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

Computer simulation of biological interactions and reactivity.

J J Wendoloski1, Z R Wasserman, F R Salemme

  • 1Central Research and Development Department, E.I. du Pont de Nemours and Co., Inc., Wilmington, DE 19898.

Journal of Computer-Aided Molecular Design
|January 1, 1988
PubMed
Summary

Computer simulations reveal molecular motion dynamics, complementing experimental data for macromolecular structure and function. These methods explore complex interactions and dynamic states beyond X-ray crystallography limitations.

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

Anomalous temperature factor behavior and crystal lattice mobility in cytochrome C'.

Biophysical journal·2009
Same author

A comparison of the chemical properties of drugs and FEMA/FDA notified GRAS chemical compounds used in the food industry.

Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association·2007
Same author

The fundamentals of pharmacophore modeling in combinatorial chemistry.

Journal of receptor and signal transduction research·2002
Same author

High-density miniaturized thermal shift assays as a general strategy for drug discovery.

Journal of biomolecular screening·2002
Same author

Design and synthesis of a series of (2R)-N(4)-hydroxy-2-(3-hydroxybenzyl)-N(1)- [(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide derivatives as potent, selective, and orally bioavailable aggrecanase inhibitors.

Journal of medicinal chemistry·2001
Same author

Discovery of macrocyclic hydroxamic acids containing biphenylmethyl derivatives at P1', a series of selective TNF-alpha converting enzyme inhibitors with potent cellular activity in the inhibition of TNF-alpha release.

Journal of medicinal chemistry·2001

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Molecular simulations offer insights into macromolecular dynamics.
  • Experimental methods like X-ray crystallography provide average flexibility estimates.
  • Bridging simulation and experimental data enhances understanding of molecular motion.

Purpose of the Study:

  • To apply molecular dynamics simulations to large molecular aggregates.
  • To investigate dynamic properties that hinder detailed structural descriptions.
  • To explore infrequent structural fluctuations and dynamic states of molecular association.

Main Methods:

  • Utilizing computer simulations of molecular motion.
  • Comparing simulation results with experimental data (e.g., X-ray crystallographic B-values).

Related Experiment Videos

  • Applying molecular dynamics to specific systems: electron transfer complexes, ion channels, and micelles.

    • Main Results:

    • Simulations provide detailed views of motions causing crystalline disorder.
    • Crystal packing effects on protein surface mobility can be evaluated.
    • Dynamics simulations regenerate the temporal dimension of experimentally defined structures.

    Conclusions:

    • Molecular dynamics simulations are valuable for analyzing macromolecular structure and function.
    • These methods enable the study of dynamic states not accessible by X-ray methods.
    • The study demonstrates applications to complex systems like protein complexes and membrane channels.