Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Valid and invalid implementations of GOR secondary structure predictions

L B Ellis1, R P Milius

  • 1Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis 55455.

Computer Applications in the Biosciences : CABIOS
|June 1, 1994
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

SIP 7: Progress in Cervical Cancer Prevention in the UK (2025 Second Edition).

BJOG : an international journal of obstetrics and gynaecology·2025
Same author

Genotype List String: a grammar for describing HLA and KIR genotyping results in a text string.

Tissue antigens·2013
Same author

Mitral Stenosis, Clinico-Physiologic Correlations, with Particular Reference to Surgical Intervention.

Transactions of the American Clinical and Climatological Association·2011
Same author

The Use of Intravenous Veriloid in the Management of the Acute Crises of Severe Hypertensive Disease.

Transactions of the American Clinical and Climatological Association·2011
Same author

Electrocardiographic abnormalities in severe malnutrition.

British heart journal·2010
Same author

Electrocardiography.

The New England journal of medicine·2010

Two validation sequences reveal errors in several protein secondary structure prediction algorithms, including commercial GOR I implementations. Correcting these errors significantly improves prediction accuracy.

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Structural Biology

Background:

  • Gor's algorithms (GOR I and GOR II) are standard for protein secondary structure prediction from amino acid sequences.
  • Accurate prediction is crucial for understanding protein function and tertiary structure.

Purpose of the Study:

  • To develop and present validation sequences for GOR I and GOR II algorithms.
  • To identify and report incorrect implementations of these widely used algorithms.
  • To quantify the impact of implementation errors on prediction accuracy.

Main Methods:

  • Development of two short validation sequences for GOR I and GOR II.
  • Testing seven commercial and non-commercial implementations using these sequences.
  • Comparison of prediction accuracy between valid and invalid implementations using known protein structures.

Related Experiment Videos

Main Results:

  • Several implementations of GOR I and GOR II were found to be incorrect.
  • Two of three commercial GOR I implementations contained errors, likely due to misinterpretation of the algorithm or data tables.
  • Valid GOR I implementations improved secondary structure prediction accuracy by 1-13 percentage points compared to invalid ones.

Conclusions:

  • Widespread errors in GOR algorithm implementations can negatively impact protein secondary and tertiary structure predictions.
  • The developed validation sequences are valuable tools for ensuring the accuracy of GOR algorithm implementations.
  • Valid GOR I and GOR II algorithm implementations are available from the authors.