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

Novel algorithms for searching conformational space

D Byrne1, J Li, E Platt

  • 1Proteus Molecular Design Ltd., Macclesfield, Cheshire, U.K.

Journal of Computer-Aided Molecular Design
|February 1, 1994
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

Generation of equine-specific local antibiograms: reproductive tract of mares and fillies in Western Australia.

Australian veterinary journal·2026
Same author

Neurological and neurodevelopmental effects of Covid and MIS-C on children.

Pediatric research·2025
Same author

Perineural tumour spread in head and neck cancer: a pictorial review.

Clinical radiology·2024
Same author

Glass box machine learning for retrospective cohort studies using many patient records. The complex example of bleeding peptic ulcer.

Computers in biology and medicine·2024
Same author

Outcomes for Emergency Department Final Diagnosis of Non-specific Complaint compared to Dyspnoea and Pain.

Acute medicine·2024
Same author

Short- and long-term mortality following acute medical admission.

QJM : monthly journal of the Association of Physicians·2023
Same journal

Repurposing bleomycin against Acinetobacter baumannii HisG: computational, biophysical, and antibacterial evidence.

Journal of computer-aided molecular design·2026
Same journal

Topological data analysis for antibody-drug conjugate payload discovery: a computational framework for mechanistic classification and target validation.

Journal of computer-aided molecular design·2026
Same journal

Commentary on the fundamentals and development of artificial intelligence models in the life sciences and best research practices.

Journal of computer-aided molecular design·2026
Same journal

RANQSAR: a standalone open-source application for reproducible machine learning-based QSAR analysis.

Journal of computer-aided molecular design·2026
Same journal

Integrating evolutionary and compositional features with ML and DL for robust and interpretable druggable protein prediction.

Journal of computer-aided molecular design·2026
Same journal

QUAD: a composite risk framework integrating uncertainty, applicability domain, and model disagreement for reliable QSAR predictions.

Journal of computer-aided molecular design·2026
See all related articles

Molecular dynamics simulations face challenges like the multiple-minima problem, trapping systems in metastable states. This study explores advanced algorithms like RUSH, Hybrid Monte Carlo, and PEACS to improve conformational space searching and system equilibration.

Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular modeling

Background:

  • Molecular dynamics (MD) simulations are crucial for studying biological molecules.
  • A key challenge in MD is the multiple-minima problem, leading to systems getting trapped in metastable states.
  • This trapping hinders proper system equilibration and accurate conformational sampling.

Purpose of the Study:

  • To investigate novel algorithms for enhancing molecular dynamics simulations.
  • To address the limitations of traditional MD, particularly the multiple-minima problem.
  • To compare the efficiency of re-engineered 'Newtonian Rules' algorithms against standard MD methods.

Main Methods:

  • Exploration of re-engineered 'Newtonian Rules' through algorithms such as RUSH, Hybrid Monte Carlo (HMC), and Parallel Tempering Enhanced Annealing with Configuration Sampling (PEACS).

Related Experiment Videos

  • Application of these advanced algorithms to molecular dynamics simulations.
  • Comparative analysis of the performance of these algorithms against traditional molecular dynamics.

    • Main Results:

    • Advanced algorithms demonstrate potential in overcoming the multiple-minima problem.
    • Improved efficiency in searching conformational space compared to traditional MD.
    • Enhanced ability to achieve proper system equilibration by avoiding metastable states.

    Conclusions:

    • Re-engineering 'Newtonian Rules' offers a promising approach to enhance molecular dynamics simulations.
    • Algorithms like RUSH, HMC, and PEACS provide effective solutions for overcoming simulation trapping.
    • These methods represent significant advancements for accurate and efficient modeling of biological systems.