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

A central partition of molecular conformational space. I. Basic structures.

Jacques Gabarro-Arpa1

  • 1Ecole Normale Supérieure de Cachan, LBPA, C.N.R.S. UMR 8532, 61, Avenue du Président Wilson, 94235 Cedex, Cachan, France. jga@infobiogen.fr

Computational Biology and Chemistry
|June 25, 2003
PubMed
Summary

Molecular conformational space is mapped using geometric cells defined by coordinate dominance. This framework precisely locates conformations within a polytope, enabling path determination between them.

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

Hamming distance geometry of a protein conformational space: application to the clustering of a 4-ns molecular dynamics trajectory of the HIV-1 integrase catalytic core.

Proteins·2002
See all related articles

Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Geometric combinatorics

Background:

  • Understanding molecular conformational space is crucial for predicting molecular behavior.
  • Current methods often lack precise geometric frameworks for conformational analysis.

Purpose of the Study:

  • To develop a novel geometric and combinatorial description of molecular conformational space.
  • To establish a precise method for locating and analyzing molecular conformations.

Main Methods:

  • Utilizing empirical evidence from molecular dynamics simulations.
  • Applying geometric and combinatorial principles to describe cell arrangements.
  • Defining a polytope structure for conformational mapping.

Main Results:

Related Experiment Videos

  • Molecular conformational space can be partitioned into characteristic conical regions (cells).
  • A 3x(N-1)-dimensional polytope provides a geometric framework for these cells.
  • Conformations are precisely locatable within the polytope's face hierarchy.

Conclusions:

  • The described polytope framework offers a robust method for conformational analysis.
  • The 1-skeleton of the polytope facilitates the determination of pathways between conformations.
  • This approach enhances the geometric and combinatorial understanding of molecular dynamics.