Web Tools for the Post-docking Processing
As discussed previously (Sect. 8.2.2), a scoring/filtering step is normally included in a docking procedure. However, to date no program can provide a single docking solution with a high enough confidence to be correct. Docking programs instead generally provide the user with an ensemble of models, corresponding to a subset (usually refined) of the solutions they generated in the conformational sampling step, which possibly contain native-like models. These models have thus to be analyzed to attempt to single out the correct ones. Some tools have been specifically devoted to the post-docking processing, i.e. the analysis, scoring and ranking of
Table 8.2 List of available web servers for the post-docking processing
|
Server name |
Algorithm |
Analyses |
URL |
|
CCharPPI (Moal et al. 2015) |
Energy/knowledge-based |
109 parameters including FireDock, PyDock, RosettaDock, SIPPER & ZRANK scores |
http://life.bsc. es/pid/ ccharppi/ |
|
CONSRANK (Chermak et al. 2014) |
Consensus-based |
Contacts analysis and visualization; re-scoring |
https://www. molnac.unisa. it/BioTools/ consrank/ |
|
DOCKRANK (Xue et al. 2014) |
Evolution-based |
Prediction of the interface; re-scoring |
http://einstein. cs.iastate.edu/ DockRank/ |
|
FastContact (Champ and Camacho 2007) |
Energy/knowledge-based |
Energy minimization; prediction of residue contact free energies; re-scoring |
http://structure. pitt.edu/ servers/ fastcontact/ |
|
FiberDock (Mashiach et al. 2010a, 2008) |
Energy/knowledge-based |
Flexible refinement; re-scoring |
http:// bioinfo3d.cs. tau.ac.il/ FiberDock/ http:// bioinfo3d.cs. tau.ac.il/ FireDock/ |
|
FILTREST3D (Gajda et al. 2010) |
User-defined restraints from experimental data |
Re-scoring |
http:// filtrest3d. genesilico.pl/ filtrest3d/ |
|
FunHunt (London and Schueler-Furman 2008) |
Energy-based |
Characterization of local energy landscape |
http://funhunt. furmanlab.cs. huji.ac.il/ |
|
PROCOS (Fink etal. 2011) |
Energy/knowledge-based |
Re-scoring |
http:// compdiag.uni- regensburg.de/ procos/ |
models representing the output of docking programs. Several of these post-processing tools are publicly available as web servers and are listed in Table 8.2, together with the corresponding URLs. The scoring approaches they mainly rely on, reflecting the ones described above (Sect. 8.2.2), are also reported in Table 8.2.
