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PreprintCited by 37Protein Structure and DynamicsEnzyme Structure and FunctionRNA and protein synthesis mechanisms

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SSDraw: software for generating comparative protein secondary structure diagrams

Open access
Chen, Ethan A., Porter, Lauren L.·2023·Protein Science
DOI 10.1101/2023.08.25.554905PMC PMC10680343

Preprint — published as 10.1002/pro.4836

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Abstract

The program SSDraw generates publication-quality protein secondary structure diagrams from three-dimensional protein structures. To depict relationships between secondary structure and other protein features, diagrams can be colored by conservation score, B-factor, or custom scoring. Diagrams of homologous proteins can be registered according to an input multiple sequence alignment. Linear visualization allows the user to stack registered diagrams, facilitating comparison of secondary structure and other properties among homologous proteins. SSDraw can be used to compare secondary structures of homologous proteins with both conserved and divergent folds. It can also generate one secondary structure diagram from an input protein structure of interest. The source code can be downloaded ( https://github.com/ethanchen1301/SSDraw ) and run locally for rapid structure generation, while a Google Colab notebook allows easy use.

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Metadata

Authors
Chen, E. A., & Porter, L. L.
Affiliations
National Institutes of Health (US)
Corresponding author
Porter, Lauren L.
ORCID
Porter, Lauren L.
Venue
Protein Science
Publisher
openRxiv
Published
2023-08-27
Volume
32
Issue
12
Pages
e4836-e4836
ISSN
0961-8368 (ISSN-L)
DOI
10.1101/2023.08.25.554905
PMC
PMC10680343
OpenAlex
W4388633862
Cited by
37
References
1
Citations by year
2026: 9 · 2025: 20 · 2024: 7 · 2023: 1
FWCI
3.30
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Protein Science (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, public-domain)
Funders
  • National Institutes of Health (LM202011)
  • U.S. National Library of Medicine (LM202011, ZIALM202011)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
protein secondary structure, homologous proteins, conservation scores, Debye-Waller factor, multiple sequence alignment, protein structure visualization

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