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Understanding Docking Complexes of Macromolecules Using HADDOCK: The Synergy between Experimental Data and Computations.使用HADDOCK理解大分子对接复合物：实验数据与计算之间的协同作用。
Bio Protoc. 2020 Oct 20;10(20):e3793. doi: 10.21769/BioProtoc.3793.
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MTMDAT-HADDOCK: high-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry.MTMDAT-HADDOCK：基于有限蛋白酶解和质谱的高通量蛋白质复合物结构建模
BMC Struct Biol. 2012 Nov 15;12:29. doi: 10.1186/1472-6807-12-29.
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HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.HADDOCK：一种基于生化或生物物理信息的蛋白质-蛋白质对接方法。
J Am Chem Soc. 2003 Feb 19;125(7):1731-7. doi: 10.1021/ja026939x.
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The HADDOCK web server for data-driven biomolecular docking.HADDOCK 网页服务器用于数据驱动的生物分子对接。
Nat Protoc. 2010 May;5(5):883-97. doi: 10.1038/nprot.2010.32. Epub 2010 Apr 15.
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Information-Driven Antibody-Antigen Modelling with HADDOCK.基于 HADDOCK 的信息驱动抗体-抗原建模
Methods Mol Biol. 2023;2552:267-282. doi: 10.1007/978-1-0716-2609-2_14.
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Modeling protein-protein complexes using the HADDOCK webserver "modeling protein complexes with HADDOCK".使用HADDOCK网络服务器“用HADDOCK对蛋白质复合物进行建模”来对蛋白质-蛋白质复合物进行建模。
Methods Mol Biol. 2014;1137:163-79. doi: 10.1007/978-1-4939-0366-5_12.
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Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server.基于信息驱动对接构建大分子组装体：介绍 HADDOCK 多体对接服务器。
Mol Cell Proteomics. 2010 Aug;9(8):1784-94. doi: 10.1074/mcp.M000051-MCP201. Epub 2010 Mar 19.
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CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.CPORT：一种共识界面预测器及其在与 HADDOCK 进行预测驱动对接中的性能。
PLoS One. 2011 Mar 25;6(3):e17695. doi: 10.1371/journal.pone.0017695.
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Quantitative use of chemical shifts for the modeling of protein complexes.定量使用化学位移来模拟蛋白质复合物。
Proteins. 2011 Sep;79(9):2662-70. doi: 10.1002/prot.23090. Epub 2011 Jul 8.
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Protein-Protein Modeling Using Cryo-EM Restraints.利用冷冻电镜约束进行蛋白质-蛋白质建模。
Methods Mol Biol. 2020;2112:145-162. doi: 10.1007/978-1-0716-0270-6_11.
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Identifying interactions between TDP-43's N-terminal and RNA-binding domains.
Protein Sci. 2025 Oct;34(10):e70295. doi: 10.1002/pro.70295.
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Mapping the interaction surface between Caβ and actin and its role in calcium channel clearance.绘制Caβ与肌动蛋白之间的相互作用表面及其在钙通道清除中的作用。
Nat Commun. 2025 May 10;16(1):4352. doi: 10.1038/s41467-025-59548-x.
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Mass spectrometry-complemented molecular modeling predicts the interaction interface for a camelid single-domain antibody targeting the circumsporozoite protein's C-terminal domain.质谱辅助分子建模预测了一种靶向环子孢子蛋白C末端结构域的骆驼科单域抗体的相互作用界面。
Comput Struct Biotechnol J. 2024 Aug 28;23:3300-3314. doi: 10.1016/j.csbj.2024.08.023. eCollection 2024 Dec.
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Capturing the catalytic intermediates of parkin ubiquitination.捕获 parkin 泛素化的催化中间体。
Proc Natl Acad Sci U S A. 2024 Aug 6;121(32):e2403114121. doi: 10.1073/pnas.2403114121. Epub 2024 Jul 30.
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The HADDOCK2.4 web server for integrative modeling of biomolecular complexes.HADDOCK2.4 网页服务器用于生物分子复合物的整合建模。
Nat Protoc. 2024 Nov;19(11):3219-3241. doi: 10.1038/s41596-024-01011-0. Epub 2024 Jun 17.
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In Silico Analysis of SARS-CoV-2 Non-Structural Proteins Reveals an Interaction with the Host's Heat Shock Proteins That May Contribute to Viral Replications and Development.2019冠状病毒非结构蛋白的计算机模拟分析揭示了其与宿主热休克蛋白的相互作用，这可能有助于病毒的复制和发展。
Curr Issues Mol Biol. 2023 Dec 18;45(12):10225-10247. doi: 10.3390/cimb45120638.
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evaluation of molecular virus-virus interactions taking place between and .评估发生在……与……之间的分子病毒-病毒相互作用。 （注：原文中“between and”之间缺少具体内容）
PeerJ. 2021 Oct 19;9:e12018. doi: 10.7717/peerj.12018. eCollection 2021.
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Tandem domain structure determination based on a systematic enumeration of conformations.基于构象系统枚举的串联结构域结构测定。
Sci Rep. 2021 Aug 19;11(1):16925. doi: 10.1038/s41598-021-96370-z.
本文引用的文献
1
Isothermal Titration Calorimetry: A Biophysical Method to Characterize the Interaction between Label-free Biomolecules in Solution.等温滴定量热法：一种表征溶液中无标记生物分子间相互作用的生物物理方法。
Bio Protoc. 2018 Aug 5;8(15):e2957. doi: 10.21769/BioProtoc.2957.
2
The HCN domain couples voltage gating and cAMP response in hyperpolarization-activated cyclic nucleotide-gated channels.HCN 结构域将电压门控和 cAMP 反应偶联在超极化激活环核苷酸门控通道中。
Elife. 2019 Nov 26;8:e49672. doi: 10.7554/eLife.49672.
3
Mechanical transduction of cytoplasmic-to-transmembrane-domain movements in a hyperpolarization-activated cyclic nucleotide-gated cation channel.机械转导超极化激活环核苷酸门控阳离子通道细胞质到跨膜结构域的运动。
J Biol Chem. 2018 Aug 17;293(33):12908-12918. doi: 10.1074/jbc.RA118.002139. Epub 2018 Jun 23.
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A synthetic peptide that prevents cAMP regulation in mammalian hyperpolarization-activated cyclic nucleotide-gated (HCN) channels.一种能阻止哺乳类超极化激活环核苷酸门控 (HCN) 通道中 cAMP 调节的合成肽。
Elife. 2018 Jun 20;7:e35753. doi: 10.7554/eLife.35753.
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Fusicoccin Activates KAT1 Channels by Stabilizing Their Interaction with 14-3-3 Proteins.福司可辛通过稳定其与 14-3-3 蛋白的相互作用来激活 KAT1 通道。
Plant Cell. 2017 Oct;29(10):2570-2580. doi: 10.1105/tpc.17.00375. Epub 2017 Sep 29.
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A reduced mechanical model for cAMP-modulated gating in HCN channels.cAMP 调节 HCN 通道门控的简化力学模型。
Sci Rep. 2017 Jan 11;7:40168. doi: 10.1038/srep40168.
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The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.HADDOCK2.2 网页服务器：生物分子复合物的用户友好型综合建模
J Mol Biol. 2016 Feb 22;428(4):720-725. doi: 10.1016/j.jmb.2015.09.014. Epub 2015 Sep 26.
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Structural mechanism for the regulation of HCN ion channels by the accessory protein TRIP8b.辅助蛋白TRIP8b对HCN离子通道进行调控的结构机制。
Structure. 2015 Apr 7;23(4):734-44. doi: 10.1016/j.str.2015.02.007. Epub 2015 Mar 19.
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Structural basis for the mutual antagonism of cAMP and TRIP8b in regulating HCN channel function.环磷酸腺苷（cAMP）与TRIP8b在调节超极化激活的环核苷酸门控（HCN）通道功能中相互拮抗作用的结构基础
Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):14577-82. doi: 10.1073/pnas.1410389111. Epub 2014 Sep 2.
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A unified conformational selection and induced fit approach to protein-peptide docking.一种统一的构象选择和诱导契合方法用于蛋白质-肽对接。
PLoS One. 2013;8(3):e58769. doi: 10.1371/journal.pone.0058769. Epub 2013 Mar 13.
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