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Updated: May 21, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
PROPTIMUS LIVE: local constrained α-carbon optimization of proteins
Tomáš Svoboda1,2, Michal Mikuš3, Lukáš Bohuš1
1National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.
PROPTIMUS LIVE enhances protein structure precision by optimizing local atom positions using a fast, physics-based force field. This free web service improves data quality for computational chemistry applications.
Area of Science:
- Structural biology
- Computational chemistry
- Biophysics
Background:
- Accurate protein structures are crucial for computational chemistry.
- Experimental and predictive methods often lack precision in local atomic details.
- This limits the reliability of downstream computational analyses.
Purpose of the Study:
- To develop a web application for optimizing local protein structure quality.
- To enhance the precision of bond lengths, angles, and atom positions.
- To provide a user-friendly tool for improving protein structural data.
Main Methods:
- Developed PROPTIMUS LIVE, a web application for constrained alpha-carbon optimization.
- Utilized the QM-accurate, physics-based GFN-Force-Field for optimization.
- Employed a divide-and-conquer approach for accelerated computation.
- Integrated Mol* Viewer for direct visualization of optimized structures.
Main Results:
- PROPTIMUS LIVE offers precise local optimization of protein structures.
- Optimizations are completed rapidly, typically within minutes.
- The web service is freely accessible, including for commercial use.
- Optimized structures are readily visualized and analyzed.
Conclusions:
- PROPTIMUS LIVE significantly improves the local quality of protein structures.
- The tool enhances the reliability of protein structures for computational applications.
- Free and open access facilitates broader adoption and research advancement.
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