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

Backbone-dependent rotamer library for proteins. Application to side-chain prediction

R L Dunbrack1, M Karplus

  • 1Department of Chemistry, Harvard University, Cambridge, MA 02138.

Journal of Molecular Biology
|March 20, 1993
PubMed
Summary

A new backbone-dependent rotamer library predicts amino acid side-chain conformations. This method accurately places side-chains, aiding protein structure determination and homology modeling.

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

All-atom empirical potential for molecular modeling and dynamics studies of proteins.

The journal of physical chemistry. B·2014
Same author

A conformational transition in the myosin VI converter contributes to the variable step size.

Biophysical journal·2011
Same author

Calculation of free-energy differences by confinement simulations. Application to peptide conformers.

The journal of physical chemistry. B·2009
Same author

CHARMM: the biomolecular simulation program.

Journal of computational chemistry·2009
Same author

Molecular dynamics studies of NMR relaxation in proteins.

Biophysical journal·2009
Same author

Protein-Protein Interactions in DNA Recognition: H-NMR Studies of Lambda cI Repressors Genetically Altered by Site-Directed Mutagenesis.

Biophysical journal·2009

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Protein structure prediction is crucial for understanding function.
  • Amino acid side-chain conformations are influenced by backbone structure.
  • Existing methods may lack accuracy or efficiency.

Purpose of the Study:

  • To develop a backbone-dependent rotamer library for predicting protein side-chain conformations.
  • To assess the accuracy and efficiency of the developed library in protein structure prediction.

Main Methods:

  • A rotamer library was created using 132 protein chains from the Brookhaven Protein Database.
  • Main-chain angles (phi, psi) were gridded to analyze side-chain dihedral angle probabilities.
  • A minimization scheme was employed for side-chain reorientation after initial placement.

Related Experiment Videos

Main Results:

  • Significant correlations were found between backbone angles and side-chain dihedral angle probabilities.
  • Initial placement accuracy for chi 1 and chi 2 values ranged from 59% to 81%.
  • Refined placement accuracy improved, ranging from 61% to 89% across different proteins.

Conclusions:

  • The developed rotamer library accurately predicts side-chain conformations based on backbone coordinates.
  • The method is computationally efficient and automatable, assisting in experimental and modeling applications.
  • The findings suggest a simplification in protein folding by reducing conformational space.