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

Induced-fit Model01:13

Induced-fit Model

Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...

You might also read

Related Articles

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

Sort by
Same author

Estimation of protein melting temperatures using small-ladder replica exchange simulations.

The Journal of chemical physics·2026
Same author

Comparison of Protein-Glycosaminoglycan Interactions in ff14sb/GLYCAM06j-1 and CHARMM36m Force Fields.

Journal of chemical information and modeling·2026
Same author

Protein-Protein Interaction Stabilizers from MD Simulation-Derived Pharmacophores.

Journal of chemical information and modeling·2026
Same author

The vacuolar tauopathy-associated mutation D395G confers redox sensitivity to p97/VCP.

bioRxiv : the preprint server for biology·2026
Same author

In Silico Analysis of Potential Stabilizer Binding Sites at Protein-RNA Interfaces.

Computational and structural biotechnology journal·2026
Same author

How cysteine oxidation affects protein stability and binding studied by free energy calculations.

Physical chemistry chemical physics : PCCP·2026

Related Experiment Video

Updated: May 8, 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

Flexible docking and refinement with a coarse-grained protein model using ATTRACT.

Sjoerd de Vries1, Martin Zacharias

  • 1Physik-Department T38, Technische Universität München, James Franck Str. 1, 85748, Garching, Germany.

Proteins
|September 3, 2013
PubMed
Summary

A coarse-grained protein model in ATTRACT successfully predicted protein complexes in CAPRI challenges. New methods improved flexible refinement, showing promise for protein-protein docking accuracy.

Keywords:
docking minimizationelastic network modelinduced fitprotein-protein complex formationprotein-protein interaction

More Related Videos

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

Related Experiment Videos

Last Updated: May 8, 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

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

Area of Science:

  • Computational biology
  • Structural biology
  • Biophysics

Background:

  • Protein-protein interactions are crucial for biological processes.
  • Accurate prediction of protein complex structures remains a challenge.
  • Coarse-grained (CG) models offer a computationally efficient approach to protein modeling.

Purpose of the Study:

  • To evaluate a CG protein model within the ATTRACT program for protein-protein docking.
  • To develop and assess new methods for rapid flexible refinement of protein complexes.
  • To predict protein-protein complex structures for CAPRI (Critical Assessment of PRedicted Interactions) rounds.

Main Methods:

  • Utilized a coarse-grained (CG) protein model implemented in the ATTRACT docking program.
  • Applied the model to predict protein-protein complex structures for CAPRI Rounds 22-27.
  • Developed novel flexible refinement techniques combining atomistic and CG representations.
  • Investigated hydration structure prediction at protein-protein interfaces.

Main Results:

  • Achieved acceptable or better quality solutions for approximately 60% of the six CAPRI targets.
  • Obtained promising results in predicting the hydration structure at a protein-protein interface for one target.
  • Developed new rapid flexible refinement approaches.

Conclusions:

  • The CG protein model in ATTRACT demonstrates effectiveness for protein-protein docking.
  • The developed flexible refinement methods show potential for improving docking accuracy.
  • Further enhancements in scoring and refinement could advance protein complex structure prediction.