Computational Drug Discovery and Design

Table 2
(continued)

S. No.

De novo design

software or

program

Year of

publication Concept of function

Receptor

(R)/Ligand

(L) based Reference

25 DycoBlock 1999 Force field and solvent accessible

surface

R[58]

26 LEA 2000 QSAR prediction based on 3D

descriptors

L[59]

27 LigBuilder 2000 Empirical scoring R [60]

28 TOPAS 2000 Molecular similarity function L [61]

29 F-DycoBlock 2001 Force field and solvent accessible

surface

R[62]

30 ADAPT 2001 Based on weighted sum of dock score,

clogP, MM, number of rotatable

bonds and hydrogen bonds

R[63]

31 Pellegrini & field 2003 QSAR prediction based on target

specific

R[64]

32 SYNOPSIS 2003 Electrical dipole moment and

empirically derived HIV-RT scoring

R[65]

33 CoG 2004 Molecular similarity scoring L [66]

35 Nikitin 2005 Hydrogen bond, grid based

electrostatic interaction

R[67]

36 LEAD3D 2005 Molecular docking with independent

property

R[68]

37 Flux 2006 Stochastic searching with ligand-based

similarity scoring

L[69, 70]

38 GANDI 2008 Force field R and L [71]

39 COLIBREE 2008 Based on chemical advance template

search topological pharmacophore

similarity

L[72]

40 SQUIRReLnovo 2008 Shape and pharmacophoric features

based generation

L[32]

41 Hecht & Fogel 2009 GOLD fitness scoring L [73]

42 MED-hybridise 2009 MED sumo score R [74]

43 MEGA 2009 Multi objective fitness scoring R [75]

44 AutoGrow 2009 Molecular docking score R [76]

45 NovoFLAP 2010 Ligand-based scoring with structural

and pharmacophoric features

L[34]

46 PhDD 2010 Pharmacophore-based de novo design L [28]

(continued)

De Novo Design of Ligands 79