ArticleStructural dynamics (Melville, N.Y.)2017
Augmenting the anisotropic network model with torsional potentials improves PATH performance, enabling detailed comparison with experimental rate data.
Article in Structural dynamics (Melville, N.Y.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Aminoacyl-tRNA synthetase urzymes optimized by deep learning behave as a quasispecies.Structural dynamics (Melville, N.Y.) · 2025Article
- Whither the protein landscape?Structural dynamics (Melville, N.Y.) · 2025Article
- Primordial aminoacyl-tRNA synthetases preferred minihelices to full-length tRNA.Nucleic acids research · 2024Article
- Domain acquisition by class I aminoacyl-tRNA synthetase urzymes coordinated the catalytic functions of HVGH and KMSKS motifs.Nucleic acids research · 2023Article
- High-throughput thermal denaturation of tryptophanyl-tRNA synthetase combinatorial mutants reveals high-order energetic coupling determinants of conformational stability.Structural dynamics (Melville, N.Y.) · 2023Article
- Microcalorimetry reveals multi-state thermal denaturation ofStructural dynamics (Melville, N.Y.) · 2023Article
- Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-Modular Coupling.International journal of molecular sciences · 2022Article
- Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis.Biomolecules · 2021Review
- Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding.International journal of molecular sciences · 2020Article
- Escapement mechanisms: Efficient free energy transduction by reciprocally-coupled gating.Proteins · 2020Article
- Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases.PLoS computational biology · 2018Article
- High-Dimensional Mutant and Modular Thermodynamic Cycles, Molecular Switching, and Free Energy Transduction.Annual review of biophysics · 2017Review
- Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis.Structural dynamics (Melville, N.Y.) · 2017Article
- Coding of Class I and II Aminoacyl-tRNA Synthetases.Advances in experimental medicine and biology · 2017Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
PATH algorithms for identifying conformational transition states provide computational parameters-time to the transition state, conformational free energy differences, and transition state activation energies-for comparison to experimental data and can be carried out sufficiently rapidly to use in the "high throughput" mode. These advantages are especially useful for interpreting results from combinatorial mutagenesis experiments. This report updates the previously published algorithm with enhancements that improve correlations between PATH convergence parameters derived from virtual variant structures generated by RosettaBackrub and previously published kinetic data for a complete, four-way combinatorial mutagenesis of a conformational switch in Tryptophanyl-tRNA synthetase.
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Registered trials
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