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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
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Related Experiment Video

Updated: Jun 8, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

BSDB: the biomolecule stretching database.

Mateusz Sikora1, Joanna I Sulkowska, Bartlomiej S Witkowski

  • 1Institute of Physics, Polish Academy of Sciences, Al Lotników 32/46, 02-668 Warsaw, Poland. sikoram@ifpan.edu.pl

Nucleic Acids Research
|October 9, 2010
PubMed
Summary
This summary is machine-generated.

The Biomolecule Stretching Data Base offers insights into protein mechanostability. It details protein stretching simulations, revealing force peaks, rupture events, and key mechanical clamp motifs.

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A Novel Stretching Platform for Applications in Cell and Tissue Mechanobiology
16:46

A Novel Stretching Platform for Applications in Cell and Tissue Mechanobiology

Published on: June 3, 2014

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Last Updated: Jun 8, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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Published on: July 16, 2017

A Novel Stretching Platform for Applications in Cell and Tissue Mechanobiology
16:46

A Novel Stretching Platform for Applications in Cell and Tissue Mechanobiology

Published on: June 3, 2014

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Understanding protein mechanics is crucial for molecular biology and drug design.
  • Experimental and computational methods are used to study protein stretching.
  • Data on protein mechanostability is fragmented and difficult to access.

Purpose of the Study:

  • To establish a comprehensive database of protein stretching simulations.
  • To provide detailed information on protein mechanostability.
  • To identify common motifs responsible for protein mechanical resistance.

Main Methods:

  • Simulations of stretching 17,134 proteins using a structure-based model.
  • Analysis of force-displacement patterns during protein stretching.
  • Identification and categorization of contact-rupturing events and mechanical clamps.

Main Results:

  • The Biomolecule Stretching Data Base (BSDB) is now available online.
  • Detailed data on maximal force peaks and force-displacement patterns are provided.
  • Characterization of mechanical clamps (motifs) contributing to protein resistance.

Conclusions:

  • The BSDB serves as a valuable resource for researchers studying protein mechanics.
  • The database facilitates comparative analysis of protein mechanostability.
  • Insights into mechanical clamps can inform protein engineering and design.