Adaptive Lambda Scheduling: A Method for Computational Efficiency in Free Energy Perturbation Simulations.

IF 5.6 2区化学 Q1 CHEMISTRY, MEDICINAL

Journal of Chemical Information and Modeling Pub Date : 2025-01-27 Epub Date: 2025-01-09 DOI:10.1021/acs.jcim.4c01668

Scott D Midgley, Sofia Bariami, Matthew Habgood, Mark Mackey

引用次数: 0

Abstract

Recent increases in the availability of computational power have improved the accessibility of ligand-protein relative binding free energy (RBFE) calculations; however, these calculations remain resource-intensive, which can limit their practical application. RBFE calculations typically use a set of thermodynamic intermediates mediated by the transformation coordinate λ. Optimizing λ offers a way to tune the computational efforts required for a given RBFE calculation. Here, we present Adaptive Lambda Scheduling (ALS), a streamlined approach for on-the-fly bespoke λ scheduling. We show it can achieve substantial reductions in computational cost while retaining predictive performance.

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自适应Lambda调度：一种提高自由能摄动模拟计算效率的方法。

最近计算能力的提高提高了配体-蛋白质相对结合自由能（RBFE）计算的可及性；然而，这些计算仍然是资源密集型的，这限制了它们的实际应用。RBFE计算通常使用一组由变换坐标λ介导的热力学中间体。优化λ提供了一种方法来调整给定RBFE计算所需的计算量。在这里，我们提出了自适应λ调度（ALS），一种简化的实时定制λ调度方法。我们证明它可以在保持预测性能的同时大幅降低计算成本。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Chemical Information and Modeling 化学-化学综合

CiteScore

9.80

自引率

10.70%

发文量

529

审稿时长

1.4 months

期刊介绍： The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.