文献检索文档翻译深度研究
Suppr Zotero 插件Zotero 插件
邀请有礼套餐&价格历史记录

新学期,新优惠

限时优惠:9月1日-9月22日

30天高级会员仅需29元

1天体验卡首发特惠仅需5.99元

了解详情
不再提醒
插件&应用
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
高级版
套餐订阅购买积分包
AI 工具
文献检索文档翻译深度研究
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2025

Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host-guest challenge.

作者信息

Hurley Matthew F D, Raddi Robert M, Pattis Jason G, Voelz Vincent A

机构信息

Department of Chemistry, Temple University, Philadelphia, PA, USA.

出版信息

Phys Chem Chem Phys. 2023 Dec 6;25(47):32393-32406. doi: 10.1039/d3cp02197a.


DOI:10.1039/d3cp02197a
PMID:38009066
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10760931/
Abstract

As part of the SAMPL9 community-wide blind host-guest challenge, we implemented an expanded ensemble workflow to predict absolute binding free energies for 13 small molecules against pillar[6]arene. Notable features of our protocol include consideration of a variety of protonation and enantiomeric states for both host and guests, optimization of alchemical intermediates, and analysis of free energy estimates and their uncertainty using large numbers of simulation replicates performed using distributed computing. Our predictions of absolute binding free energies resulted in a mean absolute error of 2.29 kcal mol and an of 0.54. Overall, results show that expanded ensemble calculations using all-atom molecular dynamics simulations are a valuable and efficient computational tool in predicting absolute binding free energies.

摘要

相似文献

[1]
Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host-guest challenge.

Phys Chem Chem Phys. 2023-12-6

[2]
SAMPL9 blind predictions using nonequilibrium alchemical approaches.

J Chem Phys. 2022-4-28

[3]
Expanded ensemble predictions of toluene-water partition coefficients in the SAMPL9 log  challenge.

Phys Chem Chem Phys. 2025-3-19

[4]
Thermodynamic integration to predict host-guest binding affinities.

J Comput Aided Mol Des. 2012-2-16

[5]
The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy.

Phys Chem Chem Phys. 2024-3-20

[6]
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.

J Comput Aided Mol Des. 2020-5

[7]
Taming multiple binding poses in alchemical binding free energy prediction: the β-cyclodextrin host-guest SAMPL9 blinded challenge.

Phys Chem Chem Phys. 2023-9-20

[8]
The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.

J Comput Aided Mol Des. 2017-1

[9]
Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies.

J Chem Theory Comput. 2021-10-12

[10]
Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations.

J Comput Aided Mol Des. 2011-12-24

引用本文的文献

[1]
Expanded ensemble predictions of toluene-water partition coefficients in the SAMPL9 log  challenge.

Phys Chem Chem Phys. 2025-3-19

[2]
The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy.

Phys Chem Chem Phys. 2024-3-20

本文引用的文献

[1]
Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations.

J Chem Theory Comput. 2023-6-27

[2]
Folding@home: Achievements from over 20 years of citizen science herald the exascale era.

Biophys J. 2023-7-25

[3]
Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations.

J Chem Theory Comput. 2023-3-28

[4]
An overview of the SAMPL8 host-guest binding challenge.

J Comput Aided Mol Des. 2022-10

[5]
CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding.

Nat Rev Chem. 2022-4

[6]
SAMPL9 blind predictions using nonequilibrium alchemical approaches.

J Chem Phys. 2022-4-28

[7]
Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design.

New J Chem. 2022-1-21

[8]
Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange.

J Comput Aided Mol Des. 2022-1

[9]
BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations.

J Chem Theory Comput. 2021-11-9

[10]
Critical assessment of methods of protein structure prediction (CASP)-Round XIV.

Proteins. 2021-12

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

推荐工具

医学文档翻译智能文献检索