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

Reduced surface: an efficient way to compute molecular surfaces

M F Sanner1, A J Olson, J C Spehner

  • 1The Scripps Research Institute, La Jolla, California 92037, USA.

Biopolymers
|March 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

Mesoscope: A Web-based Tool for Mesoscale Data Integration and Curation.

MolVa : Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2020·2023
Same author

Cuttlefish: Color Mapping for Dynamic Multi-Scale Visualizations.

Computer graphics forum : journal of the European Association for Computer Graphics·2019
Same author

Tomato bushy stunt virus at 2.9 A resolution.

Nature·2009
Same author

Analysis of large-scale sequencing of small RNAs.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2008
Same author

Recognition templates for predicting adenylate-binding sites in proteins.

Journal of molecular biology·2001
Same author

Viral evolution in response to the broad-based retroviral protease inhibitor TL-3.

Journal of virology·2001
Same journal

Untreated Rosehip Powder/Poly(Lactic Acid)/Poly(3-Hydroxybutyrate-Co-4-Hydroxybutyrate) Electrospun Mats for Wound Dressing Applications.

Biopolymers·2026
Same journal

Synthesis, Characterization, and Antidiabetic Evaluation of Sequence-Modified Liraglutide Analogs in a Drosophila melanogaster Model.

Biopolymers·2026
Same journal

Fabrication of an Antibacterial Alginate/Chitosan Hydrogel Dressing Loaded With CuO Nanoparticles for Wound Dressing Applications.

Biopolymers·2026
Same journal

Effect of Chitosan-Alginate Polyelectrolyte Complex Formation and Multilayer Polymer Configuration on the Characteristics of 3D-Printed Metronidazole-Loaded Periodontal Films.

Biopolymers·2026
Same journal

Phenolic Grafting of Oxidized Cellulose Nanofibers Using Ferulic Acid: Structural and Antioxidant Analysis Toward Bioactive Nanomaterials.

Biopolymers·2026
Same journal

Detection of a Target Nucleic Acid by Ligation-Assisted Fluorescence Enhancement of a Peptide Nucleic Acid (PNA) Twin Probe via Disulfide Binding.

Biopolymers·2026
See all related articles

MSMS is a new program for computing molecular surfaces, offering a fast and reliable method for generating solvent-accessible and solvent-excluded surfaces. It accurately handles complex molecular structures and self-intersecting surfaces, outperforming existing tools.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Molecular modeling

Background:

  • Molecular modeling relies heavily on accurate computation of molecular surfaces.
  • Existing algorithms often struggle with solvent-excluded surfaces, particularly for large molecules or complex geometries.
  • There is a need for robust and efficient methods to compute analytical molecular surface representations.

Purpose of the Study:

  • To introduce MSMS, a novel program for computing molecular surfaces.
  • To demonstrate the speed and reliability of MSMS in handling solvent-accessible and solvent-excluded surfaces.
  • To address limitations of existing methods in dealing with complex molecular structures and singularities.

Main Methods:

  • Development of MSMS program utilizing a reduced surface approach.

Related Experiment Videos

  • Implementation of four distinct algorithms for surface computation.
  • Analysis of algorithmic complexity, with a focus on handling surface singularities.
  • Comparison with Connolly's PQMS program on a diverse dataset of molecules.

    • Main Results:

    • MSMS successfully computed topologically correct molecular surfaces for all tested molecules.
    • The program exhibits a computational complexity of O[n log(n)] for n atoms.
    • MSMS demonstrates significant speed improvements, accurately computing surfaces for large molecules.

    Conclusions:

    • MSMS provides a fast, reliable, and accurate solution for computing molecular surfaces.
    • The program effectively handles challenging cases, including self-intersecting surfaces and large molecular systems.
    • MSMS represents a significant advancement in molecular surface computation methods.