ArticleStructural dynamics (Melville, N.Y.)2016
A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms.
Article in Structural dynamics (Melville, N.Y.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Whither the protein landscape?Structural dynamics (Melville, N.Y.) · 2025Article
- Domain acquisition by class I aminoacyl-tRNA synthetase urzymes coordinated the catalytic functions of HVGH and KMSKS motifs.Nucleic acids research · 2023Article
- Microcalorimetry reveals multi-state thermal denaturation ofStructural dynamics (Melville, N.Y.) · 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
- Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-Modular Coupling.International journal of molecular sciences · 2022Article
- Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes.International journal of molecular sciences · 2021Article
- 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
- Large-Scale Conformational Changes and Protein Function: Breaking theFrontiers in molecular biosciences · 2019Review
- 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
- Augmenting the anisotropic network model with torsional potentials improves PATH performance, enabling detailed comparison with experimental rate data.Structural dynamics (Melville, N.Y.) · 2017Article
- Coding of Class I and II Aminoacyl-tRNA Synthetases.Advances in experimental medicine and biology · 2017Review
- Preface to Special Topic on Protein Dynamics: Beyond Static Snapshots in Structural Biology.Structural dynamics (Melville, N.Y.) · 2016Article
- Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids.Frontiers in molecular biosciences · 2016Article
- Moving beyond static snapshots: Protein dynamics and the Protein Data Bank.The Journal of biological chemistryReview
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
PATH rapidly computes a path and a transition state between crystal structures by minimizing the Onsager-Machlup action. It requires input parameters whose range of values can generate different transition-state structures that cannot be uniquely compared with those generated by other methods. We outline modifications to estimate these input parameters to circumvent these difficulties and validate the PATH transition states by showing consistency between transition-states derived by different algorithms for unrelated protein systems. Although functional protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH.
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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.