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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview

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Updated: May 21, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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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.

Nucleic Acids Research
|May 20, 2026
PubMed
Summary

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.

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Engineering 'Golden' Fluorescence by Selective Pressure Incorporation of Non-canonical Amino Acids and Protein Analysis by Mass Spectrometry and Fluorescence
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Engineering 'Golden' Fluorescence by Selective Pressure Incorporation of Non-canonical Amino Acids and Protein Analysis by Mass Spectrometry and Fluorescence
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Engineering 'Golden' Fluorescence by Selective Pressure Incorporation of Non-canonical Amino Acids and Protein Analysis by Mass Spectrometry and Fluorescence

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Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

Published on: August 1, 2016

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.