关于明智地使用MM/PBSA和MM/GBSA近似方法进行配体结合计算研究的编辑指南。 - Suppr

Editorial Guidelines for Computational Studies of Ligand Binding Using MM/PBSA and MM/GBSA Approximations Wisely.

作者信息

Roux Benoît, Chipot Christophe

机构信息

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States.

Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, UMR n°7019, Université de Lorraine, 54506 Vandœuvre-lès-Nancy cedex, France.

出版信息

J Phys Chem B. 2024 Dec 12;128(49):12027-12029. doi: 10.1021/acs.jpcb.4c06614. Epub 2024 Dec 2.

DOI:10.1021/acs.jpcb.4c06614

PMID:39620637

Abstract

摘要

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Editorial Guidelines for Computational Studies of Ligand Binding Using MM/PBSA and MM/GBSA Approximations Wisely.关于明智地使用MM/PBSA和MM/GBSA近似方法进行配体结合计算研究的编辑指南。

J Phys Chem B. 2024 Dec 12;128(49):12027-12029. doi: 10.1021/acs.jpcb.4c06614. Epub 2024 Dec 2.

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches.评估 MM/PBSA 和 MM/GBSA 方法的性能。7. 熵效应对终点结合自由能计算方法性能的影响。

Phys Chem Chem Phys. 2018 May 30;20(21):14450-14460. doi: 10.1039/c7cp07623a.

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J Comput Chem. 2011 Apr 15;32(5):866-77. doi: 10.1002/jcc.21666. Epub 2010 Oct 14.

Assessing the performance of MM/PBSA and MM/GBSA methods. 10. Prediction reliability of binding affinities and binding poses for RNA-ligand complexes.评估 MM/PBSA 和 MM/GBSA 方法的性能。10. RNA-配体复合物结合亲和力和结合构象的预测可靠性。

Phys Chem Chem Phys. 2024 Mar 27;26(13):10323-10335. doi: 10.1039/d3cp04366e.

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring.评估MM/PBSA和MM/GBSA方法的性能。5. 使用高溶质介电常数的MM/GBSA和MM/PBSA重新评分提高对接性能。

Phys Chem Chem Phys. 2014 Oct 28;16(40):22035-45. doi: 10.1039/c4cp03179b. Epub 2014 Sep 10.

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set.评估MM/PBSA和MM/GBSA方法的性能。4. 使用PDBbind数据集通过各种模拟协议评估MM/PBSA和MM/GBSA方法的准确性。

Phys Chem Chem Phys. 2014 Aug 21;16(31):16719-29. doi: 10.1039/c4cp01388c.

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.用于估计配体结合亲和力的MM/PBSA和MM/GBSA方法。

Expert Opin Drug Discov. 2015 May;10(5):449-61. doi: 10.1517/17460441.2015.1032936. Epub 2015 Apr 2.

Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models.评估 MM/PBSA 和 MM/GBSA 方法的性能。3. 力场和配体电荷模型的影响。

J Phys Chem B. 2013 Jul 18;117(28):8408-21. doi: 10.1021/jp404160y. Epub 2013 Jul 8.

Assessing the performance of MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein-peptide complexes.评估 MM/PBSA 和 MM/GBSA 方法的性能。9. 蛋白质-肽复合物结合亲和力和结合构象的预测可靠性。

Phys Chem Chem Phys. 2019 May 15;21(19):10135-10145. doi: 10.1039/c9cp01674k.

A head-to-head comparison of MM/PBSA and MM/GBSA in predicting binding affinities for the CB cannabinoid ligands.头对头比较 MM/PBSA 和 MM/GBSA 预测 CB 大麻素配体结合亲和力。

J Mol Model. 2024 Oct 31;30(11):390. doi: 10.1007/s00894-024-06189-4.

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Editorial Guidelines for Computational Studies of Ligand Binding Using MM/PBSA and MM/GBSA Approximations Wisely.

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