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

Modeling protein complexes with BiGGER.

Ludwig Krippahl1, José J Moura, P Nuno Palma

  • 1REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Monte de Caparica, Portugal. ludi@dq.fct.unl.pt ludik@netcabo.pt

Proteins
|June 5, 2003
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

Inactivation Mechanism of the Fatty Acid Amide Hydrolase Inhibitor BIA 10-2474.

Chembiochem : a European journal of chemical biology·2022
Same author

eHooke: A tool for automated image analysis of spherical bacteria based on cell cycle progression.

Biological imaging·2022
Same author

Discovery of a Potent, Long-Acting, and CNS-Active Inhibitor (BIA 10-2474) of Fatty Acid Amide Hydrolase.

ChemMedChem·2018
Same author

Measurement of adsorption constants of laccase on gold nanoparticles to evaluate the enhancement in enzyme activity of adsorbed laccase.

Physical chemistry chemical physics : PCCP·2018
Same author

Predicting Protein-Protein Interactions Using BiGGER: Case Studies.

Molecules (Basel, Switzerland)·2016
Same author

Protein docking with predicted constraints.

Algorithms for molecular biology : AMB·2015
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 BiGGER protein docking program achieved one successful prediction in the Critical Assessment of PRediction of Interactions (CAPRI) experiment. It also generated reasonable models for other targets, potentially useful with more biochemical data.

Area of Science:

  • Computational biology
  • Structural biology
  • Bioinformatics

Background:

  • The Critical Assessment of PRediction of Interactions (CAPRI) is a community-wide experiment to assess the accuracy of protein-protein interaction structure prediction methods.
  • Evaluating and ranking protein complex models is crucial for understanding biological functions and designing drugs.

Purpose of the Study:

  • To assess the performance of the BiGGER (Bimolecular complex Generation with Global Evaluation and Ranking) program in the CAPRI experiment.
  • To evaluate the accuracy of protein docking predictions generated by BiGGER.

Main Methods:

  • Utilized the BiGGER protein docking program for structure prediction.
  • Participated in the CAPRI experiment, predicting five target protein complexes (targets 2, 4, 5, 6, and 7).

Related Experiment Videos

  • Evaluated prediction accuracy based on CAPRI criteria.

    • Main Results:

    • Achieved one successful prediction (target 6) out of five CAPRI targets.
    • Generated reasonable models for CAPRI targets 4, 5, and 7.
    • Identified limitations in prediction accuracy without additional biochemical information.

    Conclusions:

    • The BiGGER program demonstrated some capability in predicting protein-protein interactions.
    • Additional biochemical data could significantly improve the accuracy and utility of predicted models.
    • Further development of docking algorithms is warranted for complex biological systems.