ArticleJournal of chemical theory and computation2023
Reaction Coordinates for Conformational Transitions Using Linear Discriminant Analysis on Positions.
Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Mechanochemical Decoupling of ATP Hydrolysis and RNA Translocation in SARS-CoV-2 nsp13 by the L405D Mutation.bioRxiv : the preprint server for biology · 2026Article
- Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications.Chemical reviews · 2026Review
- Tutorial on quantifying and sampling biomolecular ensembles with ShapeGMM.The Journal of chemical physics · 2025Article
- Using Time Dependent Rate Analysis to Evaluate the Quality of Machine Learned Reaction Coordinates for Biasing and Computing Kinetics.The journal of physical chemistry. B · 2025Article
- The Arch from the Stones: Understanding Protein Folding Energy Landscapes via Bioinspired Collective Variables.The journal of physical chemistry letters · 2025Article
- PAL - parallel active learning for machine-learned potentials.Digital discovery · 2025Article
- Improved Data-Driven Collective Variables for Biased Sampling through Iteration on Biased Data.The journal of physical chemistry. B · 2025Article
- A direct computational assessment of vinculin-actin unbinding kinetics reveals catch-bonding behavior.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Accelerating Molecular Dynamics through Informed Resetting.Journal of chemical theory and computation · 2025Article
- Molecular simulation approaches to probing the effects of mechanical forces in the actin cytoskeleton.Cytoskeleton (Hoboken, N.J.) · 2024Article
- Good Rates From Bad Coordinates: The Exponential Average Time-dependent Rate Approach.Journal of chemical theory and computation · 2024Article
- Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase.Nucleic acids research · 2024Article
- Enhanced Sampling with Machine Learning.Annual review of physical chemistry · 2024Review
- Short-Time Infrequent Metadynamics for Improved Kinetics Inference.Journal of chemical theory and computation · 2024Article
- Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM.Journal of chemical theory and computation · 2024Article
- Improved Prediction of Molecular Response to Pulling by Combining Force Tempering with Replica Exchange Methods.The journal of physical chemistry. B · 2024Article
- Role of ATP Hydrolysis and Product Release in the Translocation Mechanism of SARS-CoV-2 NSP13.The journal of physical chemistry. B · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
In this work, we demonstrate that Linear Discriminant Analysis (LDA) applied to atomic positions in two different states of a biomolecule produces a good reaction coordinate between those two states. Atomic coordinates of a macromolecule are a direct representation of a macromolecular configuration, and yet, they are not used in enhanced sampling studies due to a lack of rotational and translational invariance. We resolve this issue using the technique of our prior work, whereby a molecular configuration is considered a member of an equivalence class in size-and-shape space, which is the set of all configurations that can be translated and rotated to a single point within a reference multivariate Gaussian distribution characterizing a single molecular state. The reaction coordinates produced by LDA applied to positions are shown to be good reaction coordinates both in terms of characterizing the transition between two states of a system within a long molecular dynamics (MD) simulation and also ones that allow us to readily produce free energy estimates along that reaction coordinate using enhanced sampling MD techniques.
Identifiers
What OpenQuestion holds
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.