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

PSI-DOCK: towards highly efficient and accurate flexible ligand docking.

Jianfeng Pei1, Qi Wang, Zhenming Liu

  • 1State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China.

Proteins
|January 6, 2006
PubMed
Summary

We introduce Pose-Sensitive Inclined (PSI)-DOCK, a novel flexible ligand docking method with an improved scoring function for accurate binding free energy prediction. PSI-DOCK demonstrates high efficiency in identifying experimental binding poses and predicting binding free energies with minimal user preparation.

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

Unveiling optimal molecular features for hERG insights with automatic machine learning.

Journal of pharmaceutical analysis·2026
Same author

Artificial intelligence guided Raman spectroscopy in biomedicine: Applications and prospects.

Journal of pharmaceutical analysis·2025
Same author

MGTbind: a comprehensive database of molecular glue ternary interactome.

Nucleic acids research·2025
Same author

Benchmarking Cofolding Methods for Molecular Glue Ternary Structure Prediction.

Journal of chemical information and modeling·2025
Same author

Identification and Functional Disparity of Pheromone-Binding Proteins from Tomato Leafminer <i>Tuta absoluta</i> in Detection of Sex Pheromone Components.

Journal of agricultural and food chemistry·2025
Same author

Predictive value of monocytes for coronary heart disease in Chinese adults: a population-based cohort study.

BMJ open·2025

Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Drug discovery

Background:

  • Accurate prediction of protein-ligand interactions is crucial for drug discovery.
  • Existing flexible ligand docking methods often require extensive preparation and lack accuracy in binding free energy evaluation.

Purpose of the Study:

  • To develop a novel, efficient, and user-friendly flexible ligand docking method.
  • To improve the accuracy of binding free energy prediction in docking simulations.

Main Methods:

  • Developed Pose-Sensitive Inclined (PSI)-DOCK, a new flexible ligand docking approach.
  • Implemented an improved SCORE function for binding free energy evaluation.
  • Utilized a hybrid genetic algorithm search strategy combining rapid shape complementarity and accurate energy scoring.

Related Experiment Videos

Main Results:

  • PSI-DOCK achieved a 67% success rate in identifying experimental binding poses for 194 complexes in a single run.
  • The improved SCORE function reproduced binding free energies with a correlation coefficient of 0.788 on a training set.
  • PSI-DOCK showed high accuracy in predicting binding free energies for a test set (r = 0.777).

Conclusions:

  • PSI-DOCK is a highly efficient and accurate method for flexible ligand docking and binding free energy prediction.
  • The method simplifies the docking process by eliminating the need for hydrogen atom addition and partial charge calculations.
  • PSI-DOCK offers a user-friendly alternative to existing docking tools, facilitating drug discovery research.