Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

    We have a manual that explains all the features 

Record number 431794
Title Solvated protein-protein docking using Kyte-Doolittle-based water preferences
Author(s) Kastritis, P.L.; Visscher, K.M.; Dijk, A.D.J. van; Bonvin, A.M.J.J.
Source Proteins : Structure, Function, and Bioinformatics 81 (2013)3. - ISSN 0887-3585 - p. 510 - 518.
DOI http://dx.doi.org/10.1002/prot.24210
Department(s) PRI BIOS Applied Bioinformatics
Biometris (WU MAT)
Publication type Refereed Article in a scientific journal
Publication year 2013
Keyword(s) ligand docking - biomolecular complexes - globular-proteins - drug design - molecules - recognition - interfaces - solvent - haddock - challenges
Abstract HADDOCK is one of the few docking programs that can explicitly account for water molecules in the docking process. Its solvated docking protocol starts from hydrated molecules and a fraction of the resulting interfacial waters is subsequently removed in a biased Monte Carlo procedure based on water-mediated contact probabilities. The latter were derived from an analysis of water contact frequencies from high-resolution crystal structures. Here, we introduce a simple water mediated amino acid - amino acid contact probability scale derived from the Kyte-Doolittle hydrophobicity scale and assess its performance on the largest high-resolution dataset developed to date for solvated docking. Both scales yield high-quality docking results. The novel and simple hydrophobicity scale, which should reflect better the physico-chemical principles underlying contact propensities, leads to a performance improvement of around 10% in ranking, cluster quality and water recovery at the interface compared to the statistics-based original solvated docking protocol.
Comments
There are no comments yet. You can post the first one!
Post a comment
 
Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.