ArticleJournal of chemical theory and computation2019
a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Structural and spectroscopic basis of excitation energy transfer in microbial rhodopsins binding xanthophylls.Chemical science · 2025Article
- Rhodopsin charge diffusion computations disclose contrasting color-tuning mechanisms.Nature communications · 2025Article
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- Mechanical Modulation of SThe journal of physical chemistry. B · 2025Article
- In-silico predicted mouse melanopsins with blue spectral shifts deliver efficient subcellular signaling.Cell communication and signaling : CCS · 2024Article
- Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct.Nature communications · 2024Article
- The OpenMolcasJournal of chemical theory and computation · 2023Article
- Surface hopping modeling of charge and energy transfer in active environments.Physical chemistry chemical physics : PCCP · 2023Review
- Alternative Strategy for Spectral Tuning of Flavin-Binding Fluorescent Proteins.The journal of physical chemistry. B · 2023Article
- Retinal chromophore charge delocalization and confinement explain the extreme photophysics of Neorhodopsin.Nature communications · 2022Article
- On the fluorescence enhancement of arch neuronal optogenetic reporters.Nature communications · 2022Article
- Article
- Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol.Topics in current chemistry (Cham) · 2022Review
- Coupled- and Independent-Trajectory Approaches Based on the Exact Factorization Using the PyUNIxMD Package.Topics in current chemistry (Cham) · 2022Review
- Pro219 is an electrostatic color determinant in the light-driven sodium pump KR2.Communications biology · 2021Article
- PyUNIxMD: A Python-based excited state molecular dynamics package.Journal of computational chemistry · 2021Article
- Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design.Communications biology · 2021Article
- Frontiers in Multiscale Modeling of Photoreceptor Proteins.Photochemistry and photobiology · 2021Review
- Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins.Advances in experimental medicine and biology · 2021Review
- Molecular Photochemistry: Recent Developments in Theory.Angewandte Chemie (International ed. in English) · 2020Review
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Authors and funding
5 authors.
Funding
Abstract
The Automatic Rhodopsin Modeling (ARM) protocol has recently been proposed as a tool for the fast and parallel generation of basic hybrid quantum mechanics/molecular mechanics (QM/MM) models of wild type and mutant rhodopsins. However, in its present version, input preparation requires a few hours long user's manipulation of the template protein structure, which also impairs the reproducibility of the generated models. This limitation, which makes model building semiautomatic rather than fully automatic, comprises four tasks: definition of the retinal chromophore cavity, assignment of protonation states of the ionizable residues, neutralization of the protein with external counterions, and finally congruous generation of single or multiple mutations. In this work, we show that the automation of the original ARM protocol can be extended to a level suitable for performing the above tasks without user's manipulation and with an input preparation time of minutes. The new protocol, called a-ARM, delivers fully reproducible (i.e., user independent) rhodopsin QM/MM models as well as an improved model quality. More specifically, we show that the trend in vertical excitation energies observed for a set of 25 wild type and 14 mutant rhodopsins is predicted by the new protocol better than when using the original. Such an agreement is reflected by an estimated (relative to the probed set) trend deviation of 0.7 ± 0.5 kcal mol
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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.