Table 1.

de novo design tools (taken and adapted from [53]).

Tool	Concept	Reference
Builder	Combinatory search by recombination of docked molecules	[54]
Caveat	Database search for fragment fitting	[55]
Concerts	Fragment-based, stochastic search	[56]
Dynamic ligand design	Atom-based, structure sampling by simulated annealing	[57]
GenStar	Atom-Based, molecules growth based on an enzyme contact model	[58]
GroupBuild	Fragment-based, combinatorial search	[59]
Grow	Peptide design, sequential growth	[60]
Growmol	Fragment-based, sequential growth, stochastic search	[61]
Hook	Linker search for fragments placed by MCSS	[62]
Legend	Atom-based, stochastic search	[63]
LUDI	Fragment-based, combinatorial search	[64]
MCDNLG	Atom-based, stochastic search	[65]
MCSS	Fragment-based, stochastic sampling	[66]
MolMaker	Graph-theoretical 3D design	[67]
NewLead	Fragment-based, builds on 3D pharmacophore-models	[68]
Pro-Ligand	Fragment-based search	[69]
Pro-Select	Fragment-based, scaffold-linker approach	[70]
Skelgen	Small-fragment based, Monte-Carlo search	[71]
SME	Peptide design, whole-molecule optimization	[72]
SMoG	Fragment-based, sequential growth, stochastic search	[73]
Splice	Recombination of ligands retrieved by a 3D database search	[74]
Sprout	Fragment-based, sequential growth, combinatorial search	[75]
Topas	Fragment-based, evolutionary search	[76]