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

Protein ligand docking based on empirical method for binding affinity estimation.

P Tao1, L Lai

  • 1Institute of Physical Chemistry, Peking University, Beijing, PR China.

Journal of Computer-Aided Molecular Design
|June 8, 2001
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

Ablation-first versus biopsy-first strategy in computed tomography (CT)-guided biopsy-cryoablation for pulmonary nodules: a retrospective cohort study.

Clinical radiology·2026
Same author

Molecular mechanisms revealed by network pharmacology of Xuebijing on the treatment of acute respiratory distress syndrome caused by novel coronavirus infection.

European review for medical and pharmacological sciences·2022
Same author

Evaluation of N-acetylcysteine dose for the treatment of massive acetaminophen ingestion.

Clinical toxicology (Philadelphia, Pa.)·2021
Same author

[Comparison of the intact and segmented dissection for surface preparation of the cochlea in mice].

Zhonghua er bi yan hou tou jing wai ke za zhi = Chinese journal of otorhinolaryngology head and neck surgery·2020
Same author

Knowledge about cancer screening programmes in Sardinia.

Journal of preventive medicine and hygiene·2020
Same author

[Hypopharyngeal angiofibroma: a case report].

Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery·2018
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

ScoreDock integrates protein-ligand binding affinity estimation with docking to improve accuracy. This computational tool aids in drug design by reliably assessing protein-ligand complexes and identifying potential drug candidates.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Protein-ligand interactions are crucial in biological processes and drug development.
  • Accurate prediction of binding affinity is essential for effective structure-based drug design.
  • Existing docking methods often require refinement for reliable affinity estimation.

Purpose of the Study:

  • To integrate the SCORE empirical binding affinity estimation method into the DOCK4 docking program.
  • To develop and validate a quality assessment method for the enhanced docking tool, ScoreDock.
  • To evaluate ScoreDock's utility in screening potential drug candidates based on predicted binding affinities.

Main Methods:

  • Incorporation of the SCORE method into the DOCK4 program to create ScoreDock.

Related Experiment Videos

  • Reconstruction of 200 known protein-ligand complex structures using ScoreDock.
  • Development of a quality assessment method for docking results based on a comprehensive test set.
  • Testing the quality assessment method on additional selected protein-ligand complexes.

    • Main Results:

    • ScoreDock demonstrated good performance in reconstructing protein-ligand complexes, particularly those with high binding affinities.
    • The developed quality assessment method significantly improved the accuracy of docking results.
    • The quality assessment method proved reliable for evaluating docking outcomes.
    • ScoreDock effectively handles structural water molecules and metal atoms in complexes.

    Conclusions:

    • ScoreDock enhances protein-ligand docking by incorporating accurate binding affinity estimation.
    • The integrated quality assessment method provides reliable evaluation of docking results.
    • ScoreDock serves as a valuable tool for structure-based drug design, enabling direct screening of potential drug candidates.