ArticleJournal of computer-aided molecular design2020
SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations.
Article in Journal of computer-aided molecular design, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Host Dynamics under General-Purpose Force Fields.Molecules (Basel, Switzerland) · 2023Article
- A General Picture of Cucurbit[8]uril Host-Guest Binding: Recalibrating Bonded Interactions.Molecules (Basel, Switzerland) · 2023Article
- Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation.Molecules (Basel, Switzerland) · 2023Article
- Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant.Journal of computer-aided molecular design · 2022Article
- Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure.Journal of computer-aided molecular design · 2022Article
- Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy.Journal of chemical theory and computation · 2021Article
- Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations.Journal of computer-aided molecular design · 2021Article
- Accurate Receptor-Ligand Binding Free Energies from Fast QM Conformational Chemical Space Sampling.International journal of molecular sciences · 2021Article
- SAMPL7 TrimerTrip host-guest binding poses and binding affinities from spherical-coordinates-biased simulations.Journal of computer-aided molecular design · 2021Article
- SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations.Journal of computer-aided molecular design · 2021Article
- Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics.Journal of computer-aided molecular design · 2020Article
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Authors and funding
4 authors.
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Abstract
Host-guest binding is a challenging problem in computer simulation. The prediction of binding affinities between hosts and guests is an important part of the statistical assessment of the modeling of proteins and ligands (SAMPL) challenges. In this work, the volume-based variant of well-tempered metadynamics is employed to calculate the binding affinities of the host-guest systems in the SAMPL6 challenge. By biasing the spherical coordinates describing the relative position of the host and the guest, the initial-configuration-induced bias vanishes and all possible binding poses are explored. The agreement between the predictions and the experimental results and the observation of new binding poses indicate that the volume-based technique serves as a nice candidate for the calculation of binding free energies and the search of the binding poses.
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