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

A kinematic view of loop closure.

Evangelos A Coutsias1, Chaok Seok, Matthew P Jacobson

  • 1Department of Mathematics and Statistics, University of New Mexico, Albuquerque, New Mexico 87131, USA.

Journal of Computational Chemistry
|January 22, 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

MotifLeadDB: A Hierarchical Structural Data Set for Congeneric Ligand Binding Activity Change.

Journal of chemical information and modeling·2026
Same author

Structural basis of the sweat odorant HMHA recognition by the human odorant receptor OR52E8.

Communications biology·2026
Same author

Nonequilibrium Theory for Molecular Machine Design.

ArXiv·2026
Same author

Seeking Biology's Physics Stories: Simplify, Simplify.

Annual review of biophysics·2026
Same author

GalaxyCDock: Webserver for Covalent Protein-Ligand Binding Mode Prediction.

Journal of molecular biology·2026
Same author

A principled basis for nonequilibrium network flows.

Nature communications·2026
Same journal

Electric-Field Effects on Structure and Conductance in a Cytochrome b<sub>562</sub> Junction.

Journal of computational chemistry·2026
Same journal

Quantum Chemistry Study of Luminescence Quenching in the Eu<sup>3+</sup>@UiO-67 Sensor Induced by Ag<sup>+</sup> Ions.

Journal of computational chemistry·2026
Same journal

Projection-Modified Direct Inversion in the Iterative Subspace: A Memory-Efficient Convergence Method for the Extended Molecular Ornstein-Zernike Theory.

Journal of computational chemistry·2026
Same journal

PES2MP: A Python Application for Automating Collisional Dynamics of Linear Rigid-Rotors.

Journal of computational chemistry·2026
Same journal

The Anionic States of Ubiquinone Characterized by Second-Order Approximate Coupled-Cluster Theory.

Journal of computational chemistry·2026
Same journal

Hydrogen Bond Energy Estimation in Large Molecular Clusters via the Method of Synergistic Cyclic Cooperativity: A Software Update H-BEE 2.0.

Journal of computational chemistry·2026
See all related articles

This study presents a new analytical method for protein loop closure, reducing complex conformational problems to solving a polynomial equation. This approach efficiently models protein structures and enhances molecular modeling techniques.

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Protein structure determination is crucial for understanding function.
  • Predicting protein loop conformations remains a significant challenge in structural biology.
  • Existing methods often struggle with flexibility and non-consecutive torsions.

Purpose of the Study:

  • To develop an efficient analytical method for protein loop closure.
  • To generalize existing loop closure techniques to handle non-consecutive torsions and flexible bond angles.
  • To provide a computational tool for modeling protein loop structures.

Main Methods:

  • Reduced the loop closure problem to finding real roots of a 16th-degree polynomial.
  • Utilized robotics kinematics for analyzing rotator linkages.

Related Experiment Videos

  • Developed an intuitive derivation for a specific case of torsional axes.
  • Incorporated flexibility in bond and peptide torsion angles.

    • Main Results:

    • The method successfully models cyclic pentapeptides.
    • Analytical loop closure algorithm efficiently samples loops longer than three residues when combined with existing algorithms.
    • Monte Carlo minimization of an eight-residue loop was severalfold more efficient using this algorithm's local moves.

    Conclusions:

    • The developed analytical loop closure method is a powerful tool for protein structure prediction.
    • It offers significant improvements in efficiency and scope compared to previous methods.
    • The algorithm is publicly available for broader scientific application.