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

Contact interactions method: a new algorithm for protein folding simulations

L Toma1, S Toma

  • 1Dipartimento di Chimica Organica, Università di Pavia, Italy. burdisso@ipv85.unipv.it

Protein Science : a Publication of the Protein Society
|January 1, 1996
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

Activation of the visual system by space radiation: A novel study on Ca<sup>2+</sup> signalling in ex-vivo rabbit eyes exposed to visible light, X-rays and high-energy protons.

Life sciences in space research·2025
Same author

Increasing Octupole Collectivity across the Z=64 Isotopic Chain: B(E3) Values in ^{150}Gd.

Physical review letters·2025
Same author

Argas ticks (Ixodida: Argasidae) on migratory birds from Africa: first record of a genotype close to Argas africolumbae in Italy.

Ticks and tick-borne diseases·2023
Same author

COVID-19 AND THE THYROID FUNCTION IN PATIENTS WITH HCV- ASSOCIATED HEPATOCELLULAR CARCINOMA.

Acta endocrinologica (Bucharest, Romania : 2005)·2023
Same author

The impact of COVID 19 infection on HCV-induced thyroid disease.

Acta endocrinologica (Bucharest, Romania : 2005)·2022
Same author

Estimation of genetic parameter for feed efficiency and resilience traits in three pig breeds.

Animal : an international journal of animal bioscience·2021

A new Contact Interactions (CI) algorithm enhances protein folding simulations by exploring low-energy conformations. This method, improving on Monte Carlo simulations, identifies energy minima missed by other algorithms.

Area of Science:

  • Computational Biology
  • Biophysics
  • Protein Folding Dynamics

Background:

  • Computer simulations of lattice models aid protein folding studies.
  • Previous methods have limitations in conformational searching.

Purpose of the Study:

  • Introduce a novel algorithm, Contact Interactions (CI), for protein conformational search.
  • Improve the efficiency and scope of protein folding simulations.

Main Methods:

  • Developed the CI algorithm, an extension of Monte Carlo, using nonlocal contact interactions.
  • Modeled protein chains as copolymers on square and cubic lattices.
  • Utilized residue-specific cooling factors for conformational acceptance criteria.

Main Results:

Related Experiment Videos

  • The CI algorithm demonstrated high efficiency in 2D and 3D lattice simulations.
  • Successfully localized energy minima missed by existing algorithms.
  • Tested on sequences of varying lengths (20-136 residues).

Conclusions:

  • The CI algorithm is effective for conformational search in protein folding.
  • It enables exploration of thermodynamic and kinetic behaviors of model protein chains.
  • Offers a significant advancement over traditional simulation methods.