Three-Dimensional Searching for Recurrent Structural Motifs in Data Bases of Protein Structures

Mauro Rustici, Arthur Lesk

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

The problem of searching a data base of coordinates of proteins for substructures similar to a probe structure or motif is an important problem in computational molecular biology. It is the three-dimensional analog of the one-dimensional case of pattern matching in strings, procedures for which are widely used in molecular biology to search data bases of gene sequences. Typical applications of substructure searching are: (i) Determining whether structural features observed in one protein structure are unique or recurrent, and (ii) in predictions of protein structures, to bridge gaps in an incomplete structural model, by searching the data base for peptides that link the given starting and ending points. We describe our analysis of the problem and our experience in developing software.

Original languageEnglish (US)
Pages (from-to)121-132
Number of pages12
JournalJournal of Computational Biology
Volume1
Issue number2
DOIs
StatePublished - Jan 1 1994

Fingerprint

Protein Structure
Molecular biology
Databases
Substructure
Proteins
Three-dimensional
Computational Molecular Biology
Pattern matching
Molecular Biology
Structural Models
Structural Model
Pattern Matching
Computational Biology
Peptides
Probe
Software
Genes
Strings
Gene
Analogue

All Science Journal Classification (ASJC) codes

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

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abstract = "The problem of searching a data base of coordinates of proteins for substructures similar to a probe structure or motif is an important problem in computational molecular biology. It is the three-dimensional analog of the one-dimensional case of pattern matching in strings, procedures for which are widely used in molecular biology to search data bases of gene sequences. Typical applications of substructure searching are: (i) Determining whether structural features observed in one protein structure are unique or recurrent, and (ii) in predictions of protein structures, to bridge gaps in an incomplete structural model, by searching the data base for peptides that link the given starting and ending points. We describe our analysis of the problem and our experience in developing software.",
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Three-Dimensional Searching for Recurrent Structural Motifs in Data Bases of Protein Structures. / Rustici, Mauro; Lesk, Arthur.

In: Journal of Computational Biology, Vol. 1, No. 2, 01.01.1994, p. 121-132.

Research output: Contribution to journalArticle

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