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

Protein topology prediction through parallel constraint logic programming

D A Clark1, C J Rawlings, J Shirazi

  • 1Biomedical Informatics Unit, Imperial Cancer Research Fund Laboratories, London, UK.

Proceedings. International Conference on Intelligent Systems for Molecular Biology
|January 1, 1993
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

Coronal STIR MRI sequences in unexplained limping in children under 6 years old: A single-center retrospective study of 130 cases.

Archives de pediatrie : organe officiel de la Societe francaise de pediatrie·2022
Same author

Pollutant Pb burden in Mediterranean Centroscymnus coelolepis deep-sea sharks.

Marine pollution bulletin·2022
Same author

Chlorophyll a might structure a community of potentially pathogenic culturable Vibrionaceae. Insights from a one-year study of water and mussels surveyed on the French Atlantic coast.

Environmental microbiology reports·2013
Same author

Erdheim-Chester disease: a rare diagnosis with evocative imaging.

Diagnostic and interventional imaging·2013
Same author

Acute pulmonary embolism revealing Ivemark syndrome in an adult.

Diagnostic and interventional imaging·2013
Same author

Properties of the static NMR response of a confined thin nematic film of 5CB-d2 under crossed electric and magnetic fields: theory and experiments.

Physical review. E, Statistical, nonlinear, and soft matter physics·2012
Same journal

Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB 2000). San Diego, California, USA. August 19-23, 2000.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2001
Same journal

Analysis of gene expression data with pathway scores.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
Same journal

Towards a complete map of the protein space based on a unified sequence and structure analysis of all known proteins.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
Same journal

Mining for putative regulatory elements in the yeast genome using gene expression data.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
Same journal

A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
Same journal

Sequence database search using jumping alignments.

Proceedings. International Conference on Intelligent Systems for Molecular Biology·2000
See all related articles

Two new programs, CBS1e and CBS2e, use parallel constraint logic programming to predict protein topology. These AI tools significantly improve speed and handle complex folding rules for molecular biology problems.

Area of Science:

  • Computational Biology
  • Artificial Intelligence
  • Bioinformatics

Background:

  • Protein structure prediction is crucial for understanding biological function.
  • Traditional logic programming languages face limitations in scalability for complex biological problems.

Purpose of the Study:

  • To introduce two novel programs, CBS1e and CBS2e, for protein topology prediction.
  • To demonstrate the advantages of parallel constraint logic programming (PCLP) over traditional methods like Prolog for large-scale combinatorial problems in molecular biology.

Main Methods:

  • Implementation of CBS1e and CBS2e using the ElipSys PCLP language.
  • Utilizing secondary structure assignments and topological folding rules as constraints.
  • Developing CBS2e to integrate uncertain (weighted) protein folding constraints with categorical ones via cost function minimization.

Related Experiment Videos

Main Results:

  • CBS1e showed a 60-fold speed improvement over an equivalent Prolog implementation (CBS1) for large topological problems.
  • PCLP overcomes limitations of traditional logic programming in declarative features and scalability.
  • CBS2e effectively integrates weighted and categorical constraints with minimal performance reduction.

Conclusions:

  • PCLP offers a powerful approach for solving complex, large-scale problems in protein structure prediction.
  • CBS1e and CBS2e significantly extend the capabilities of AI in addressing advanced protein structure prediction challenges.
  • These advancements pave the way for more sophisticated computational methods in molecular biology research.