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

Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

You might also read

Related Articles

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

Sort by
Same author

Molecular insights into the dual-glycoprotein surface layer of the oral bacterium Tannerella serpentiformis.

Journal of molecular graphics & modelling·2026
Same author

Navigating the Pre- and Post-AlphaFold Divide: CAPRI 8th Evaluation Meeting, February 12-14, Grenoble, FR.

Proteins·2025
Same author

Updates to the CASP Infrastructure in 2024.

Proteins·2025
Same author

Improved prediction of antibody and their complexes with clustered generative modelling ensembles.

Bioinformatics advances·2025
Same author

Biomolecular Interaction Prediction in the Pre- and Post-AlphaFold Era: The 8th CAPRI Evaluation.

Proteins·2025
Same author

Molecular determinants for recognition of serotonylated chromatin.

Nucleic acids research·2025

Related Experiment Video

Updated: Jun 3, 2026

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

CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.

Sjoerd J de Vries1, Alexandre M J J Bonvin

  • 1Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands. a.m.j.j.bonvin@uu.nl

Plos One
|April 6, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces CPORT, a consensus interface prediction method, combined with HADDOCK for protein-protein complex structure prediction. This prediction-driven docking approach offers a competitive alternative to ab initio methods, especially with limited experimental data.

More Related Videos

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

Related Experiment Videos

Last Updated: Jun 3, 2026

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

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

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Macromolecular complexes are essential cellular machinery, but their atomic-level structures are challenging to determine using traditional methods like NMR and X-ray crystallography.
  • A significant number of protein-protein complexes are difficult to study, necessitating advanced computational approaches for structural elucidation.
  • Large-scale computational methods are crucial for advancing structural biology and understanding molecular functions at the atomic level.

Purpose of the Study:

  • To develop and evaluate a computational strategy for determining atomic-level structures of protein-protein complexes.
  • To combine interface prediction and docking methods to overcome limitations of studying transient complexes.
  • To provide an alternative to *ab initio* docking for cases with limited experimental data.

Main Methods:

  • Developed CPORT (Consensus Prediction Of interface Residues in Transient complexes), a consensus method integrating six interface prediction web servers.
  • Integrated CPORT predictions into the HADDOCK (High Ambiguity Driven DOCKing) program for a prediction-driven docking protocol.
  • Performed blind, prediction-driven docking on a diverse set of protein-protein complexes.

Main Results:

  • CPORT demonstrated more stable and reliable interface predictions compared to individual web servers.
  • The HADDOCK-CPORT combination achieved performance competitive with state-of-the-art *ab initio* docking methods like ZDOCK-ZRANK.
  • Interface post-prediction analysis further improved the accuracy of the initial interface predictions.

Conclusions:

  • Blind, prediction-driven docking using CPORT and HADDOCK is a viable and competitive approach for structural studies of protein-protein complexes.
  • This method serves as a foundational 'bottom line' for data-driven docking, with potential for significant improvement with additional biological information.
  • Further optimization of prediction-driven docking is possible, indicating its potential has not yet been fully realized.