Rigid substructure search

David Shirvanyants, Anastassia N. Alexandrova, Nikolay V. Dokholyan

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Motivation: Identifying the location of binding sites on proteins is of fundamental importance for a wide range of applications, including molecular docking, de novo drug design, structure identification and comparison of functional sites. Here we present Erebus, a web server that searches the entire Protein Data Bank for a given substructure defined by a set of atoms of interest, such as the binding scaffolds for small molecules. The identified substructure contains atoms having the same names, belonging to same amino acids and separated by the same distances (within a given tolerance) as the atoms of the query structure. The accuracy of a match is measured by the root-mean-square deviation or by the normal weight with a given variance. Tests show that our approach can reliably locate rigid binding scaffolds of drugs and metal ions.

Original languageEnglish (US)
Article numberbtr129
Pages (from-to)1327-1329
Number of pages3
JournalBioinformatics
Volume27
Issue number9
DOIs
StatePublished - May 1 2011

Fingerprint

Substructure
Scaffold
Scaffolds
Atoms
Drug Design
Root mean square deviation
Molecular Docking
Structure Identification
Names
Proteins
Protein
Metals
Binding Sites
Web Server
Databases
Binding sites
Ions
Amino Acids
Weights and Measures
Pharmaceutical Preparations

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Shirvanyants, D., Alexandrova, A. N., & Dokholyan, N. V. (2011). Rigid substructure search. Bioinformatics, 27(9), 1327-1329. [btr129]. https://doi.org/10.1093/bioinformatics/btr129
Shirvanyants, David ; Alexandrova, Anastassia N. ; Dokholyan, Nikolay V. / Rigid substructure search. In: Bioinformatics. 2011 ; Vol. 27, No. 9. pp. 1327-1329.
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Shirvanyants, D, Alexandrova, AN & Dokholyan, NV 2011, 'Rigid substructure search', Bioinformatics, vol. 27, no. 9, btr129, pp. 1327-1329. https://doi.org/10.1093/bioinformatics/btr129

Rigid substructure search. / Shirvanyants, David; Alexandrova, Anastassia N.; Dokholyan, Nikolay V.

In: Bioinformatics, Vol. 27, No. 9, btr129, 01.05.2011, p. 1327-1329.

Research output: Contribution to journalArticle

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Shirvanyants D, Alexandrova AN, Dokholyan NV. Rigid substructure search. Bioinformatics. 2011 May 1;27(9):1327-1329. btr129. https://doi.org/10.1093/bioinformatics/btr129