ArticleJournal of biomolecular structure & dynamics2019
Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning.
Article in Journal of biomolecular structure & dynamics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed, 21 citations in OpenAlex.
- Generative adversarial network (GAN) model-based design of potent SARS-CoV-2 MMolecular diversity · 2025Article
- Using Machine Learning to Analyze Molecular Dynamics Simulations of Biomolecules.The journal of physical chemistry. B · 2025Article
- The Light Chain Allosterically Enhances the Protease Activity of Murine Urokinase-Type Plasminogen Activator.Biochemistry · 2024Article
- Article
- Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods.Journal of chemical information and modeling · 2023Article
- Machine learning and protein allostery.Trends in biochemical sciences · 2023Review
- Simulations suggest double sodium binding induces unexpected conformational changes in thrombin.Journal of molecular modeling · 2022Article
- Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands.International journal of molecular sciences · 2021Review
- Light Chain Mutation Effects on the Dynamics of Thrombin.Journal of chemical information and modeling · 2021Article
- Interaction of the synthetic antithrombotic peptide P10 with thrombin: a spectroscopy study.RSC advances · 2019Article
- NaPhysical chemistry chemical physics : PCCP · 2019Article
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 at 1 institution in 1 country.
Funding
Abstract
Thrombin is a key component for chemotherapeutic and antithrombotic therapy development. As the physiologic and pathologic roles of the light chain still remain vague, here, we continue previous efforts to understand the impacts of the disease-associated single deletion of LYS9 in the light chain. By combining supervised and unsupervised machine learning methodologies and more traditional structural analyses on data from 10 μs molecular dynamics simulations, we show that the conformational ensemble of the ΔK9 mutant is significantly perturbed. Our analyses consistently indicate that LYS9 deletion destabilizes both the catalytic cleft and regulatory functional regions and result in some conformational changes that occur in tens to hundreds of nanosecond scaled motions. We also reveal that the two forms of thrombin each prefer a distinct binding mode of a Na
Indexed as
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.