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Visualizing Ligand Molecules
in Twilight Electron Density
Christian X.
Weichenbergera*,
Edwin
Pozharskib*
and
Bernhard
Ruppc
aCenter
for Biomedicine,
European
Academy of Bozen/Bolzano (EURAC),
Viale Druso 1,
Bozen/Bolzano,
I-39100,
Italy,
bUniversity
of Maryland,
Baltimore,
MD,
USA,
and ck.k.
Hofkristallamt,
991 Audrey
Place,
Vista,
CA,
92084,
USA
Correspondence email:
Christian.Weichenberger@eurac.edu;
epozh001@umaryland.edu
Synopsis
We present a software
script for facilitating analysis and visual inspection of ligand
molecules in context of the electron density maps calculated from
experimental data associated with protein structures determined
by X-ray crystallography.
Abstract
Three-dimensional models of protein structures
determined by X-ray crystallography are based on the
interpretation of experimentally derived electron density maps.
The real-space correlation coefficient (RSCC)
provides an easily comprehensible, objective measure for
residue-based fit of atom coordinates with electron density.
Among protein structure models, protein-ligand complexes are of
special interest, given their contribution to understanding the
molecular underpinnings of biological activity and to drug
design. For consumers of such models it is not trivial to
determine the degree to which ligand structure modelling is
biased by subjective electron density interpretation. We present
a standalone script, Twilight, for analysis, visualization, and annotation of a
pre-filtered set of 2,815 protein/ligand complexes deposited
with the PDB as of January 15, 2012, with ligand
RSCC values that are
below a threshold of 0.6. The script runs on various platforms
and is available for download at
http://www.ruppweb.org/twilight/.
Download this
Acta Crystallographica F paper
and its companion in
Acta Crystallographica D
describing the actual findings from the IUCr web site
(preferred) or
request a link by email. Please read also the editorial
Expectation bias and information content
Z. Dauter,
M. S. Weiss,
H. Einspahr and
E. N. Baker,
Acta Crystallogr. D69, 141 (2013).
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Citation |
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Techniques, tools and best practices for
ligand electron-density analysis and results from their application
to deposited crystal structures.
E. Pozharski,
C. X. Weichenberger and
B. Rupp,
Acta Crystallogr D69, 150-167 (2013)
Visualizing Ligand
Molecules in Twilight Electron Density.
C. X. Weichenberger,
E. Pozharski and
B. Rupp,
Acta Crystallogr. F69(2), 195-200(2013) |
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Download
program |
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The program distribution comes in a zip archive file which can be
downloaded here.
Here is the readme file for installing
Twilight |
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 Update
and
current data files |
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The distribution comes packaged with the original published datafile
current to the January 15 2012 PDB release (ligands-2012-01-15.tsv). In
the meantime, analysis of the PDB release January 16 2013, has
delivered about 500 more entries that match the twilight selection
criteria. You can update either
(a) the complete data file current up to January 16, 2013 (ligands-2013-01-16.tsv)
(b) or if you have annotated and wish to keep the
old file, concatenate your old file with the file containing
only new entries
newligands-2012.tsv, which holds the entries that have
changed during the last update (be
sure to remove the header line of the appended file, though). The
new entries are to a great extent those released in 2012, but the file also
contains a good number of older
PDB entries that became accessible through EDS during last year.
Therefore, this 'update' for the year 2012 also presents entries
from before 2012. When you
add the update file to the ligand table 'ligands-2012-01-15.tsv'
which we have included in our
TWILIGHT distribution package, you will end up with a complete
updated file equivalent to
'ligands-2013-01-16.tsv':
ligands-2013-01-16.tsv = ligands-2012-01-15.tsv +
newligands-2012.tsv
Here is the readme file for installing
Twilight |
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My
texbook |
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A useful resource if you want to learn more about
protein crystallography, ligand structures, and structure validation |
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For now |
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You can still use the web tutorial for free! |
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