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 Concept Videos

Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Utilizing rat kidney gene co-expression networks to enhance safety assessment biomarker identification and human translation.

iScience·2025
Same author

A preclinical secondary pharmacology resource illuminates target-adverse drug reaction associations of marketed drugs.

Nature communications·2023
Same author

Identifying multiscale translational safety biomarkers using a network-based systems approach.

iScience·2023
Same author

Neurofilament light chain and dorsal root ganglia injury after adeno-associated virus 9 gene therapy in nonhuman primates.

Molecular therapy. Methods & clinical development·2023
Same author

"3D, human renal proximal tubule (RPTEC-TERT1) organoids 'tubuloids' for translatable evaluation of nephrotoxins in high-throughput".

PloS one·2022
Same author

Structural determinants of dual incretin receptor agonism by tirzepatide.

Proceedings of the National Academy of Sciences of the United States of America·2022

Related Experiment Video

Updated: Jul 10, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Lessons in molecular recognition. 2. Assessing and improving cross-docking accuracy.

Jeffrey J Sutherland1, Ravi K Nandigam, Jon A Erickson

  • 1Discovery Informatics and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA. sutherlandje@lilly.com

Journal of Chemical Information and Modeling
|October 25, 2007
PubMed
Summary

Cross-docking accuracy for molecular docking programs improves by selecting protein structures with ligands similar to the target. This "similarity selection" enhances prediction reliability for drug discovery.

More Related Videos

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Related Experiment Videos

Last Updated: Jul 10, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Molecular docking predicts ligand-protein interactions, crucial for drug design.
  • Self-docking tests assess program success but lack real-world applicability.
  • Cross-docking, using different ligand-protein complexes, offers a more realistic evaluation.

Purpose of the Study:

  • To evaluate the cross-docking performance of CDocker, Fred, and Rocs.
  • To investigate strategies for improving cross-docking accuracy.
  • To identify predictors of docking accuracy for method selection.

Main Methods:

  • Cross-docking simulations were performed using CDocker, Fred, and Rocs.
  • Eight protein targets (kinases, nuclear hormone receptor, proteases, phosphodiesterases) with multiple X-ray structures were used.
  • Ligand similarity and protein conformer selection strategies were applied.

Main Results:

  • Average cross-docking accuracy was generally low.
  • "Similarity selection" (using protein structures with similar ligands) significantly improved accuracy for all methods.
  • "Best selection" (identifying the most successful protein conformer) also enhanced accuracy.

Conclusions:

  • Ligand similarity and protein conformer selection are critical for improving cross-docking reliability.
  • Predictors of docking accuracy can be identified and used to build models for selecting optimal docking methods.