ArticleJournal of chemical information and modeling2025
An Empirical Biasing Force Constant to Minimize Overfitting in Cryo-EM Flexible Fitting Refinement.
Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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
0 citing papers in PubMed.
No citing paper in PubMed yet.
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
No grant is acknowledged in the PubMed record.
Abstract
Reliable modeling of protein structures from a cryo-EM density map is one of the central issues in structural biology. Typically, the constructed model is refined using a flexible fitting method combined with molecular dynamics, where a biasing potential is introduced to guide the protein structure toward the density map. However, the appropriate force constant for the biasing potential is generally unknown a priori. Here, we propose an empirical force constant that enables flexible fitting refinement with minimal overfitting. The rule is derived from systematic flexible fitting calculations performed on 29 selected systems (map resolution = 3.0-6.8 Å) using a range of force constants from weak to strong values. The refined structures are evaluated based on the MolProbity score and secondary-structure-forming tendencies. Our analysis shows that in most systems, the MolProbity score increases monotonically as the force constant increases. In addition, α-helix and β-strand tend to collapse beyond a certain force constant depending on the system size or number of fitting atoms (
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.