Jove
Visualize
Contact Us

Related Experiment Videos

Cluster distance geometry of polypeptide chains.

Gordon M Crippen1

  • 1College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, USA. gcrippen@unich.edu

Journal of Computational Chemistry
|May 13, 2004
PubMed
Summary

This study generalizes distance geometry for low-resolution protein conformational calculations. New methods incorporate radii of gyration for sets of points, improving protein conformer prediction.

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

Purely in silico BCS classification: science based quality standards for the world's drugs.

Molecular pharmaceutics·2013
Same author

SAGA: rapid automatic mainchain NMR assignment for large proteins.

Journal of biomolecular NMR·2010
Same author

Predicting pKa.

Journal of chemical information and modeling·2009
Same author

A statistical measure of association and a series expansion of chain conformations.

Computational biology and chemistry·2009
Same author

pKa prediction of monoprotic small molecules the SMARTS way.

Journal of chemical information and modeling·2008
Same author

Data mining the NCI60 to predict generalized cytotoxicity.

Journal of chemical information and modeling·2008
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

Area of Science:

  • Computational chemistry
  • Structural biology
  • Biophysics

Background:

  • Distance geometry is a key tool for conformational calculations in molecular modeling.
  • Traditional methods represent atoms as points, suitable for small proteins but limited for lower-resolution analyses.
  • A need exists for methods applicable to larger systems or when lower resolution is desired.

Purpose of the Study:

  • To generalize distance geometry for analyzing sets of points, enabling lower-resolution conformational calculations.
  • To explore the role of radii of gyration in these generalized methods.
  • To demonstrate the utility of this approach for predicting protein structures.

Main Methods:

  • Generalization of distance geometry to handle distances between sets of points.
  • Incorporation of radii of gyration as a key parameter.
  • Application of techniques to sample configurations subject to distance constraints.

Main Results:

  • The generalized distance geometry successfully produces configurations of point sets consistent with constraints.
  • Radii of gyration play a significant role in the sampling of configurations.
  • A simple example shows effective protein conformer calculation at low resolution.

Conclusions:

  • Generalized distance geometry offers a powerful approach for low-resolution conformational analysis.
  • This method effectively integrates packing constraints and distance information for protein structure prediction.
  • The approach is advantageous for studying large systems or when atomic detail is not required.

Related Experiment Videos