| Affinity |
N/A |
www.accelrys.com/products/datasheets/i2_affinity_data.pdf |
MC |
| ADAM |
(Yamada and Itai, 1993; Mizutani et al., 1994, 2006) |
www.immd.co.jp/en/product_2.html |
RBD |
| Autodock 4.0 |
(Morris et al., 1998; Osterberg et al., 2002) |
autodock.scripps.edu/ |
GA |
| CDOCKER |
(Wu et al., 2003a) |
N/A |
MD-SA |
| CHARMM |
(Vieth et al., 1998b, 1998a) |
www.charmm.org/ |
GA and MC |
| CLIX |
(Lawrence and Davis, 1992) |
N/A |
RBD |
| DARWIN |
(Taylor and Burnett, 2000) |
N/A |
GA |
| DIVALI |
(Clark and Ajay, 1995) , |
N/A |
GA |
| DOCK 6 |
(Oshiro et al., 1995; Knegtel et al., 1997; Kang et al., 2004; Moustakas et al., 2006) |
dock.compbio.ucsf.edu/ |
IC |
| DockIt |
N/A |
www.metaphorics.com/products/dockit.html |
N/A |
| DockVision 1.0.3 |
(Hart and Read, 1992) , |
www.dockvision.com |
MC |
| DoMCoSAR |
(Vieth and Cummins, 2000) |
N/A |
SA |
| DragHOME |
(Schafferhans and Klebe, 2001) |
N/A |
RBD |
| EADock |
(Grosdidier et al., 2007) |
N/A |
EA |
| eHiTs |
(Zsoldos et al., 2006) |
www.simbiosys.ca/ehits/index.html |
RBD of fragments followed by reconstruction |
| EUDOC |
(Pang et al., 2001) , |
N/A |
RBD |
| FDS |
(Taylor et al., 2003) |
N/A |
MC |
| DAIM-SEED-FFLD |
(Majeux et al., 1999; Budin et al., 2001; Kolb and Caflisch, 2006) |
biocroma.uzh.ch/SDL/DAIM-SEED-FFLD_agreement.pdf |
RBD |
| FITTED |
(Corbeil et al., 2007) |
www.fitted.ca |
GA |
| FlexX 2.2 |
(Rarey et al., 1996) |
www.biosolveit.de/ |
IC |
| FlexE |
(Rarey et al., 1999; Claußen et al., 2001) |
|
|
| FlipDock (formerly pyDock) |
(Zhao and Sanner, 2007) |
www.scripps.edu/~yongzhao/FLIPDock/ |
GA |
| FLOG |
(Miller et al., 1994) |
N/A |
IC |
| FRED |
(McGann et al., 2003) |
www.eyesopen.com/products/applications/fred.html |
RBD |
| FTDock |
(Gabb et al., 1997) |
www.bmm.icnet.uk/docking/ftdock.html |
RBD |
| GAMBLER |
(Charifson et al., 1999) |
N/A |
GA |
| GasDock |
(Li et al., 2004) |
N/A |
GA |
| GEMDOCK |
(Yang and Chen, 2004) |
N/A |
EA |
| GlamDock |
(Tietze and Apostolakis, 2007) |
N/A |
MC/SA |
| Glide 4.0 |
(Friesner et al., 2004; Sherman et al., 2006) |
www.schrodinger.com/ProductDescription.php?mID=6&sID=6&cID=0 |
Hierarchical filters and MC |
| GOLD 3.1 |
(Verdonk et al., 2003, 2005) |
www.ccdc.cam.ac.uk/products/life_sciences/gold/ |
GA |
| Hammerhead |
(Welch et al., 1996) |
N/A |
IC |
| HADDOCK |
(Dominguez et al., 2003) |
www.nmr.chem.uu.nl/haddock/ |
SA |
| HierDOCK/HierVLS |
(Floriano et al., 2004; Trabanino et al., 2004) |
N/A |
IC |
| ICM |
(Abagyan et al., 1994b; Totrov and Abagyan, 1997) |
www.molsoft.com/docking.html |
MC |
| LibDock |
(Diller and Merz, 2001) |
N/A |
MA |
| LIDAEUS |
(Wu et al., 2003b) |
N/A |
MA |
| LIGIN |
(Sobolev et al., 1996) |
N/A |
RBD |
| MacDOCK |
(Fradera et al., 2004) |
N/A |
IC |
| MCDOCK |
(Liu and Wang, 1999) |
N/A |
MC |
| MolDock |
(Thomsen and Christensen, 2006) |
N/A |
DE |
| MVP |
N/A |
N/A |
IC |
| PatchDOCK |
(Schneidman-Duhovny et al., 2005) |
N/A |
Shape complementarity |
| PAS-Dock |
(Tøndel et al., 2006) |
N/A |
TS |
| PhDOCK |
(Joseph-McCarthy et al., 2003) |
N/A |
MA |
| Ph4DOCK |
(Goto et al., 2004) |
N/A |
MA |
| PIPER |
(Kozakov et al., 2006) |
N/A |
Fast Fourier transform |
| Plants |
(Korb et al., 2006) |
N/A |
Ant colony optimisation |
| Prodock |
(Trosset and Scheraga, 1999) |
N/A |
MC |
| PRO_LEADS |
(Murray et al., 1999) |
N/A |
TS |
| ProPose |
(Seifert, 2005) |
N/A |
IC |
| PSI_DOCK |
(Pei et al., 2006) |
N/A |
GA with TS |
| Q-fit |
(Jackson, 2002) |
N/A |
MA |
| Quantum |
N/A |
www.q-lead.com/cnt/quantum |
N/A |
| QXP/Flo+ |
(McMartin and Bohacek, 1997) |
N/A |
MC |
| RiboDock |
(Morley and Afshar, 2004) |
N/A |
MC |
| ROSETTALIGAND |
(Meiler and Baker, 2006) |
N/A |
MC |
| SANDOCK |
(Burkhard et al., 1998) |
N/A |
MA |
| SDOCKER |
(Wu and Vieth, 2004) |
N/A |
Random walk |
| SLIDE |
(Schnecke and Kuhn, 2000; Zavodszky and Kuhn, 2005) |
N/A |
IC |
| SKELGEN |
(Alberts et al., 2005) |
N/A |
IC |
| SODOCK |
(Chen et al., 2007) |
N/A |
Swarm Optimisation |
| SG-DOCK/SP-DOCK |
(Fradera et al., 2000) |
N/A |
IC |
| Surflex 2.1 |
(Jain, 2003, 2007) |
N/A |
IC with MA |
| Yucca |
(Choi, 2005) |
N/A |
MC |
