt)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Histone Deacetylase Inhibitors Research
- Keywords
- HDAC11, AlphaFold, protein structure prediction, structure-based drug design, zinc binding, molecular docking, molecular dynamics simulation, structure-guided optimization
- MeSH terms
- Feasibility Studies, Histone Deacetylases, Drug Discovery, Molecular Dynamics Simulation, Histone Deacetylase Inhibitors
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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