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Screening a peptidyl database for potential ligands to proteins with side-chain flexibility

Academic Article
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Overview

authors

  • Schnecke, V.
  • Swanson, C. A.
  • Getzoff, Elizabeth
  • Tainer, John
  • Kuhn, L. A.

publication date

  • October 1998

journal

  • Proteins-Structure Function and Genetics  Journal

abstract

  • The three key challenges addressed in our development of SPECITOPE, a tool for screening large structural databases for potential ligands to a protein, are to eliminate infeasible candidates early in the search, incorporate ligand and protein side-chain flexibility upon docking, and provide an appropriate rank for potential new ligands. The protein ligand-binding site is modeled by a shell of surface atoms and by hydrogen-bonding template points for the ligand to match, conferring specificity to the interaction. SPECITOPE combinatorially matches all hydrogen-bond donors and acceptors of the screened molecules to the template points. By eliminating molecules that cannot match distance or hydrogen-bond constraints, the transformation of potential docking candidates into the ligand-binding site and the shape and hydrophobic complementarity evaluations are only required for a small subset of the database. SPECITOPE screens 140,000 peptide fragments in about an hour and has identified and docked known inhibitors and potential new ligands to the free structures of four distinct targets: a serine protease, a DNA repair enzyme, an aspartic proteinase, and a glycosyltransferase. For all four, protein side-chain rotations were critical for successful docking, emphasizing the importance of inducible complementarity for accurately modeling ligand interactions. SPECITOPE has a range of potential applications for understanding and engineering protein recognition, from inhibitor and linker design to protein docking and macromolecular assembly.

subject areas

  • Aspartic Acid Endopeptidases
  • Binding Sites
  • DNA Glycosylases
  • Databases, Factual
  • Glucosyltransferases
  • Ligands
  • N-Glycosyl Hydrolases
  • Peptides
  • Subtilisins
  • Uracil-DNA Glycosidase
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Research

keywords

  • DNA repair enzyme
  • aspartic proteinase
  • distance geometry
  • docking
  • drug design
  • glycosyltransferase
  • inducible complementarity
  • peptidyl inhibitors
  • protein-peptide interactions
  • serine protease
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Identity

International Standard Serial Number (ISSN)

  • 0887-3585

Digital Object Identifier (DOI)

  • 10.1002/(sici)1097-0134(19981001)33:1<74::aid-prot7>3.0.co;2-l

PubMed ID

  • 9741846
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Additional Document Info

start page

  • 74

end page

  • 87

volume

  • 33

issue

  • 1

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