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

CASP2 experiences with docking flexible ligands using FlexX

B Kramer1, M Rarey, T Lengauer

  • 1German National Research Center for Information Technology (GMD), Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Germany. bernd.kramer@gmd.de

Proteins
|January 1, 1997
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

Dissecting heterogeneity in cortical thickness abnormalities in major depressive disorder: a large-scale ENIGMA MDD normative modelling study.

bioRxiv : the preprint server for biology·2025
Same author

Taking shape: A geometric morphometric analysis of the immature human palate in relation to dental eruption and growth.

Morphologie : bulletin de l'Association des anatomistes·2024
Same author

Collaborative study for the characterisation of the BINACLE Assay for <i>in vitro</i> detection of tetanus toxicity in toxoids - Part 1.

Pharmeuropa bio & scientific notes·2024
Same author

The challenge of replicating putative genetic risk factors in a population-based database.

Journal of gastroenterology and hepatology·2024
Same author

Impact of Bepanthen<sup>®</sup> and dexpanthenol on human nasal ciliary beat frequency in vitro.

European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery·2023
Same author

NT-proBNP and stem cell factor plasma concentrations are independently associated with cardiovascular outcomes in end-stage renal disease hemodialysis patients.

European heart journal open·2023
Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026
Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026
Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026
Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026
Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026
Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026
See all related articles

The FlexX docking program successfully predicted protein-ligand complexes for CASP2 targets, demonstrating competitive quality and remarkable speed. Further development could enhance its accuracy by incorporating receptor flexibility and optimizing scoring functions.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Protein-ligand interactions are crucial for biological processes and drug development.
  • Accurate prediction of these complexes aids in understanding molecular mechanisms and designing novel therapeutics.

Purpose of the Study:

  • To evaluate the performance of the FlexX docking program on protein-ligand targets from the CASP2 experiment.
  • To assess the speed and quality of FlexX predictions compared to other methods.

Main Methods:

  • Applied the FlexX docking program to eight CASP2 targets involving protein complexes with small ligands.
  • Analyzed prediction results for seven targets included in the CASP2 experiment.

Main Results:

Related Experiment Videos

  • Successfully solved two out of seven CASP2 targets.
  • Achieved partial solutions for four additional targets.
  • Demonstrated rapid prediction times (minutes per run) on standard workstations.

Conclusions:

  • FlexX shows competitive prediction quality and exceptional speed, making it suitable for real-time demonstrations.
  • Areas for improvement include incorporating receptor flexibility, handling water molecules, post-optimization, and refining the scoring function.