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

Conformer generation under restraints.

Paul I W de Bakker1, Nicholas Furnham, Tom L Blundell

  • 1Department of Molecular Biology and Center for Human Genetic Research, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114-2790, USA.

Current Opinion in Structural Biology
|February 18, 2006
PubMed
Summary
This summary is machine-generated.

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

Workflow for Crystallographic Fragment Screening by Crystal Soaking for Protein Targets: A Case Study on Thioredoxin Glutathione Reductase From <i>Schistosoma mansoni</i>.

Bio-protocol·2026
Same author

Crystal structure of Schistosoma mansoni cathepsin D1 in complex with a nanobody reveals the conformation of the propeptide-bound state.

Acta crystallographica. Section D, Structural biology·2026
Same author

Tools and challenges in the use of routine clinical data for antimicrobial resistance surveillance.

npj antimicrobials and resistance·2025
Same author

Molecular subtyping of hypertensive disorders of pregnancy.

Nature communications·2025
Same author

Unveiling the ghost: machine learning's impact on the landscape of virology.

The Journal of general virology·2025
Same author

Fragment library screening by X-ray crystallography and binding site analysis on thioredoxin glutathione reductase of Schistosoma mansoni.

Scientific reports·2024
Same journal

Tomogram exploration through template matching and deep learning.

Current opinion in structural biology·2026
Same journal

A comparative review of cryo-electron ptychography: Biological applications and future perspectives.

Current opinion in structural biology·2026
Same journal

Metabolic disruptions through a three-dimensional genomic lens.

Current opinion in structural biology·2026
Same journal

Collective variable design for biomolecular conformational dynamics.

Current opinion in structural biology·2026
Same journal

Polymer scaling in protein crowding: From dilute coils to semidilute meshes.

Current opinion in structural biology·2026
Same journal

Tuning the physicochemical properties of rationally designed protein-based biomolecular condensates.

Current opinion in structural biology·2026
See all related articles

Discrete sampling methods offer a more effective approach to conformational sampling for predicting molecular structures. This computational strategy aids in overcoming challenges in determining complex macromolecular systems.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Biophysics

Background:

  • Direct optimization of all-atom energy functions for conformational sampling is hindered by rugged energy landscapes.
  • Accurate prediction of molecular structures is increasingly limited by conformational sampling methods rather than energy functions.

Purpose of the Study:

  • To explore discrete sampling schemes as an alternative for generating molecular conformers.
  • To address the challenges in predicting structures of large macromolecular systems and incorporating dynamic properties.

Main Methods:

  • Utilizing discrete sampling schemes to generate ensembles of conformers.
  • Integrating dense, discrete sampling with all-atom energy evaluation and refinement.

Main Results:

Related Experiment Videos

  • Discrete sampling schemes provide an attractive alternative for generating conformers consistent with empirical spatial restraints.
  • Computational approaches combining discrete sampling with energy evaluation show promise for overcoming structural determination barriers.

Conclusions:

  • Discrete sampling is crucial for advancing conformational sampling in structure prediction.
  • Combined computational strategies may resolve limitations in modeling complex biological systems, including their dynamics and heterogeneity.