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Related Experiment Video

Updated: Jul 18, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage.

José Ignacio Garzón1, Julio Kovacs, Ruben Abagyan

  • 1Centro de Investigaciones Biológicas, CSIC Ramiro de Maeztu 9, 28040 Madrid, Spain.

Bioinformatics (Oxford, England)
|December 8, 2006
PubMed
Summary

A new algorithm efficiently fits atomic models into low-resolution density maps. This method uses spherical harmonics and translational scanning for fast and accurate atomic structure docking, enabling high-throughput analysis.

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Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Advancements in atomic modeling and low-resolution density map generation necessitate efficient fitting tools.
  • Current methods struggle with the rapid integration of diverse structural data.

Purpose of the Study:

  • To develop a novel algorithm for fast and exhaustive fitting of atomic models into low-resolution density maps.
  • To improve the accuracy and efficiency of atomic structure docking.

Main Methods:

  • A novel fitting algorithm combining spherical harmonics (SH) for fast rotational search and translational scanning.
  • Exhaustive overlay of partial high-resolution models into low-resolution density maps.

Main Results:

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Last Updated: Jul 18, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Whole-cell Super-Resolution Imaging via DNA-PAINT on a Spinning Disk Confocal with Optical Photon Reassignment
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Whole-cell Super-Resolution Imaging via DNA-PAINT on a Spinning Disk Confocal with Optical Photon Reassignment

Published on: January 6, 2026

  • Accurate docking of atomic structures into low-resolution electron-density maps achieved in seconds to minutes.
  • High-efficiency, robustness, and high-throughput coverage demonstrated on simulated and experimental data.
  • Preservation of exhaustiveness crucial for heterogeneous-resolution merging.

    • Conclusions:

    • The developed algorithm offers an efficient and accurate solution for fitting atomic models into low-resolution density maps.
    • This method supports the integration of diverse structural data for molecular assembly analysis.
    • The tool facilitates high-throughput structural biology research.