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

Knowledge-based protein secondary structure assignment

D Frishman1, P Argos

  • 1European Molecular Biology Laboratory, Heidelberg, Germany.

Proteins
|December 1, 1995
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

Prediction of protein folding pathways: Bovine pancreatic trypsin inhibitor.

Cytotechnology·2012
Same author

Rapid access to genes of biotechnologically useful enzymes by partial genome sequencing: the thermoalkaliphile Anaerobranca gottschalkii.

Journal of molecular microbiology and biotechnology·2008
Same author

MIPS: analysis and annotation of genome information in 2007.

Nucleic acids research·2007
Same author

MIPS: analysis and annotation of proteins from whole genomes in 2005.

Nucleic acids research·2005
Same author

Alternative splicing and protein function.

BMC bioinformatics·2005
Same author

MIPS: analysis and annotation of proteins from whole genomes.

Nucleic acids research·2003
Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026
Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026
Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026
Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026
Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026
Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026
See all related articles

We developed STRIDE, an algorithm for protein secondary structure assignment using hydrogen bond energy and torsional angles. STRIDE demonstrates higher accuracy compared to DSSP, aligning better with crystallographer-defined protein structures.

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Chemistry

Background:

  • Accurate protein secondary structure assignment is crucial for understanding protein function and dynamics.
  • Existing methods like DSSP have limitations in precise residue-by-residue assignments.

Purpose of the Study:

  • To develop and validate an automated algorithm, STRIDE, for improved protein secondary structure assignment.
  • To compare the performance of STRIDE against the established DSSP algorithm.

Main Methods:

  • STRIDE combines hydrogen bond energy calculations with statistically derived backbone torsional angle information.
  • Algorithm parameters were optimized using crystallographer-defined secondary structure assignments as the ground truth.
  • Performance was evaluated by comparing STRIDE and DSSP assignments against crystallographer definitions across 226 protein chains.

Related Experiment Videos

Main Results:

  • STRIDE achieved greater agreement with crystallographer-defined secondary structures than DSSP in 58% of protein chains, compared to DSSP's 31%.
  • In 11% of cases, both STRIDE and DSSP yielded identical assignments.
  • STRIDE showed improved delineation of helical and strand regions compared to published assignments.

Conclusions:

  • STRIDE offers a more accurate and reliable method for automated protein secondary structure assignment.
  • The algorithm's performance suggests its utility in structural biology and drug discovery.
  • STRIDE's improved accuracy enhances the interpretation of protein structures from atomic coordinates.