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 Video

Updated: Jul 12, 2026

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

zsasa: a Zig-based engine for high-throughput solvent accessible surface area at proteome scale.

Tsubasa Nagae, Kentaro Tomii

    Biorxiv : the Preprint Server for Biology
    |July 10, 2026
    PubMed
    Summary

    We developed zsasa, a fast and memory-efficient tool for calculating solvent accessible surface area (SASA) in structural biology. It offers reproducible, high-throughput analysis for large datasets and complex structures.

    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

    Oligomer-based functions of mitochondrial porin.

    Nature communications·2025
    Same author

    Application of Anomaly Detection to Identify Important Features of Protein Dynamics.

    ACS omega·2025
    Same author

    Neuronal and non-neuronal functions of the synaptic cell adhesion molecule neurexin in Nematostella vectensis.

    Nature communications·2024
    Same author

    PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins.

    Journal of chemical information and modeling·2023
    Same author

    Predicting global distributions of eukaryotic plankton communities from satellite data.

    ISME communications·2023
    Same author

    Author Correction: A multipoint guidance mechanism for β-barrel folding on the SAM complex.

    Nature structural & molecular biology·2023

    Area of Science:

    • Structural biology
    • Computational chemistry
    • Biophysics

    Background:

    • Solvent accessible surface area (SASA) is crucial for understanding protein stability, ligand interactions, and molecular recognition.
    • Existing SASA calculation tools face challenges with throughput, memory usage, and handling large, complex structural datasets, hindering large-scale analyses.

    Purpose of the Study:

    • To develop and present zsasa, a new, high-performance engine for calculating SASA.
    • To provide a tool that is reproducible, memory-efficient, and suitable for large-scale structural biology workloads.

    Main Methods:

    • Implementation of Shrake-Rupley and Lee-Richards algorithms in a Zig-based engine.
    • Support for exact double/single precision modes, an optional bitmask approximation, batch processing, trajectory analysis, and compressed structure inputs.

    More Related Videos

    Modeling Amyloid-β42 Toxicity and Neurodegeneration in Adult Zebrafish Brain
    10:01

    Modeling Amyloid-β42 Toxicity and Neurodegeneration in Adult Zebrafish Brain

    Published on: October 25, 2017

    A Femtoliter Droplet Array for Massively Parallel Protein Synthesis from Single DNA Molecules
    10:45

    A Femtoliter Droplet Array for Massively Parallel Protein Synthesis from Single DNA Molecules

    Published on: June 20, 2020

    Related Experiment Videos

    Last Updated: Jul 12, 2026

    Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
    09:42

    Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

    Published on: January 16, 2016

    Modeling Amyloid-β42 Toxicity and Neurodegeneration in Adult Zebrafish Brain
    10:01

    Modeling Amyloid-β42 Toxicity and Neurodegeneration in Adult Zebrafish Brain

    Published on: October 25, 2017

    A Femtoliter Droplet Array for Massively Parallel Protein Synthesis from Single DNA Molecules
    10:45

    A Femtoliter Droplet Array for Massively Parallel Protein Synthesis from Single DNA Molecules

    Published on: June 20, 2020

  • Configurable atom classification, including Chemical Component Dictionary (CCD)-based radii for non-standard components.

    • Main Results:

    • zsasa demonstrated near-numerical identity with FreeSASA for Shrake-Rupley calculations on AlphaFold structures.
    • Achieved significant speedups (2.94x in exact mode, up to 9.70x in bitmask mode) compared to FreeSASA batch processing.
    • Exhibited substantial memory reduction (12.5%-25% of comparator peak memory) and high-speed trajectory analysis (>1000 frames/s).

    Conclusions:

    • zsasa is a practical and efficient tool for reproducible, large-scale SASA calculations.
    • Its performance characteristics make it suitable for analyzing predicted structures, molecular dynamics trajectories, and large protein assemblies.
    • zsasa facilitates the generation of surface-derived structural features essential for various biological investigations.