ArticleJournal of computer-aided molecular design2015
BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge.
Article in Journal of computer-aided molecular design, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge.Journal of computer-aided molecular design · 2022Article
- Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges.Journal of computer-aided molecular design · 2018Article
- SAMPL6 host-guest challenge: binding free energies via a multistep approach.Journal of computer-aided molecular design · 2018Article
- The aqueous supramolecular chemistry of cucurbit[n]urils, pillar[n]arenes and deep-cavity cavitands.Chemical Society reviews · 2017Review
- Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.Journal of computer-aided molecular design · 2017Article
- Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.Journal of computer-aided molecular design · 2017Article
- A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.Journal of computer-aided molecular design · 2017Article
- Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase.ACS omega · 2016Article
- Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.Journal of computer-aided molecular design · 2016Article
- Computational methods in drug discovery.Beilstein journal of organic chemistry · 2016Review
- Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.Journal of molecular recognition : JMR · 2016Article
- Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing.Computer physics communications · 2015Article
- A unique binding mode of the eukaryotic translation initiation factor 4E for guiding the design of novel peptide inhibitors.Protein science : a publication of the Protein Society · 2015Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
The binding energy distribution analysis method (BEDAM) protocol has been employed as part of the SAMPL4 blind challenge to predict the binding free energies of a set of octa-acid host-guest complexes. The resulting predictions were consistently judged as some of the most accurate predictions in this category of the SAMPL4 challenge in terms of quantitative accuracy and statistical correlation relative to the experimental values, which were not known at the time the predictions were made. The work has been conducted as part of a hands-on graduate class laboratory session. Collectively the students, aided by automated setup and analysis tools, performed the bulk of the calculations and the numerical and structural analysis. The success of the experiment confirms the reliability of the BEDAM methodology and it shows that physics-based atomistic binding free energy estimation models, when properly streamlined and automated, can be successfully employed by non-specialists.
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