Technology transfer
Pydock-figure 1 protein association [8] (10.1002/prot.20285);
been specially highlighted in the most recent
References (DOI)
2) pydockNIP, for the prediction of hot-spot
editions of CAPRI, where in addition to the
1. 10.1002/prot.21419
residues in a specific protein-protein complex
standard prediction of protein-protein complex
2. 10.1016/s0092-8674(00)80922-8
based on the identification of the higher
assemblies, additional challenges have been
3. 10.1038/nmeth.2289, 10.1038/nmeth.1280
interface propensity residues within a docking
proposed, including binding affinity predictions,
simulation
(10.1186/1471-2105-9-
free-energy changes upon mutation, as well as
447); and finally, 3) pyDockEneRes for the
the prediction of sugar binding and interface
7. 10.1016/j.jmb.2006.01.001
prediction of the most energetically relevant
water molecules, multimeric complexes and
8. 10.1002/prot.20285
residues within a complex by the estimation
protein-peptide complexes. Indeed, pyDock
9. 10.1186/1471-2105-9-447
of the corresponding binding affinity changes
occupied fifth position in the overall ranking
10. 10.1093/bioinformatics/btz884
upon mutation to alanine [10](10.1093/
in the Fifth Edition [12] (10.1002/prot.24387),
11. 10.1093/bioinformatics/btt262
bioinformatics/btz884).
and sixth position in the Sixth Edition [13]
[9]
How has pyDock evolved and been evaluated?
(10.1002/prot.25184). Furthermore, in CAPRI Round 46, a special CASP-CAPRI protein
4. 10.1006/jmbi.1997.1203 5. 10.1186/1471-2105-9-441 6. 10.1093/nar/gkv368
12. 10.1002/prot.24387 13. 10.1002/prot.25184 14. 10.1002/prot.25838 15. 10.1016/j.molonc.2014.04.002
assembly prediction challenge [14](10.1002/
16. 10.1016/j.bbabio.2015.09.006
Thanks to the work of Jimenez and co-workers
prot.25838), pyDock hit the top position as
17. 10.1371/journal.ppat.1003382
[11](10.1093/bioinformatics/btt262), a new
scorers and second position as predictors.
version of the pyDock scoring algorithm has
As further confirmation of its prowess, in
been recently published, consisting of a new
the last few years pyDock has also been
custom parallel FTDock implementation, with
successfully applied in several projects. These
adjusted grid size for optimal FFT calculations,
include initiatives relating to the effect of
and a new parallel version of pyDock code,
mutations upon p53 tetramerization process
which dramatically speeds up its docking
[15]
simulations by a factor of up to 40 and paves
structural prediction of Photosystem I in
the way for the application of pyDock within
complex to different electron carrier proteins
HTC (High-throughput computing) and HPC
[16]
(high performance computing) frameworks.
the structural characterization of the human Rab1
(10.1016/j.molonc.2014.04.002),
(10.1016/j.bbabio.2015.09.006) De-AMPylation
Since its first publication, pyDock has
pneumophila
SidD
been periodically tested in CAPRI (Critical
journal.ppat.1003382).
by protein
the
the
and
Legionella
[17](10.1371/
Assessment of PRediction of Interactions), a worldwide community contest aimed at
Read about NBD’s latest product launch in the
assessing the performance of protein-protein
News section.
docking methods in blind conditions, generally achieving excellent results. Along these lines,
CAPRI:
ebi.ac.uk/msd-srv/capri
the all-round applicability of pyDock has
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