ArticleThe journal of physical chemistry. B2019
Exploring the Effectiveness of Binding Free Energy Calculations.
Article in The journal of physical chemistry. B, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
5 citing papers in PubMed.
- High throughput mutational scanning of a protein via alchemistry on a high-performance computing resource.bioRxiv : the preprint server for biology · 2024Article
- Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors.Journal of computer-aided molecular design · 2023Article
- Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of α-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2.Biochemistry · 2020Article
- Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches.Molecules (Basel, Switzerland) · 2020Review
- Pharmacoinformatics approaches to identify potential hits against tetraacyldisaccharide 4'-kinase (LpxK) ofRSC advances · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Increasing the accuracy of the evaluation of ligand-binding energies is one of the most important tasks of current computational biology. Here we explore the accuracy of free energy perturbation (FEP) approaches by comparing the performance of a "regular" FEP method to the one using replica exchange to enhance the sampling on a well-defined benchmark. The examination was limited to the so-called alchemical perturbations which are restricted to a fragment of the drug, and therefore, the calculation is a relative one rather than the absolute binding energy of the drug. Overall, our calculations reach the 1 kcal/mol accuracy limit. It is also shown that the accurate prediction of the position of water molecules around the binding pocket is important for FEP calculations. Interestingly, the replica exchange method does not significantly improve the accuracy of binding energies, suggesting that we reach the limit where the force field quality is a critical factor for accurate calculations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.