design, synthesis, and evaluation of novel
nonsteroidal phenanthrene ligands for the
estrogen receptor. J Med Chem
46:1408–1418
- Haitao Ji et al (2003) Structure-basedde novo
design, synthesis, and biological evaluation of
non-azole inhibitors specific for Lanosterol
14 α-Demethylase of fungi. J Med Chem
46:474–485
- Liu YZ, Wang XL, Wang XY, Yu RL, Liu DQ,
Kang CM (2016)De novodesign of VEGFR-
2 tyrosine kinase inhibitors based on a linked-
fragment approach. J Mol Model 22:222
- Kankanala J, Latham AM, Johnson AP,
Homer-Vanniasinkam S, Fishwick CW, Pon-
nambalam S (2012) A combinatorialin silico
and cellular approach to identify a new class of
compounds that target VEGFR2 receptor
tyrosine kinase activity and angiogenesis. Br J
Pharmacol 166:737–748
- Bo ̈hm HJ, Banner DW, Weber L (1999)
Combinatorial docking and combinatorial
chemistry: design of potent non-peptide
thrombin inhibitors. J Comput Aided Mol
Des 13:51–56
- Pierce AC, Rao G, Bemis GW (2004)
BREED: generating novel inhibitors through
hybridization of known ligands. Application
to CDK2, P38, and HIV protease. J Med
Chem 47:2768–2775
- Rogers-Evans M, Alanine AI, Bleicher KH,
Kube D, Schneider G (2004) Identification
of novel cannabinoid receptor ligands via evo-
lutionaryde novodesign and rapid parallel
synthesis. QSAR Comb Sci 23:426–430
- Huang Q, Li LL, Sheng-Yong Y (2010)
PhDD: a new pharmacophore-basedde novo
design method of drug-like molecules com-
bined with assessment of synthetic accessibil-
ity. J Mol Graph Model 28:775–787
- Heikkil€a T, Thirumalairajan S, Davies M, Par-
sons MR, McConkey AG, Fishwick CWG,
Johnson AP (2006) The firstde novodesigned
inhibitors of plasmodium falciparum dihy-
droorotate dehydrogenase. Bioorg Med
Chem Lett 16:88–92
- Babine RE, Bleckman TM, Kissinger CR,
Showalter R, Pelletier LA, Lewis C,
Tucker K, Moomaw E, Parge HE, Villafranca
JE (1995) Design synthesis and X-ray crystal-
lographic studies of novel FKBP-12 ligand.
Bioorg Med Chem Lett 5:1719–1724
- Heartenfeller M, Zettl H, Walter M, Rupp M,
Reisen F, Proschak E, Wegen S, Stark H,
Schneider G (2012) DOGS: reaction-driven
de novodesign of bioactive compounds. PLoS
Comput Biol 8:1–12
32. Proschak E, Sander K, Zettl H, Tanrikulu Y,
Rau O, Schneider P, Schubert-Zsilavecz M,
Stark H, Schneider G (2009) From molecular
shape to potent bioactive agents II: fragment-
based de novo design. ChemMedChem
4:45–48
33. Dhanjal JK, Sreenidhi AK, Bafna K, Katiyar
SP, Goyal S, Grover A, Sundar D (2015)
Computational structure-based de novo
design of hypothetical inhibitors against the
anti-inflammatory target COX-2. PLoS One
10:e0134691
34. Damewood JR, Lerman CL, Masek BB
(2010) NovoFLAP: a ligand-basedde novo
design approach for the generation of medici-
nally relevant ideas. J Chem Inf Model
50:1296–1303
35. Danziger DJ, Dean PM (1989) Automated
site-directed drug design: a general algorithm
for knowledge acquisition about hydrogen
bonding regions at protein surfaces. Proc R
Soc Lond B Biol Sci 236:101–113
36. Lewis RA (1990) Automated site-directed
drug design: approaches to the formation of
3D molecular graphs. J Comput Aided Mol
Des 4:205–210
37. Nishibata Y, Itai A (1991) Automatic creation
of dug candidate structures based on receptor
structure. Starting point for artificial lead gen-
eration. Tetrahedron 47:8985–8990
38. Lewis RA, Roe DC, Huang C, Ferrin TE,
Langridge R, Kuntz ID (1992) Automated
site-directed drug design using molecular lat-
tices. J Mol Graph 10:66–78
39. Bo ̈hm HJ (1992) The computer program
LUDI: a new simple method for the
de-novo design of enzyme inhibitors. J Com-
put Aided Mol Des 6:61–78
40. Tschinke V, Cohen NC (1993) The NEW-
LEAD program: a new method for the design
of candidate structures from pharmacophoric
hypothesis. J Med Chem 36:3863–3870
41. Rotstein SH, Murcko MA (1993) Group
build: a fragment-based method forde novo
drug design. J Med Chem 36:1700–1710
42. Ho CMW, Marshall GR (1993) SPLICE: a
program to assemble partial query solutions
from three-dimensional database searches
into novel ligands. J Comput Aided Mol Des
7:623–647
43. Rotstein SH, Murcko MA (1993) GenStar: a
method forde novodrug design. J Comput
Aided Mol Des 7:23–43
44. Pearlman DA, Murcko MA (1993) CON-
CEPTS: new dynamic algorithm forde novo
design suggestion. J Comput Chem
14:1184–1193
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