Ligand binding free-energy calculations with funnel metadynamics
Author:
Publisher
Springer Science and Business Media LLC
Subject
General Biochemistry, Genetics and Molecular Biology
Link
https://www.nature.com/articles/s41596-020-0342-4.pdf
Reference83 articles.
1. Pollard, T. D. A guide to simple and informative binding assays. Mol. Biol. Cell. 21, 4061–4067 (2010).
2. Huang, N. & Jacobson, M. P. Physics-based methods for studying protein–ligand interactions. Curr. Opin. Drug Discov. Devel. 10, 325–331 (2007).
3. Broomhead, N. K. & Soliman, M. E. Can we rely on computational predictions to correctly identify ligand binding sites on novel protein drug targets? Assessment of binding site prediction methods and a protocol for validation of predicted binding sites. Cell Biochem. Biophys. 75, 15–23 (2017).
4. Limongelli, V. Ligand binding free energy and kinetics calculations in 2020. WIREs Comp. Mol. Sci. 10, e1455 (2020).
5. Limongelli, V., Bonomi, M. & Parrinello, M. Funnel-metadynamics as accurate binding free-energy method. Proc. Natl Acad. Soc. USA 110, 6358–6363 (2013).
Cited by 108 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献
1. Free energy landscape of the PI3Kα C-terminal activation;Computational and Structural Biotechnology Journal;2024-12
2. AlphaFold-SFA: Accelerated sampling of cryptic pocket opening, protein-ligand binding and allostery by AlphaFold, slow feature analysis and metadynamics;PLOS ONE;2024-08-27
3. Host-Guest binding free energies à la carte: an automated OneOPES protocol;2024-08-24
4. Pathways and mechanism of MRTX1133 binding to KRAS G12D elucidated by molecular dynamics simulations and Markov state models;International Journal of Biological Macromolecules;2024-08
5. Pseudoirreversible inhibition elicits persistent efficacy of a sphingosine 1-phosphate receptor 1 antagonist;Nature Communications;2024-07-19
1.学者识别学者识别
2.学术分析学术分析
3.人才评估人才评估
"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370
www.globalauthorid.com
TOP
Copyright © 2019-2024 北京同舟云网络信息技术有限公司 京公网安备11010802033243号 京ICP备18003416号-3