Prediction of models for ordered solvent in macromolecular structures by a classifier based upon resolution-independent projections of local feature data

Acta Crystallographica. Section D, Structural Biology
Laurel JonesPaul Smith

Abstract

Current software tools for the automated building of models for macromolecular X-ray crystal structures are capable of assembling high-quality models for ordered macromolecule and small-molecule scattering components with minimal or no user supervision. Many of these tools also incorporate robust functionality for modelling the ordered water molecules that are found in nearly all macromolecular crystal structures. However, no current tools focus on differentiating these ubiquitous water molecules from other frequently occurring multi-atom solvent species, such as sulfate, or the automated building of models for such species. PeakProbe has been developed specifically to address the need for such a tool. PeakProbe predicts likely solvent models for a given point (termed a `peak') in a structure based on analysis (`probing') of its local electron density and chemical environment. PeakProbe maps a total of 19 resolution-dependent features associated with electron density and two associated with the local chemical environment to a two-dimensional score space that is independent of resolution. Peaks are classified based on the relative frequencies with which four different classes of solvent (including water) are observed within a gi...Continue Reading

References

Mar 25, 1999·Acta Crystallographica. Section D, Biological Crystallography·F van den Akker, W G Hol
May 20, 1999·Nature Structural Biology·A PerrakisV S Lamzin
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
May 20, 2000·Acta Crystallographica. Section D, Biological Crystallography·T HoltonJ C Sacchettini
Apr 26, 2001·Acta Crystallographica. Section D, Biological Crystallography·T J Oldfield
Nov 22, 2001·Acta Crystallographica. Section D, Biological Crystallography·T C Terwilliger
Apr 19, 2002·Acta Crystallographica. Section A, Foundations of Crystallography·V Y LuninA G Urzhumtsev
Dec 25, 2002·Acta Crystallographica. Section D, Biological Crystallography·Peter MüllerGeorge M Sheldrick
Jul 1, 1963·Journal of Molecular Biology·G N RAMACHANDRANV SASISEKHARAN
Dec 31, 2003·Methods in Enzymology·Richard J MorrisVictor S Lamzin
Dec 2, 2004·Acta Crystallographica. Section D, Biological Crystallography·Paul Emsley, Kevin Cowtan
Jul 21, 2006·Acta Crystallographica. Section D, Biological Crystallography·Thomas C TerwilligerJudith D Cohn
Aug 25, 2006·Acta Crystallographica. Section D, Biological Crystallography·Kevin Cowtan
Feb 1, 2008·Journal of Medicinal Chemistry·Alessio AmadasiGlen E Kellogg
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Paul D AdamsPeter H Zwart
Jan 1, 2009·Journal of Cheminformatics·Tobias Lippert, Matthias Rarey
Jun 1, 2009·Journal of Applied Crystallography·Robbie P JoostenGert Vriend
Apr 5, 2014·Acta Crystallographica. Section D, Biological Crystallography·Nathaniel EcholsPaul D Adams
Mar 6, 2015·Journal of Chemical Information and Modeling·Eva NittingerMatthias Rarey
May 7, 2015·Acta Crystallographica. Section D, Biological Crystallography·Christian X WeichenbergerBernhard Rupp
May 7, 2015·Acta Crystallographica. Section D, Biological Crystallography·Nader MorshedPaul D Adams
Nov 4, 2015·Acta Crystallographica. Section D, Biological Crystallography·Lada Biedermannová, Bohdan Schneider
Mar 10, 2016·Acta Crystallographica. Section D, Structural Biology·Julien JordaTodd O Yeates
Sep 17, 2016·Nature Communications·Scott HorowitzJames C A Bardwell
Oct 6, 2017·Journal of Chemical Information and Modeling·Agnes MeyderMatthias Rarey
Jul 24, 2018·Journal of Chemical Information and Modeling·Eva NittingerMatthias Rarey

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Methods Mentioned

BETA
X-ray
feature extraction
PCA
feature-extraction

Software Mentioned

ProteinPlus
WaterScore
Buccaneer
RESOLVE
EDIA
LIGAND
TEXTAL
wARP
PeakProbe
PHENIX

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