Chemistry Reference
In-Depth Information
The objective of SAMPL is to test protein and small molecule modeling. It is a
'blind' assessment (methods applied to data not seen by participants). Ideally,
blind tests helps avoid the tendency to bias our theories and approaches to known
answers. It is conceived as an opportunity for groups to test their methods, learn
from the experience and share lessons learned. The objective of SAMPL4 is to
build a series of successful blind challenges for computational chemistry
(hydration free energy, host-guest, binding free prediction components)
http://ccl.net/chemistry/resources/messages/2013/01/28.007-dir/index.html.
Critical assessment of predicted interactions (CAPRI) (http://capr
i.e.
bi.ac.uk) is a
forum (conducted every other year since 2001) for evaluating methods for
computational (protein complex interaction prediction) and protein-protein
docking. Groups are invited yearly to test their computational methods and predict
the structures of protein complexes (experimentally solved and made public that
year).
Some of the protein-protein docking computational methods that have competed
in Capri include the following.
AutoDock (autodock.scripps.edu)
DOT (http://sdsc.edu/CCMS/DOT/
3dDockSuite(http://sbg.bio.ic.ac.ud/docking/)
Fiber Dock (http://bioinfo3d.cs.tau.ac.il/FiberDock).
BiGGER (http://centriafct.unl.pt-ludi/bigger.html).
KFC Server (http://kfc.itchell-ab.org/).
SymmDock(http://bioinfo.ed.cs.tau.ac.il/SymmDock/)
PI2PE(
http://pipe.scs.fsu.edu/meta-ppisp.html)
DOCK/PIE
;DOCK(http//:clsb.ices.utexas.edu/dock-by-pic/
