ArticleBMC biophysics2013
Time-resolved force distribution analysis.
Article in BMC biophysics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 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
40 citing papers in PubMed.
- Dynamic Coupling between Tom22 Motions and Tom40 Pore Dynamics Modulates Ion Transport in the Mitochondrial TOM Complex.Journal of chemical information and modeling · 2025Article
- Article
- Allosteric Mechanisms Triggering Substrate and Cofactor Binding in the SULT1A1 Dimer as Revealed by Molecular Dynamics Simulations.Journal of chemical information and modeling · 2025Article
- Identifying the interactions conferring functional mechanical rigidity on RNase-resistant RNA from Zika virus.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The accomplices: Heparan sulfates and N-glycans foster SARS-CoV-2 spike:ACE2 receptor binding and virus priming.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular Dynamics Reveal Key Steps in BAR-Related Membrane Remodeling.Pathogens (Basel, Switzerland) · 2024Article
- Integrin mechanosensing relies on a pivot-clip mechanism to reinforce cell adhesion.Biophysical journal · 2024Article
- Unveiling dissociation mechanisms and binding patterns in the UHRF1-DPPA3 complex via multi-replica molecular dynamics simulations.Journal of molecular modeling · 2024Article
- Insights into the Dissociation Process and Binding Pattern of the BRCT7/8-PHF8 Complex.ACS omega · 2024Article
- Emergence of slip-ideal-slip behavior in tip-links serve as force filters of sound in hearing.Nature communications · 2024Article
- Probing binding and occlusion of substrate in the human creatine transporter-1 by computation and mutagenesis.Protein science : a publication of the Protein Society · 2024Article
- What Strengthens Protein-Protein Interactions: Analysis and Applications of Residue Correlation Networks.Journal of molecular biology · 2023Article
- Mechanical forces control the valency of the malaria adhesin VAR2CSA by exposing cryptic glycan binding sites.PLoS computational biology · 2023Article
- Article
- Key Factors Regulating the Interdomain Dynamics May Contribute to the Assembly of ASC.Biology · 2023Article
- IDH3γ functions as a redox switch regulating mitochondrial energy metabolism and contractility in the heart.Nature communications · 2023Article
- Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all-atom simulations.Protein science : a publication of the Protein Society · 2022Article
- Recognizing the Binding Pattern and Dissociation Pathways of the p300 Taz2-p53 TAD2 Complex.JACS Au · 2022Article
- Article
- Bending-torsional elasticity and energetics of the plus-end microtubule tip.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBiomolecules or other complex macromolecules undergo conformational transitions upon exposure to an external perturbation such as ligand binding or mechanical force. To follow fluctuations in pairwise forces between atoms or residues during such conformational changes as observed in Molecular Dynamics (MD) simulations, we developed Time-Resolved Force Distribution Analysis (TRFDA).
resultsThe implementation focuses on computational efficiency and low-memory usage and, along with the wide range of output options, makes possible time series analysis of pairwise forces variation in long MD simulations and for large molecular systems. It also provides an exact decomposition of pairwise forces resulting from 3- and 4-body potentials and a unified treatment of pairwise forces between atoms or residues. As a proof of concept, we present a stress analysis during unfolding of ubiquitin in a force-clamp MD simulation.
conclusionsTRFDA can be used, among others, in tracking signal propagation at atomic level, for characterizing dynamical intermolecular interactions (e.g. protein-ligand during flexible docking), in development of force fields and for following stress distribution during conformational changes.
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.