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

Conformational sampling for the impatient.

Kaihsu Tai1

  • 1Department of Biochemistry, University of Oxford, Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK. kaihsu@biop.ox.ac.uk

Biophysical Chemistry
|February 18, 2004
PubMed
Summary

New biomolecular simulation methods offer advanced ways to study molecular shapes. Four key techniques, including Replica-Exchange Molecular Dynamics, are highlighted for their effectiveness in various biological systems.

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

Quality Assurance for Biomolecular Simulations.

Journal of chemical theory and computation·2015
Same author

A novel congenital myasthenic syndrome due to decreased acetylcholine receptor ion-channel conductance.

Brain : a journal of neurology·2012
Same author

Ion-blocking sites of the Kir2.1 channel revealed by multiscale modeling.

Biochemistry·2009
Same author

Molecular modeling and simulation studies of ion channel structures, dynamics and mechanisms.

Methods in cell biology·2009
Same author

Ion channel gates: comparative analysis of energy barriers.

European biophysics journal : EBJ·2008
Same author

The selectivity of K+ ion channels: testing the hypotheses.

Biophysical journal·2008

Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Modeling

Background:

  • Accurate sampling of biomolecular conformations is crucial for understanding biological function.
  • Traditional simulation methods face challenges in exploring complex conformational landscapes.
  • Recent advancements have introduced novel approaches to enhance conformational sampling.

Purpose of the Study:

  • To review recently developed methods for sampling biomolecular conformations.
  • To evaluate the published applications and system suitability of these new methods.
  • To identify practical and effective techniques for biomolecular simulations.

Main Methods:

  • Review of recent literature on biomolecular conformation sampling.
  • Analysis of applications and system compatibility for selected methods.
  • Focus on four specific methods: RESPA, replica-exchange molecular dynamics, CONCOORD, and Gaussian network method.

Main Results:

  • Several new methods for biomolecular conformation sampling have emerged.
  • The review emphasizes published applications and system-specific suitability.
  • Four methods (RESPA, replica-exchange molecular dynamics, CONCOORD, Gaussian network method) are identified as readily applicable.

Conclusions:

  • The reviewed methods provide powerful tools for exploring biomolecular conformational space.
  • The choice of method depends on the specific system and research question.
  • These techniques facilitate deeper insights into biomolecular mechanisms and functions.

Related Experiment Videos