ArticleBiophysical journal2008
A comparison of step-detection methods: how well can you do?
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
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- Biophysical Interaction Landscape of Mycobacterial Mycolic Acids and Phenolic Glycolipids with Host Macrophage Membranes.ACS applied bio materials · 2023Article
- Single-molecule investigations of single-chain cellulose biosynthesis.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Observing the base-by-base search for native structure along transition paths during the folding of single nucleic acid hairpins.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Transmembrane topology and oligomeric nature of an astrocytic membrane protein, MLC1.Open biology · 2021Article
- Single-molecule measurements reveal that PARP1 condenses DNA by loop stabilization.Science advances · 2021Article
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- Evidence for S2 flexibility by direct visualization of quantum dot-labeled myosin heads and rods within smooth muscle myosin filaments moving on actin in vitro.The Journal of general physiology · 2021Article
- Direct evaluation of self-quenching behavior of fluorophores at high concentrations using an evanescent field.PloS one · 2021Article
- Optical tweezers in single-molecule biophysics.Nature reviews. Methods primers · 2021Article
- DNA replication:Computational and structural biotechnology journal · 2021Review
- Ultra-fast force-clamp spectroscopy data on the interaction between skeletal muscle myosin and actin.Data in brief · 2019Article
- Myosin V fluorescence imaging dataset for single-molecule localization and tracking.Data in brief · 2019Article
- Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis.Chemical reviews · 2017Article
- Shuttling along DNA and directed processing of D-loops by RecQ helicase support quality control of homologous recombination.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Unsupervised Idealization of Ion Channel Recordings by Minimum Description Length: Application to Human PIEZO1-Channels.Frontiers in neuroinformatics · 2017Article
- A novel method to accurately locate and count large numbers of steps by photobleaching.Molecular biology of the cell · 2016Article
- Dual-Color Herpesvirus Capsids Discriminate Inoculum from Progeny and Reveal Axonal Transport Dynamics.Journal of virology · 2016Article
- Single molecule measurements of DNA helicase activity with magnetic tweezers and t-test based step-finding analysis.Methods (San Diego, Calif.) · 2016Article
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Authors and funding
3 authors.
Funding
Abstract
Many biological machines function in discrete steps, and detection of such steps can provide insight into the machines' dynamics. It is therefore crucial to develop an automated method to detect steps, and determine how its success is impaired by the significant noise usually present. A number of step detection methods have been used in previous studies, but their robustness and relative success rate have not been evaluated. Here, we compare the performance of four step detection methods on artificial benchmark data (simulating different data acquisition and stepping rates, as well as varying amounts of Gaussian noise). For each of the methods we investigate how to optimize performance both via parameter selection and via prefiltering of the data. While our analysis reveals that many of the tested methods have similar performance when optimized, we find that the method based on a chi-squared optimization procedure is simplest to optimize, and has excellent temporal resolution. Finally, we apply these step detection methods to the question of observed step sizes for cargoes moved by multiple kinesin motors in vitro. We conclude there is strong evidence for sub-8-nm steps of the cargo's center of mass in our multiple motor records.
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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.