HELFIT: Helix fitting by a total least squares method
Abstract
The problem of fitting a helix to data arises in analysis of protein structure, in nuclear physics, and in engineering. A continuous helix is described by five parameters: helix axis, helix radius, and helix pitch. One of these helix parameters is frequently predefined in the helix fitting. Other algorithms find only the helix axis or determine separately the helix axis, the helix radius, or the helix pitch. Here we describe a total least squares method, HELFIT, for helix fitting. HELFIT enables one to calculate simultaneously all five of the helix parameters with high accuracy. The minimum number of data points required for the analysis is only four. HELFIT is very insensitive to noise even in short helices. HELFIT also calculates a parameter, p=rmsd/(N-1)(1/2), which estimates the regularity of helical structures independent of the number of data points, where rmsd is the root mean square distance from the best-fit helix to data points and N is the number of data points. It should become a basic tool of structural bioinformatics.
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The BISON CRISPR library targets 713 E1, E2, and E3 ubiquitin ligases, deubiquitinases, and control genes and contains 2,852 guide RNAs.
“The BISON CRISPR library targets 713 E1, E2, and E3 ubiquitin ligases, deubiquitinases, and control genes and contains 2,852 guide RNAs.”
From Small-molecule-induced polymerization triggers degradation of BCL6 (2020) · cites this paper as [35]
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Small-molecule-induced polymerization triggers degradation of BCL6
Słabicki, M., Yoon, H., Koeppel, J., Nitsch, L., Roy Burman, S. S., Di Genua, C., Donovan, K. A., Sperling, A. S., Hunkeler, M., Tsai, J. M., et al. (2020) · Nature · doi:10.1038/s41586-020-2925-1 · Cited by 270 · see citing works
- Authors
- Enkhbayar, P., Damdinsuren, S., Osaki, M., & Matsushima, N.
- Affiliations
- Sapporo Medical University (JP)
- National University of Mongolia (MN)
- Hokkaido University (JP)
- Corresponding author
- Matsushima, Norio
- Venue
- Computational Biology and Chemistry
- Publisher
- Elsevier BV
- Published
- 2008-08
- Volume
- 32
- Issue
- 4
- Pages
- 307-310
- ISSN
- 1476-9271 (ISSN-L)
- OpenAlex
- W2038862514
- Cited by
- 58
- References
- 16
- Citations by year
- 2025: 1 · 2024: 5 · 2023: 3 · 2022: 4 · 2021: 3 · 2020: 7 · 2019: 4 · 2018: 6 · 2017: 2 · 2016: 2 · 2015: 2 · 2014: 6 · 2013: 5 · 2012: 2
- FWCI
- 0.82
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Computational Biology and Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Funders
- University of Virginia
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Mathematics › Applied Mathematics › Statistical and numerical algorithms
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- total least squares, helix radius, helical pitch, structural bioinformatics, protein structure analysis, noise immunity
- MeSH terms
- Algorithms, Proteins, Software, Least-Squares Analysis, Protein Structure, Secondary, Computational Biology
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