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

Constraint Logic Programming approach to protein structure prediction.

Alessandro Dal Palù1, Agostino Dovier, Federico Fogolari

  • 1Dipartimento di Matematica e Informatica, Università di Udine, Via delle Scienze 206, 33100 Udine, Italy. dalpalu@dimi.uniud.it <dalpalu@dimi.uniud.it>

BMC Bioinformatics
|December 2, 2004
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

Structural characterization and thermodynamic behavior of melittin-derived peptide interactions with gram-positive bacterial cell membranes using molecular dynamics simulation.

RSC advances·2026
Same author

The Single-Parameter Bragg-Williams Model for Eutectic Solvents.

International journal of molecular sciences·2025
Same author

Adenine nucleotide translocator and ATP synthase cooperate in mediating the mitochondrial permeability transition.

The Journal of physiology·2025
Same author

Bluues_cplx: Electrostatics at Protein-Protein and Protein-Ligand Interfaces.

Molecules (Basel, Switzerland)·2025
Same author

Exploring patient stratification in head and neck squamous cell carcinoma using machine learning techniques: Preliminary results.

Current problems in cancer·2024
Same author

Statistical accuracy of molecular dynamics-based methods for sampling conformational ensembles of disordered proteins.

Physical chemistry chemical physics : PCCP·2024

Constraint Logic Programming effectively models protein structure prediction using simplified lattice models. This approach yields acceptable results for small proteins, offering advantages in prototyping and search space pruning.

Area of Science:

  • Computational Biology
  • Biophysics
  • Bioinformatics

Background:

  • Protein structure prediction is a major challenge in biological sciences.
  • Existing methods often use database information or simplified models.
  • The problem is an optimization challenge rarely addressed by Constraint Logic Programming (CLP).

Purpose of the Study:

  • To investigate the application of Constraint Logic Programming (CLP) to protein structure prediction.
  • To explore CLP on a face-centered cube lattice model for simplified protein structures.

Main Methods:

  • Applied Constraint Logic Programming (CLP) techniques to the face-centered cube lattice model.
  • Utilized molecular dynamics with constraints.
  • Incorporated known secondary structure and disulfide bridges as constraints.

Related Experiment Videos

  • Converted simplified models to all-atom models.

    • Main Results:

    • Achieved acceptable results for small protein structure prediction using CLP on the lattice model.
    • Simplified structures were converted to plausible all-atom models.
    • Compared favorably with molecular dynamics approaches.

    Conclusions:

    • CLP techniques are viable for studying simplified protein models.
    • These models can be converted into realistic all-atom structures.
    • CLP offers advantages in rapid prototyping, heuristic encoding, and search space pruning.