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AutoGrow: a novel algorithm for protein inhibitor design.自动生长：一种用于蛋白质抑制剂设计的新算法。
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AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design.AutoGrow 3.0：一种改进的算法，用于可化学处理、半自动的蛋白质抑制剂设计。
J Mol Graph Model. 2013 Jul;44:104-12. doi: 10.1016/j.jmgm.2013.05.006. Epub 2013 May 23.
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In silico fragment-based drug design with SEED.基于 SEED 的基于片段的计算机药物设计。
Eur J Med Chem. 2018 Aug 5;156:907-917. doi: 10.1016/j.ejmech.2018.07.042. Epub 2018 Jul 17.
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Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening.提炼蛋白质表面的基本特征以改进蛋白质-配体对接、评分和虚拟筛选。
J Comput Aided Mol Des. 2002 Dec;16(12):883-902. doi: 10.1023/a:1023866311551.
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In silico fragment-based drug discovery: setup and validation of a fragment-to-lead computational protocol using S4MPLE.基于片段的计算机药物发现：使用 S4MPLE 建立和验证片段至先导物的计算方案。
J Chem Inf Model. 2013 Apr 22;53(4):836-51. doi: 10.1021/ci4000163. Epub 2013 Apr 11.
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Ligand-protein docking and rational drug design.配体-蛋白质对接与合理药物设计。
Curr Opin Struct Biol. 1995 Apr;5(2):224-8. doi: 10.1016/0959-440x(95)80080-8.
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Improving docking results via reranking of ensembles of ligand poses in multiple X-ray protein conformations with MM-GBSA.通过使用 MM-GBSA 对多个 X 射线蛋白质构象中的配体构象进行重新排序，从而提高对接结果。
J Chem Inf Model. 2014 Oct 27;54(10):2697-717. doi: 10.1021/ci5003735. Epub 2014 Sep 30.
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Importance of molecular computer modeling in anticancer drug development.分子计算机建模在抗癌药物研发中的重要性。
J BUON. 2007 Sep;12 Suppl 1:S101-18.
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FlexE: efficient molecular docking considering protein structure variations.FlexE：考虑蛋白质结构变异的高效分子对接
J Mol Biol. 2001 Apr 27;308(2):377-95. doi: 10.1006/jmbi.2001.4551.
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From drug target to leads--sketching a physicochemical pathway for lead molecule design in silico.从药物靶点到先导化合物——勾勒计算机辅助先导分子设计的物理化学途径
Curr Pharm Des. 2007;13(34):3454-70. doi: 10.2174/138161207782794220.
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PharmacoForge: pharmacophore generation with diffusion models.药物铸造厂：基于扩散模型的药效团生成
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Moldrug algorithm for an automated ligand binding site exploration by 3D aware molecular enumerations.用于通过3D感知分子枚举自动探索配体结合位点的Moldrug算法。
J Cheminform. 2025 May 26;17(1):85. doi: 10.1186/s13321-025-01022-3.
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AILDE Computer-Aided Discovery of Novel Ibuprofen-Coumarin Antitumor Lead Compounds Targeting Cyclooxygenase-2.AILDE计算机辅助发现靶向环氧合酶-2的新型布洛芬-香豆素抗肿瘤先导化合物
ACS Omega. 2024 Sep 19;9(39):41021-41031. doi: 10.1021/acsomega.4c06596. eCollection 2024 Oct 1.
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Design of RNA Polymerase Inhibitors as Therapeutics for Tuberculous Meningitis.作为结核性脑膜炎治疗药物的RNA聚合酶抑制剂的设计
Infect Disord Drug Targets. 2025;25(3):e18715265341228. doi: 10.2174/0118715265341228240827062721.
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Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening.通过基于配体的虚拟预筛选信息指导的进化优化，简化基于片段的药物发现的计算流程。
J Chem Inf Model. 2024 May 13;64(9):3826-3840. doi: 10.1021/acs.jcim.4c00234. Epub 2024 May 2.
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Cheminformatics and artificial intelligence for accelerating agrochemical discovery.用于加速农用化学品发现的化学信息学与人工智能
Front Chem. 2023 Nov 29;11:1292027. doi: 10.3389/fchem.2023.1292027. eCollection 2023.
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An open-source molecular builder and free energy preparation workflow.一个开源分子构建器和自由能制备工作流程。
Commun Chem. 2022;5(1):136. doi: 10.1038/s42004-022-00754-9. Epub 2022 Oct 27.
8
A molecular evolution algorithm for ligand design in DOCK.DOCK 中配体设计的分子进化算法。
J Comput Chem. 2022 Nov 5;43(29):1942-1963. doi: 10.1002/jcc.26993. Epub 2022 Sep 8.
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Systemic evolutionary chemical space exploration for drug discovery.用于药物发现的系统进化化学空间探索。
J Cheminform. 2022 Apr 1;14(1):19. doi: 10.1186/s13321-022-00598-4.
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Efficient Hit-to-Lead Searching of Kinase Inhibitor Chemical Space via Computational Fragment Merging.通过计算片段融合进行激酶抑制剂化学空间的高效从头至先导化合物搜索。
J Chem Inf Model. 2021 Dec 27;61(12):5967-5987. doi: 10.1021/acs.jcim.1c00630. Epub 2021 Nov 11.
本文引用的文献
1
Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei.布氏锥虫中一种必需的RNA编辑连接酶的类药物抑制剂的发现。
Proc Natl Acad Sci U S A. 2008 Nov 11;105(45):17278-83. doi: 10.1073/pnas.0805820105. Epub 2008 Nov 3.
2
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase.基于集成学习的虚拟筛选揭示了针对禽流感神经氨酸酶的潜在新型抗病毒化合物。
J Med Chem. 2008 Jul 10;51(13):3878-94. doi: 10.1021/jm8001197. Epub 2008 Jun 18.
3
FEP-guided selection of bicyclic heterocycles in lead optimization for non-nucleoside inhibitors of HIV-1 reverse transcriptase.在HIV-1逆转录酶非核苷抑制剂的先导化合物优化中，基于自由能扰动引导选择双环杂环化合物。
J Am Chem Soc. 2006 Dec 6;128(48):15372-3. doi: 10.1021/ja066472g.
4
The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design.H5N1禽流感神经氨酸酶的结构为药物设计提供了新机遇。
Nature. 2006 Sep 7;443(7107):45-9. doi: 10.1038/nature05114. Epub 2006 Aug 16.
5
Protein-ligand docking: current status and future challenges.蛋白质-配体对接：现状与未来挑战。
Proteins. 2006 Oct 1;65(1):15-26. doi: 10.1002/prot.21082.
6
Designing molecules by optimizing potentials.通过优化势能来设计分子。
J Am Chem Soc. 2006 Mar 15;128(10):3228-32. doi: 10.1021/ja0572046.
7
Variational particle number approach for rational compound design.用于合理化合物设计的变分粒子数方法
Phys Rev Lett. 2005 Oct 7;95(15):153002. doi: 10.1103/PhysRevLett.95.153002.
8
Computer-based de novo design of drug-like molecules.基于计算机的类药物分子从头设计。
Nat Rev Drug Discov. 2005 Aug;4(8):649-63. doi: 10.1038/nrd1799.
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A component-based software environment for visualizing large macromolecular assemblies.一个用于可视化大型大分子组装体的基于组件的软件环境。
Structure. 2005 Mar;13(3):447-62. doi: 10.1016/j.str.2005.01.010.
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ZINC--a free database of commercially available compounds for virtual screening.锌数据库——一个可用于虚拟筛选的商业可用化合物免费数据库。
J Chem Inf Model. 2005 Jan-Feb;45(1):177-82. doi: 10.1021/ci049714+.
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