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Updated: Jul 10, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Geometry-based sampling of conformational transitions in proteins.
Daniel Seeliger1, Jürgen Haas, Bert L de Groot
1Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
We introduce tCONCOORD, a computational method for predicting protein flexibility and conformational changes. This tool efficiently samples protein movements, aiding in understanding biological processes like enzyme activity and ligand binding.
Area of Science:
- Protein science
- Computational biology
- Structural biology
Background:
- Protein flexibility and conformational changes are crucial for biological functions.
- Predicting these dynamics computationally is a significant challenge.
Purpose of the Study:
- To develop a computationally efficient method for sampling protein conformational transitions.
- To identify essential biological degrees of freedom in proteins.
Main Methods:
- Reimplementation of the CONCOORD approach as tCONCOORD.
- Utilizing geometrical considerations for efficient conformational sampling.
- Estimating the stability of interactions within protein structures.
Main Results:
- tCONCOORD accurately predicts experimentally known conformational transitions.
- The method successfully identified essential degrees of freedom.
- Applications demonstrated on multiple proteins including adenylate kinase and ubiquitin.
Conclusions:
- tCONCOORD offers an efficient and reliable approach for studying protein flexibility.
- The method aids in understanding dynamic processes vital to protein function.
- This tool advances the prediction of protein conformational changes.
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