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Journal of Biomolecular Structure and Dynamics Volume 35, 2017 - Issue 15
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Research Articles

Evaluation of protein–ligand affinity prediction using steered molecular dynamics simulations

Noriaki OkimotoLaboratory for Computational Molecular Design, Computational Biology Research Core, Quantitative Biology Center (QBiC), RIKEN, QBiC Building B, 6-2-4 Furuedai, Suita, Osaka565-0874, JapanCorrespondence[email protected]
,
Atsushi SuenagaData Management and Integration Team, Molecular Profiling Research Center for Drug Discovery, AIST, Tokyo Waterfront Bio-IT Research Building, 2-4-7 Aomi, Koto-ku, Tokyo135-0064, Japan;Department of Biosciences, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajyosui, Setagaya-ku, Tokyo156-8550, Japan
&
Makoto TaijiLaboratory for Computational Molecular Design, Computational Biology Research Core, Quantitative Biology Center (QBiC), RIKEN, QBiC Building B, 6-2-4 Furuedai, Suita, Osaka565-0874, Japan
Pages 3221-3231 | Received 02 Aug 2016, Accepted 16 Oct 2016, Published online: 07 Nov 2016

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Qianqian Zhang, Nannan Zhao, Xiaoxiao Meng, Fansen Yu, Xiaojun Yao & Huanxiang Liu. (2022) The prediction of protein–ligand unbinding for modern drug discovery. Expert Opinion on Drug Discovery 17:2, pages 191-205.
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Visvaldas Kairys, Lina Baranauskiene, Migle Kazlauskiene, Daumantas Matulis & Egidijus Kazlauskas. (2019) Binding affinity in drug design: experimental and computational techniques. Expert Opinion on Drug Discovery 14:8, pages 755-768.
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Grégory Menchon, Laurent Maveyraud & Georges Czaplicki. 2024. Computational Drug Discovery and Design. Computational Drug Discovery and Design 33 83 .
Yi-Xiao Hu, Jun-wen Fei, Li-Hua Bie & Jun Gao. (2023) Simulation of the ligand-leaving process of the human heat shock protein. Physical Chemistry Chemical Physics 25:41, pages 28465-28472.
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Hoang Linh Nguyen, Nguyen Quoc Thai & Mai Suan Li. (2022) Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution. Journal of Chemical Theory and Computation 18:6, pages 3860-3872.
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Willmor J. Peña Ccoa & Glen M. Hocky. (2022) Assessing models of force-dependent unbinding rates via infrequent metadynamics. The Journal of Chemical Physics 156:12.
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Sergio Decherchi & Andrea Cavalli. (2020) Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation. Chemical Reviews 120:23, pages 12788-12833.
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Quentin Vanhaelen, Yen-Chu Lin & Alex Zhavoronkov. (2020) The Advent of Generative Chemistry. ACS Medicinal Chemistry Letters 11:8, pages 1496-1505.
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Qiankun Gong, Haomiao Zhang, Haozhe Zhang & Changjun Chen. (2020) Calculating the absolute binding free energy of the insulin dimer in an explicit solvent. RSC Advances 10:2, pages 790-800.
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An-hui Wang, Zhi-chao Zhang & Guo-hui Li. (2019) Advances in enhanced sampling molecular dynamics simulations for biomolecules. Chinese Journal of Chemical Physics 32:3, pages 277-286.
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Iman Katouzian & Seid Mahdi Jafari. 2019. Biopolymer Nanostructures for Food Encapsulation Purposes. Biopolymer Nanostructures for Food Encapsulation Purposes 101 124 .
Jelisa Iglesias, Suwipa Saen‐oon, Robert Soliva & Victor Guallar. (2018) Computational structure‐based drug design: Predicting target flexibility. WIREs Computational Molecular Science 8:5.
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Nicolai Popov, Lawrence W. Honaker, Maia Popova, Nadezhda Usol’tseva, Elizabeth K. Mann, Antal Jákli & Piotr Popov. (2017) Thermotropic Liquid Crystal-Assisted Chemical and Biological Sensors. Materials 11:1, pages 20.
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Damian Bartuzi, Agnieszka Kaczor, Katarzyna Targowska-Duda & Dariusz Matosiuk. (2017) Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors. Molecules 22:2, pages 340.
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