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Indeterminate structures refer to structures where internal forces and reactions cannot be determined using only the equations of static equilibrium.  Indeterminate structures have more unknown forces and reaction forces than equations of static equilibrium that can be used to determine them. Indeterminate structures are often used in engineering to create complex, efficient, and aesthetically pleasing structures. There are various types of indeterminate structures used in engineering and some...
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Related Experiment Video

Updated: Jun 3, 2026

Hierarchical and Programmable One-Pot Oligosaccharide Synthesis
09:56

Hierarchical and Programmable One-Pot Oligosaccharide Synthesis

Published on: September 6, 2019

Rigid substructure search.

David Shirvanyants1, Anastassia N Alexandrova, Nikolay V Dokholyan

  • 1Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599-7260, USA.

Bioinformatics (Oxford, England)
|April 5, 2011
PubMed
Summary
This summary is machine-generated.

Erebus is a new web server that accurately finds protein binding sites by searching the Protein Data Bank for specific molecular substructures. This tool aids in drug design and protein structure analysis.

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Last Updated: Jun 3, 2026

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Chemistry

Background:

  • Protein binding site identification is crucial for drug design and structural analysis.
  • Existing methods require precise structural information for accurate site identification.

Purpose of the Study:

  • To introduce Erebus, a novel web server for identifying protein binding sites.
  • To enable the search for specific substructures within the Protein Data Bank (PDB).

Main Methods:

  • Erebus searches the PDB for user-defined substructures based on atom identity, amino acid context, and inter-atomic distances.
  • Match accuracy is assessed using root-mean-square deviation (RMSD) and normal weight calculations.

Main Results:

  • The Erebus server reliably locates rigid binding scaffolds for small molecules, drugs, and metal ions.
  • The server utilizes a robust algorithm for substructure matching within the PDB.

Conclusions:

  • Erebus provides an accurate and efficient method for identifying protein binding sites.
  • This tool facilitates applications in molecular docking, drug design, and functional site comparison.