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Related Experiment Video

Updated: Jan 12, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Sampling protein conformations and pathways.

Ming Lei¹, Maria I Zavodszky, Leslie A Kuhn

¹Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA.

Journal of Computational Chemistry

|April 30, 2004

Summary

This summary is machine-generated.

Constraint theory analyzes protein flexibility and rigidity. The ROCK algorithm generates new protein conformations by tracking flexible regions while preserving rigid structures, enabling analysis of protein motion and pathways.

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Last Updated: Jan 12, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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Published on: March 1, 2022

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Published on: July 16, 2017

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

Biophysics
Structural Biology
Computational Biology

Background:

Proteins function through dynamic conformational changes.
Understanding protein flexibility and rigidity is crucial for molecular mechanisms.
Constraint theory provides a framework for analyzing protein structures as networks.

Purpose of the Study:

To introduce the Rigidity Optimized Conformational Kinetics (ROCK) algorithm.
To generate novel protein conformations while preserving structural constraints.
To analyze protein flexibility, rigidity, and conformational pathways.

Main Methods:

Developed the ROCK algorithm to model proteins as 3D constraint networks.
Applied ROCK to generate new conformations for complex protein networks.
Tracked conformational changes in flexible protein regions, leaving rigid regions intact.

Main Results:

Demonstrated large flap motion in HIV protease using ROCK.
Generated conformational pathways between distinct protein states.
Determined directed trajectories between closed and occluded conformations of dihydrofolate reductase.

Conclusions:

ROCK effectively generates new protein conformations and pathways.
The algorithm aids in understanding large-scale protein motions.
ROCK is valuable for analyzing protein dynamics and conformational landscapes.