ArticlePLoS computational biology2018
Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics.
Article in PLoS computational biology, 2018. 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.
- Article
- Accurate conformational ensembles of intrinsically disordered proteins using reweighting based on NMR chemical shifts.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Characterization and modulation of human insulin degrading enzyme conformational dynamics to control enzyme activity.bioRxiv : the preprint server for biology · 2025Article
- PackPPI: An integrated framework for protein-protein complex side-chain packing and ΔΔG prediction based on diffusion model.Protein science : a publication of the Protein Society · 2025Article
- Temperature-dependent fold-switching mechanism of the circadian clock protein KaiB.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- A curated rotamer library for common post-translational modifications of proteins.Bioinformatics (Oxford, England) · 2024Article
- Article
- HDX-MS finds that partial unfolding with sequential domain activation controls condensation of a cellular stress marker.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Cyclic peptides discriminate BCL-2 and its clinical mutants from BCL-XNature communications · 2024Article
- Invariant point message passing for protein side chain packing.bioRxiv : the preprint server for biology · 2023Article
- Folding of prestin's anion-binding site and the mechanism of outer hair cell electromotility.eLife · 2023Article
- An end-to-end deep learning method for protein side-chain packing and inverse folding.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling.Quarterly reviews of biophysics · 2023Review
- Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.The journal of physical chemistry. B · 2022Article
- The protein folding rate and the geometry and topology of the native state.Scientific reports · 2022Article
- Prediction and Validation of a Protein's Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence.Journal of chemical theory and computation · 2022Article
- Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Step-by-step design of proteins for small molecule interaction: A review on recent milestones.Protein science : a publication of the Protein Society · 2021Review
- Computational reconstruction of atomistic protein structures from coarse-grained models.Computational and structural biotechnology journal · 2020Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we present a rapid self-consistent approximation of the side chain free energy at every integration step. In analogy with the adiabatic Born-Oppenheimer approximation for electronic structure, the protein backbone dynamics are simulated as preceding according to the dictates of the free energy of an instantaneously-equilibrated side chain potential. The side chain free energy is computed on the fly, allowing the protein backbone dynamics to traverse a greatly smoothed energetic landscape. This computation results in extremely rapid equilibration and sampling of the Boltzmann distribution. Our method, termed Upside, employs a reduced model involving the three backbone atoms, along with the carbonyl oxygen and amide proton, and a single (oriented) side chain bead having multiple locations reflecting the conformational diversity of the side chain's rotameric states. We also introduce a novel, maximum-likelihood method to parameterize the side chain interactions using protein structures. We demonstrate state-of-the-art accuracy for predicting χ1 rotamer states while consuming only milliseconds of CPU time. Our method enables rapidly equilibrating coarse-grained simulations that can nonetheless contain significant molecular detail. We also show that the resulting free energies of the side chains are sufficiently accurate for de novo folding of some proteins.
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