Docking Predictions of Protein-Protein Interactions and Their Assessment: The CAPRI Experiment - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 90

Table 5.1 Web servers for protein-protein docking
Protein structure and benchmark sets
Protein Data Bank (PDB) http://www.rcsb.org/pdb/

CAPRI experiment http://capri.ebi.ac.uk/

Docking benchmark http://zlab.bu.edu/zdock/benchmark.shtml

Structure/af fi nity benchmark http://bmm.cancerresearchuk.

org/~bmmadmin/Af fi nity

FFT correlation and related docking algorithms
ClusPro http://cluspro.bu.edu/login.php
DOT http://www.sdsc.edu/CCMS/Papers/DOT_
sc95.html
FTDOCK http://www.sbg.bio.ic.ac.uk/docking/
ftdock.html
GRAMM-X http://vakser.bioinformatics.ku.edu/
resources/gramm/grammx/
HEX http://www.loria.fr/~ritchied/hex/
MolFit http://www.weizmann.ac.il/Chemical_
Research_Support//mol fi t/
ZDOCK http://zlab.bu.edu/zdock/
Molecular dynamics, Monte-Carlo and related flexible docking algorithms
ATTRACT http://www.ibpc.fr/chantal/www/ptools/
HADDOCK http://www.nmr.chem.uu.nl/haddock/
ICM-DISCO http://www.molsoft.com/icm_pro.html
RosettaDock http://graylab.jhu.edu/docking/rosetta/
Geometric hashing and related flexible docking algorithms
PatchDock

http://bioinfo3d.cs.tau.ac.il/PatchDock

FireDock http://bioinfo3d.cs.tau.ac.il/FireDock/

SymmDock http://bioinfo3d.cs.tau.ac.il/SymmDock

FiberDock http://bioinfo3d.cs.tau.ac.il/FiberDock/

MultiFit http://salilab.org/multi fi t/ and http://

bioinfo3d.cs.tau.ac.il/

3D-Garden http://www.sbg.bio.ic.ac.uk/3dgarden

SKE-Dock http://www.pharm.kitasato-u.ac.jp/

bmd/ fi les/SKE_DOCK.html

5.3.4 Template-Based Docking

An alternative to docking is to use a template, and build a model of a protein-protein
complex by analogy to one of known structure. When both components of two com-
plexes are close homologs with a high level of sequence identity (40% or more),
it is straightforward to model build both the components and their assembly, but the
method has a very limited field of application. It can be extended by accepting tem-
plates with a low level of sequence identity, or templates that have similar three-
dimensional structures irrespective of their sequences, under the assumption that the
mode of interaction is conserved (Lu et al. 2002 ; Sinha et al. 2010 ; Kundrotas et al.
2012 ). Although the limits of validity of this assumption are uncertain, genome-wide