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

FlexE: efficient molecular docking considering protein structure variations.

H Claussen1, C Buning, M Rarey

  • 1German National Research Center for Information Technology (GMD), Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany. Holger.Claussen@gmd.de

Journal of Molecular Biology
|May 1, 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

Vedolizumab in the treatment of chronic, antibiotic-dependent or refractory pouchitis.

Alimentary pharmacology & therapeutics·2017
Same author

The C/C_₁₃₉₁₀ and G/G_₂₂₀₁₈ Genotypes for Adult-type Hypolactasia are not Associated with Inflammatory Bowel Disease.

Scandinavian journal of gastroenterology·2017
Same author

Ferric maltol therapy for iron deficiency anaemia in patients with inflammatory bowel disease: long-term extension data from a Phase 3 study.

Alimentary pharmacology & therapeutics·2016
Same author

A rare cause of peripheral arthralgia in inflammatory bowel disease: multifocal osteonecrosis.

Zeitschrift fur Gastroenterologie·2014
Same author

Full genome ultra-deep pyrosequencing associates G-to-A hypermutation of the hepatitis B virus genome with the natural progression of hepatitis B.

Journal of viral hepatitis·2013
Same author

[Importance of bioinformatics in personalised medicine].

Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz·2013
Same journal

UPF3A and UPF3B shape the transcriptome cooperatively yet oppose cell function.

Journal of molecular biology·2026
Same journal

Antibody-secreting cells integrate efficient NMD with non‑canonical UPR signaling to maintain proteostasis and support massive immunoglobulin synthesis.

Journal of molecular biology·2026
Same journal

Small molecule stabilization of diverse amyloidogenic immunoglobulin light chains revealed by hydrogen-deuterium exchange mass spectrometry.

Journal of molecular biology·2026
Same journal

UPF1 at Work: Structural and Mechanistic Insights Into a Master Regulator of Nonsense-Mediated mRNA Decay.

Journal of molecular biology·2026
Same journal

Structural basis for the pro-amyloidogenic action and ligand binding of a novel W72R variant of human apolipoprotein A-I.

Journal of molecular biology·2026
Same journal

Cryo-EM Structure of the C. Elegans Septin Tetramer Reveals a Revised Architecture and Conserved Positional Orthology.

Journal of molecular biology·2026
See all related articles

FlexE software accounts for protein structure variations in molecular docking, improving ligand binding predictions. This approach enhances accuracy and efficiency compared to traditional methods by considering protein flexibility and mutations.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Drug Discovery

Background:

  • Protein structures exhibit variations like induced fit, point mutations, and modeling uncertainties, impacting molecular docking accuracy.
  • Existing docking methods often overlook these protein structural variations, limiting their predictive power.
  • Accurate ligand-protein interactions are crucial for understanding biological processes and designing therapeutics.

Purpose of the Study:

  • To introduce FlexE, a novel software tool designed to address protein structure variations in molecular docking calculations.
  • To enable flexible ligand docking into ensembles of protein structures, representing diverse conformations and mutations.
  • To improve the accuracy and efficiency of docking by integrating protein flexibility into the computational workflow.

Related Experiment Videos

Main Methods:

  • FlexE utilizes a united protein description generated from superimposed ensemble structures.
  • It explicitly considers discrete alternative conformations for varying protein regions, combinatorially joining them.
  • The software was evaluated using ten protein structure ensembles (105 PDB structures) and one modeled structure with 60 ligands.

Main Results:

  • FlexE successfully placed 83% of ligands with an RMSD below 2.0 Å to the crystal structure.
  • Results demonstrated comparable quality to cross-docking while significantly reducing computation time.
  • Average docking time per ligand was approximately 5.5 minutes on a standard workstation.

Conclusions:

  • Considering protein structure variations is essential for accurate molecular docking, as exemplified by aldose reductase inhibitor studies.
  • FlexE effectively handles protein flexibility, mutations, and alternative models, outperforming single-structure docking.
  • The tool offers a computationally efficient and accurate solution for docking flexible ligands into dynamic protein targets.