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

Efficient molecular surface generation using level-set methods.

Tolga Can1, Chao-I Chen, Yuan-Fang Wang

  • 1Department of Computer Engineering, Middle East Technical University, 06531 Ankara, Turkey. tcan@ceng.metu.edu.tr

Journal of Molecular Graphics & Modelling
|April 20, 2006
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

Comparative transcriptome profiling reveals molecular mechanisms of freezing stress responses in cultivated and wild Cicer species.

Scientific reports·2025
Same author

Phosphorylation of SNAP-25 at Ser187 is enhanced following its cleavage by Botulinum Neurotoxin Serotype A, promoting the dominant-negative effect of the resulting fragment.

PLoS pathogens·2025
Same author

E2-regulated transcriptome complexity revealed by long-read direct RNA sequencing: from isoform discovery to truncated proteins.

RNA biology·2025
Same author

Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets.

BMC bioinformatics·2025
Same author

Sleep deprivation modulates pain sensitivity through alterations in lncRNA and mRNA expression in the nucleus accumbens and ventral midbrain.

Neuropharmacology·2025
Same author

Probabilistic memory auto-encoding network for abnormal behavior detection in surveillance video.

Neural networks : the official journal of the International Neural Network Society·2025
Same journal

Covalent character of Cellobiose-Water hydrogen bonds revealed by ELF and QTAIM for enhanced dewatering and reactivity.

Journal of molecular graphics & modelling·2026
Same journal

Residue-level insights into SGLT2 inhibition and Nav1.5 selectivity of gliflozin derivatives: A molecular dynamics and pharmacophore-guided study.

Journal of molecular graphics & modelling·2026
Same journal

A benchmarking-informed structure-based virtual screening strategy targeting Lm-PTR1: Leveraging the Northern African natural products database.

Journal of molecular graphics & modelling·2026
Same journal

In Silico identification of natural and synthetic inhibitors targeting KRAS mutants (G12D, G12V, and G12C) and wild-type in pancreatic cancer.

Journal of molecular graphics & modelling·2026
Same journal

Structural evolution, mechanical and thermal stability of 7-40 mol% yttria-stabilized zirconia: First-principles investigation.

Journal of molecular graphics & modelling·2026
Same journal

Halide-encapsulated C<sub>24</sub> fullerenes as molecular redox hosts for alkali metals: A density functional theory study.

Journal of molecular graphics & modelling·2026
See all related articles

This study introduces a fast, level-set-based method for computing molecular surfaces. The new approach efficiently calculates surfaces and cavities for large protein complexes, outperforming existing tools.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Molecular modeling

Background:

  • Molecular surface calculation is crucial for understanding protein function.
  • Existing methods struggle with speed and efficiency for large molecular complexes.
  • There is a need for faster, more accurate molecular surface computation tools.

Purpose of the Study:

  • To present a novel level-set-based approach for computing and visualizing molecular surfaces.
  • To offer a uniform framework for calculating solvent-accessible, solvent-excluded surfaces, and interior cavities.
  • To demonstrate the efficiency and accuracy of the method for large molecular complexes.

Main Methods:

  • Utilized a level-set-based algorithm for molecular surface computation.

Related Experiment Videos

  • Implemented a method capable of handling large molecular complexes with tens of thousands of atoms.
  • Compared the performance against widely used molecular visualization tools: Swiss-PDBViewer, PyMol, and Chimera.

    • Main Results:

    • The level-set method computes molecular surfaces efficiently, even for very large complexes.
    • The new approach is 1.5-3.14 times faster on average than Swiss-PDBViewer, PyMol, and Chimera.
    • The method successfully identifies interior inaccessible cavities suitable for water molecules.

    Conclusions:

    • The developed level-set method provides a significant speed improvement for molecular surface calculations.
    • This technique offers a robust and efficient solution for analyzing molecular surfaces and cavities in large complexes.
    • The method enhances functional analysis by accurately computing detailed molecular surface properties.