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

Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

1.9K
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
1.9K
Fast Fourier Transform01:10

Fast Fourier Transform

1.3K
The Fast Fourier Transform (FFT) is a computational algorithm designed to compute the Discrete Fourier Transform (DFT) efficiently. By breaking down the calculations into smaller, manageable sections, the FFT significantly reduces the computational complexity involved. Direct computation of an N-point DFT requires N2 complex multiplications, whereas the FFT algorithm needs only (N/2)log⁡2N multiplications, offering a much faster performance.
The computational efficiency of the FFT becomes...
1.3K

You might also read

Related Articles

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

Sort by
Same author

The influence of ligands on AlphaFold3 prediction of cryptic pockets.

Communications biology·2026
Same author

From memorization to generalization: Why physics will improve machine learning -based prediction of protein complexes.

Current opinion in structural biology·2026
Same author

Assessment of Alphafold Protein Models for Small-Molecule Ligand Docking versus Co-Folding.

Journal of chemical information and modeling·2026
Same author

Hierarchical decoding of targeting tripeptide motif by the cytosolic iron-sulfur cluster assembly targeting complex.

bioRxiv : the preprint server for biology·2026
Same author

A Customizable Antibody Delivery Strategy Using Fc-Affinity Ligands.

ACS biomaterials science & engineering·2026
Same author

Bias in the AlphaFold3 prediction of ligand-induced domain motion in enzymes.

Proceedings of the National Academy of Sciences of the United States of America·2026

Related Experiment Video

Updated: May 2, 2026

SNARE-mediated Fusion of Single Proteoliposomes with Tethered Supported Bilayers in a Microfluidic Flow Cell Monitored by Polarized TIRF Microscopy
10:58

SNARE-mediated Fusion of Single Proteoliposomes with Tethered Supported Bilayers in a Microfluidic Flow Cell Monitored by Polarized TIRF Microscopy

Published on: August 24, 2016

10.6K

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating

David W Ritchie1, Dima Kozakov, Sandor Vajda

  • 1Department of Computing Science, University of Aberdeen, Aberdeen, Scotland, UK. d.w.ritchie@abdn.ac.uk

Bioinformatics (Oxford, England)
|July 2, 2008
PubMed
Summary

This study introduces a new 6D spherical polar Fourier correlation method for faster protein docking. This advanced technique accelerates calculations and improves accuracy, especially when incorporating prior knowledge of binding sites.

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

1.6K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.3K

Related Experiment Videos

Last Updated: May 2, 2026

SNARE-mediated Fusion of Single Proteoliposomes with Tethered Supported Bilayers in a Microfluidic Flow Cell Monitored by Polarized TIRF Microscopy
10:58

SNARE-mediated Fusion of Single Proteoliposomes with Tethered Supported Bilayers in a Microfluidic Flow Cell Monitored by Polarized TIRF Microscopy

Published on: August 24, 2016

10.6K
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

1.6K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.3K

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Biophysics

Background:

  • Protein-protein interactions are crucial but computationally challenging to predict.
  • Existing fast Fourier transform (FFT) correlation methods for protein docking are limited in dimensionality and flexibility.
  • There is a need for more efficient and versatile FFT-based docking techniques.

Purpose of the Study:

  • To develop a novel 6D spherical polar Fourier correlation expression for enhanced protein docking.
  • To enable multi-dimensional, multi-property, and multi-resolution FFT correlations.
  • To accelerate rigid body protein-protein docking calculations.

Main Methods:

  • Developed a closed-form 6D spherical polar Fourier correlation expression.
  • Calculated 1D, 3D, and 5D rotational correlations using 3D shape and electrostatic expansions.
  • Applied angular constraints based on prior knowledge of binding sites.

Main Results:

  • Demonstrated the generation of arbitrary multi-dimensional FFT correlations.
  • Observed that 5D correlations can be advantageous for multi-term potentials, despite sometimes being slower than 3D.
  • Achieved significant improvements in docking accuracy and speed by applying binding site constraints.

Conclusions:

  • The presented 6D spherical polar Fourier correlation approach offers a practical and fast tool for rigid body protein-protein docking.
  • Incorporating prior knowledge of binding sites dramatically enhances the efficiency and success rate of the docking process.
  • This method provides a versatile platform for future advancements in computational protein interaction prediction.