-
1
-
-
0024549279
-
Automated site-directed drug design: a general algorithm for knowledge acquisition about hydrogen-bonding regions at protein surfaces
-
Danziger, D. J. and Dean, P. M. (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, 101–13.
-
(1989)
Proc R Soc Lond B Biol Sci
, vol.236
, pp. 101-113
-
-
Danziger, D. J.1
Dean, P. M.2
-
2
-
-
23844449940
-
Computer-based de novo design of drug-like molecules
-
Schneider, G. and Fechner, U. (2005) Computer-based de novo design of drug-like molecules. Nat Rev Drug Discov 4, 649–63.
-
(2005)
Nat Rev Drug Discov
, vol.4
, pp. 649-663
-
-
Schneider, G.1
Fechner, U.2
-
3
-
-
42449095567
-
Recent developments in de novo design and scaffold hopping
-
Mauser, H. and Guba, W. (2008) Recent developments in de novo design and scaffold hopping. Curr Opin Drug Discov Devel 11, 365–74.
-
(2008)
Curr Opin Drug Discov Devel
, vol.11
, pp. 365-374
-
-
Mauser, H.1
Guba, W.2
-
4
-
-
20344378493
-
A very large diversity space of synthetically accessible compounds for use with drug design programs
-
Nikitin, S., Zaitseva, N., Demina, O., Solovieva, V., Mazin, E., Mikhalev, S., Smolov, M., Rubinov, A., Vlasov, P., Lepikhin, D., Khachko, D., Fokin, V., Queen, C., and Zosimov, V. (2005) A very large diversity space of synthetically accessible compounds for use with drug design programs. J Comput Aided Mol Des 19, 47–63.
-
(2005)
J Comput Aided Mol Des
, vol.19
, pp. 47-63
-
-
Nikitin, S.1
Zaitseva, N.2
Demina, O.3
Solovieva, V.4
Mazin, E.5
Mikhalev, S.6
Smolov, M.7
Rubinov, A.8
Vlasov, P.9
Lepikhin, D.10
Khachko, D.11
Fokin, V.12
Queen, C.13
Zosimov, V.14
-
5
-
-
17144419244
-
LEA3D: a computer-aided ligand design for structure-based drug design
-
Douguet, D., Munier-Lehmann H., Labesse G., and Pochet S. (2005) LEA3D: a computer-aided ligand design for structure-based drug design. J Med Chem 48, 2457–68.
-
(2005)
J Med Chem
, vol.48
, pp. 2457-2468
-
-
Douguet, D.1
Munier-Lehmann, H.2
Labesse, G.3
Pochet, S.4
-
6
-
-
33646265985
-
Flux (1): a virtual synthesis scheme for fragment-based de novo design
-
Fechner, U. and Schneider, G. (2006) Flux (1): a virtual synthesis scheme for fragment-based de novo design. J Chem Inf Model 46, 699–707.
-
(2006)
J Chem Inf Model
, vol.46
, pp. 699-707
-
-
Fechner, U.1
Schneider, G.2
-
7
-
-
34247191329
-
Flux (2): comparison of molecular mutation and crossover operators for ligand-based de novo design
-
Fechner, U., and Schneider, G. (2007) Flux (2): comparison of molecular mutation and crossover operators for ligand-based de novo design. J Chem Inf Model 47, 656–67.
-
(2007)
J Chem Inf Model
, vol.47
, pp. 656-667
-
-
Fechner, U.1
Schneider, G.2
-
8
-
-
33748652464
-
FlexNovo: structure-based searching in large fragment spaces
-
Degen, J. and Rarey, M. (2006) FlexNovo: structure-based searching in large fragment spaces. ChemMedChem 1, 854–68.
-
(2006)
ChemMedChem
, vol.1
, pp. 854-868
-
-
Degen, J.1
Rarey, M.2
-
9
-
-
38049014405
-
The use of ligand-based de novo design for scaffold hopping and sidechain optimization: two case studies
-
Feher, M., Gao, Y., Baber, C., Shirley, W. A., and Saunders, J. (2008) The use of ligand-based de novo design for scaffold hopping and sidechain optimization: two case studies. Bioorg Med Chem 16, 422–7.
-
(2008)
Bioorg Med Chem
, vol.16
, pp. 422-427
-
-
Feher, M.1
Gao, Y.2
Baber, C.3
Shirley, W. A.4
Saunders, J.5
-
10
-
-
42149174453
-
Fragment-based de novo ligand design by multiobjective evolutionary optimization
-
Dey, F., and Caflisch, A. (2008) Fragment-based de novo ligand design by multiobjective evolutionary optimization. J Chem Inf Model 48, 679–90.
-
(2008)
J Chem Inf Model
, vol.48
, pp. 679-690
-
-
Dey, F.1
Caflisch, A.2
-
11
-
-
58549110666
-
From molecular shape to potent bioactive agents I: bioisosteric replacement of molecular fragments
-
Proschak, E., Zettl, H., Tanrikulu, Y., Weisel, M., Kriegl, J. M., Rau, O., Schubert-Zsilavecz, M., and Schneider, G. (2009) From molecular shape to potent bioactive agents I: bioisosteric replacement of molecular fragments. ChemMedChem 4, 41–4.
-
(2009)
ChemMedChem
, vol.4
, pp. 41-44
-
-
Proschak, E.1
Zettl, H.2
Tanrikulu, Y.3
Weisel, M.4
Kriegl, J. M.5
Rau, O.6
Schubert-Zsilavecz, M.7
Schneider, G.8
-
12
-
-
58549112609
-
From molecular shape to potent bioactive agents II: fragment-based de novo design
-
Proschak, E., Sander, K., Zettl, H., Tanrikulu, Y., Rau, O., Schneider, P., Schubert-Zsilavecz, M., Stark, H., and Schneider, G. (2009) From molecular shape to potent bioactive agents II: fragment-based de novo design. ChemMedChem 4, 45–8.
-
(2009)
ChemMedChem
, vol.4
, pp. 45-48
-
-
Proschak, E.1
Sander, K.2
Zettl, H.3
Tanrikulu, Y.4
Rau, O.5
Schneider, P.6
Schubert-Zsilavecz, M.7
Stark, H.8
Schneider, G.9
-
13
-
-
66149089880
-
A novel in silico approach to drug discovery via computational intelligence
-
Hecht, D. and Fogel, G. B. (2009) A novel in silico approach to drug discovery via computational intelligence. J Chem Inf Model 49, 1105–21.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 1105-1121
-
-
Hecht, D.1
Fogel, G. B.2
-
14
-
-
68149124133
-
FOG: fragment optimized growth algorithm for the de novo generation of molecules occupying druglike chemical space
-
Kutchukian, P. S., Lou, D., and Shakhnovich, E. I. (2009) FOG: fragment optimized growth algorithm for the de novo generation of molecules occupying druglike chemical space. J Chem Inf Model 49, 1630–42.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 1630-1642
-
-
Kutchukian, P. S.1
Lou, D.2
Shakhnovich, E. I.3
-
15
-
-
65249116422
-
Computational fragment-based approach at PDB scale by protein local similarity
-
Moriaud, F., Doppelt-Azeroual, O., Martin, L., Oguievetskaia, K., Koch, K., Vorotyntsev, A., Adcock, S. A., and Delfaud, F. (2009) Computational fragment-based approach at PDB scale by protein local similarity. J Chem Inf Model 49, 280–94.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 280-294
-
-
Moriaud, F.1
Doppelt-Azeroual, O.2
Martin, L.3
Oguievetskaia, K.4
Koch, K.5
Vorotyntsev, A.6
Adcock, S. A.7
Delfaud, F.8
-
16
-
-
65249111062
-
De novo drug design using multiobjective evolutionary graphs
-
Nicolaou, C. A., Apostolakis, J., and Pattichis, C. S. (2009) De novo drug design using multiobjective evolutionary graphs. J Chem Inf Model 49, 295–307.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 295-307
-
-
Nicolaou, C. A.1
Apostolakis, J.2
Pattichis, C. S.3
-
17
-
-
66249100884
-
Fragment shuffling: an automated workflow for three-dimensional fragment-based ligand design
-
Nisius, B., and Rester, U. (2009) Fragment shuffling: an automated workflow for three-dimensional fragment-based ligand design. J Chem Inf Model 49, 1211–22.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 1211-1222
-
-
Nisius, B.1
Rester, U.2
-
18
-
-
58849145223
-
AutoGrow: a novel algorithm for protein inhibitor design
-
Durrant, J. D., Amaro, R. E., and McCammon, J. A. (2009) AutoGrow: a novel algorithm for protein inhibitor design. Chem Biol Drug Des 73, 168–78.
-
(2009)
Chem Biol Drug Des
, vol.73
, pp. 168-178
-
-
Durrant, J. D.1
Amaro, R. E.2
McCammon, J. A.3
-
20
-
-
57849156863
-
Voyages to the (un)known: adaptive design of bioactive compounds
-
Schneider, G., Hartenfeller, M., Reutlinger, M., Tanrikulu, Y., Proschak, E., and Schneider, P. (2009) Voyages to the (un)known: adaptive design of bioactive compounds. Trends Biotechnol 27, 18–26.
-
(2009)
Trends Biotechnol
, vol.27
, pp. 18-26
-
-
Schneider, G.1
Hartenfeller, M.2
Reutlinger, M.3
Tanrikulu, Y.4
Proschak, E.5
Schneider, P.6
-
21
-
-
0038748179
-
Virtual screening of virtual libraries
-
Green, D. V. (2003) Virtual screening of virtual libraries. Prog Med Chem 41, 61–97.
-
(2003)
Prog Med Chem
, vol.41
, pp. 61-97
-
-
Green, D. V.1
-
23
-
-
0026619394
-
Looking at proteins: representations, folding, packing, and design
-
Richardson, J. S., Richardson, D. C., Tweedy, N. B., Gernert, K. M., Quinn, T. P., Hecht, M. H., Erickson, B. W., Yan, Y., McClain, R. D., and Donlan, M. E. (1992) Looking at proteins: representations, folding, packing, and design. Biophys J 63, 1185–209.
-
(1992)
Biophys J
, vol.63
, pp. 1185-1209
-
-
Richardson, J. S.1
Richardson, D. C.2
Tweedy, N. B.3
Gernert, K. M.4
Quinn, T. P.5
Hecht, M. H.6
Erickson, B. W.7
Yan, Y.8
McClain, R. D.9
Donlan, M. E.10
-
24
-
-
34247217238
-
Designing active template molecules by combining computational de novo design and human chemist’s expertise
-
Lameijer, E. W., Tromp, R. A., Spanjersberg, R. F., Brussee, J., and Ijzerman, A. P. (2007) Designing active template molecules by combining computational de novo design and human chemist’s expertise. J Med Chem 50, 1925–32.
-
(2007)
J Med Chem
, vol.50
, pp. 1925-1932
-
-
Lameijer, E. W.1
Tromp, R. A.2
Spanjersberg, R. F.3
Brussee, J.4
Ijzerman, A. P.5
-
25
-
-
0036489455
-
Combinatorial library design using a multiobjective genetic algorithm
-
Gillet, V. J., Khatib, W., Willett, P., Fleming, P. J. and Green, D. V. (2002) Combinatorial library design using a multiobjective genetic algorithm. J Chem Inf Comput Sci 42, 375–85.
-
(2002)
J Chem Inf Comput Sci
, vol.42
, pp. 375-385
-
-
Gillet, V. J.1
Khatib, W.2
Willett, P.3
Fleming, P. J.4
Green, D. V.5
-
26
-
-
44949243928
-
New directions in library design and analysis
-
Gillet V. J. (2008) New directions in library design and analysis. Curr Opin Chem Biol 12, 372–8.
-
(2008)
Curr Opin Chem Biol
, vol.12
, pp. 372-378
-
-
Gillet, V. J.1
-
27
-
-
1942453243
-
Ligand efficiency: a useful metric for lead selection
-
Hopkins A. L., Groom C. R., and Alex A. (2004) Ligand efficiency: a useful metric for lead selection. Drug Discov Today 15, 430–1.
-
(2004)
Drug Discov Today
, vol.15
, pp. 430-431
-
-
Hopkins, A. L.1
Groom, C. R.2
Alex, A.3
-
29
-
-
0034130399
-
De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks
-
Schneider, G., Lee, M., Stahl, M., and Schneider, P. (2000) De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks. J Comput Aided Mol Des 14, 487–94.
-
(2000)
J Comput Aided Mol Des
, vol.14
, pp. 487-494
-
-
Schneider, G.1
Lee, M.2
Stahl, M.3
Schneider, P.4
-
30
-
-
2442647742
-
BREED: generating novel inhibitors through hybridization of known ligands. Application to CDK2, P38, and HIV protease
-
Pierce, A. C., Rao, G., and Bemis, G. W. (2004) BREED: generating novel inhibitors through hybridization of known ligands. Application to CDK2, P38, and HIV protease. J Med Chem 47, 2768–75.
-
(2004)
J Med Chem
, vol.47
, pp. 2768-2775
-
-
Pierce, A. C.1
Rao, G.2
Bemis, G. W.3
-
31
-
-
0025916872
-
Functionality maps of binding sites: a multiple copy simultaneous search method
-
Miranker, A. and Karplus, M. (1991) Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins 11, 29–34.
-
(1991)
Proteins
, vol.11
, pp. 29-34
-
-
Miranker, A.1
Karplus, M.2
-
32
-
-
84860134058
-
-
(accessed September 28, 2009)
-
RCSB Protein Data Bank, http://www.rcsb. org/pdb/(accessed September 28, 2009).
-
RCSB Protein Data Bank
-
-
-
33
-
-
33748807805
-
-
(accessed September 28)
-
The PubChem Project, http://pubchem. ncbi.nlm.nih.gov/(accessed September 28, 2009).
-
(2009)
The PubChem Project
-
-
-
34
-
-
0029965861
-
CONCERTS: dynamic connection of fragments as an approach to de novo ligand design
-
Pearlman, D. A. and Murcko, M. A. (1996) CONCERTS: dynamic connection of fragments as an approach to de novo ligand design. J Med Chem 39, 1651–63.
-
(1996)
J Med Chem
, vol.39
, pp. 1651-1663
-
-
Pearlman, D. A.1
Murcko, M. A.2
-
35
-
-
0030277958
-
RASSE: a new method for structure-based drug design
-
Luo, Z., Wang, R., and Lai, L. (1996) RASSE: a new method for structure-based drug design. J Chem Inf Comput Sci 36, 1187–94.
-
(1996)
J Chem Inf Comput Sci
, vol.36
, pp. 1187-1194
-
-
Luo, Z.1
Wang, R.2
Lai, L.3
-
36
-
-
0028036120
-
Multiple highly diverse structures complementary to enzyme binding sites: results of extensive application of a de novo design method incorporating combinatorial growth
-
Bohacek, R. S. and McMartin, C. (1994) Multiple highly diverse structures complementary to enzyme binding sites: results of extensive application of a de novo design method incorporating combinatorial growth. J Am Chem Soc 116, 5560–71.
-
(1994)
J Am Chem Soc
, vol.116
, pp. 5560-5571
-
-
Bohacek, R. S.1
McMartin, C.2
-
37
-
-
0011803040
-
Automated structure design in 3D
-
Gillett, V. A., Johnson, A. P., Mata, P., and Sike, S. (1990) Automated structure design in 3D. Tetrahedron Comput Method 3, 681–96.
-
(1990)
Tetrahedron Comput Method
, vol.3
, pp. 681-696
-
-
Gillett, V. A.1
Johnson, A. P.2
Mata, P.3
Sike, S.4
-
39
-
-
0000934205
-
SMoG: de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence
-
DeWitte, R. S. and Shakhnovich, E. I. (1996) SMoG: de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence. J Am Chem Soc 118, 11733–44.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 11733-11744
-
-
DeWitte, R. S.1
Shakhnovich, E. I.2
-
40
-
-
0037142298
-
SMall molecule growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein – ligand interactions
-
Ishchenko, A. V. and Shakhnovich, E. I. (2002) SMall molecule growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein – ligand interactions. J Med Chem 45, 2770–80.
-
(2002)
J Med Chem
, vol.45
, pp. 2770-2780
-
-
Ishchenko, A. V.1
Shakhnovich, E. I.2
-
41
-
-
0027586682
-
SPROUT: a program for structure generation
-
Gillet, V. J., Johnson, A. P., Mata P., Sike, S., and Williams P. (1993) SPROUT: a program for structure generation. J Comput Aided Mol Des 7, 127–53.
-
(1993)
J Comput Aided Mol Des
, vol.7
, pp. 127-153
-
-
Gillet, V. J.1
Johnson, A. P.2
Mata, P.3
Sike, S.4
Williams, P.5
-
42
-
-
0028167547
-
SPROUT: recent developments in the de novo design of molecules
-
Gillet, V. J., Newell, W., Mata, P., Myatt, G., Sike, S., Zsoldos, Z. and Johnson, A. P. (1994) SPROUT: recent developments in the de novo design of molecules. J Comput Aided Mol Des 34, 207–17.
-
(1994)
J Comput Aided Mol Des
, vol.34
, pp. 207-217
-
-
Gillet, V. J.1
Newell, W.2
Mata, P.3
Myatt, G.4
Sike, S.5
Zsoldos, Z.6
Johnson, A. P.7
-
43
-
-
0002820943
-
SPROUT, HIPPO and CAESA: tools for de novo structure generation and estimation of synthetic accessibility
-
Gillett, V. J., Myatt, G., Zsoldos, Z., and Johnson, A. P. (1995) SPROUT, HIPPO and CAESA: tools for de novo structure generation and estimation of synthetic accessibility. Perspect Drug Discov Des 3, 34–50.
-
(1995)
Perspect Drug Discov Des
, vol.3
, pp. 34-50
-
-
Gillett, V. J.1
Myatt, G.2
Zsoldos, Z.3
Johnson, A. P.4
-
44
-
-
0026813925
-
The computer program LUDI: a new simple method for the de-novo design of enzyme inhibitors
-
Böhm, H.-J. (1992) The computer program LUDI: a new simple method for the de-novo design of enzyme inhibitors. J Comput Aided Mol Des 6, 61–78.
-
(1992)
J Comput Aided Mol Des
, vol.6
, pp. 61-78
-
-
Böhm, H.-J.1
-
45
-
-
0027027467
-
LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads
-
Böhm, H.-J. (1992) LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J Comput Aided Mol Des 6, 593–606.
-
(1992)
J Comput Aided Mol Des
, vol.6
, pp. 593-606
-
-
Böhm, H.-J.1
-
46
-
-
0027658106
-
A novel computational tool for automated structure-based drug design
-
Böhm, H.-J. (1993) A novel computational tool for automated structure-based drug design. Journal of Molecular Recognition, 6, 131–7.
-
(1993)
Journal of Molecular Recognition
, vol.6
, pp. 131-137
-
-
Böhm, H.-J.1
-
47
-
-
0028454828
-
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
-
Böhm, H.-J. (1994). The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Des 8, 243–56.
-
(1994)
J Comput Aided Mol Des
, vol.8
, pp. 243-256
-
-
Böhm, H.-J.1
-
48
-
-
0032112137
-
Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs
-
Böhm, H.-J. (1998). Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J Comput Aided Mol Des 12, 309–23.
-
(1998)
J Comput Aided Mol Des
, vol.12
, pp. 309-323
-
-
Böhm, H.-J.1
-
49
-
-
0027136267
-
The NEWLEAD program: a new method for the design of candidate structures from pharmacophoric hypothesis
-
Tschinke, V. and Cohen, N. C. (1993) The NEWLEAD program: a new method for the design of candidate structures from pharmacophoric hypothesis. J Med Chem 36, 3863–70.
-
(1993)
J Med Chem
, vol.36
, pp. 3863-3870
-
-
Tschinke, V.1
Cohen, N. C.2
-
50
-
-
52249108519
-
CONFIRM: connecting fragments found in receptor molecules
-
Thompson, D. C., Denny, R. A., Nilakantan, R., Humblet, C., Joseph-McCarthy, D., and Feyfant, E. (2008) CONFIRM: connecting fragments found in receptor molecules. J Comput Aided Mol Des 22, 761–72.
-
(2008)
J Comput Aided Mol Des
, vol.22
, pp. 761-772
-
-
Thompson, D. C.1
Denny, R. A.2
Nilakantan, R.3
Humblet, C.4
Joseph-McCarthy, D.5
Feyfant, E.6
-
51
-
-
12944286886
-
Extension of the limit theorems of probability theory to a sum of variables connected in a chain
-
Howard, R. (Ed), John Wiley and Sons, Hoboken
-
Markov, A.A., (1971) Extension of the limit theorems of probability theory to a sum of variables connected in a chain. In: Howard, R. (Ed.), Dynamic Probabilistic Systems, vol. 1, Markov Chains (reprinted in Appendix B), John Wiley and Sons, Hoboken.
-
(1971)
Dynamic Probabilistic Systems, vol. 1, Markov Chains (reprinted in Appendix B)
-
-
Markov, A.A.1
-
52
-
-
0032058905
-
RECAP – retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry
-
Lewell, X. Q., Judd, D., Watson, S., and Hann, M. (1998) RECAP – retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry. J Chem Inf Comput Sci 38, 511–22.
-
(1998)
J Chem Inf Comput Sci
, vol.38
, pp. 511-522
-
-
Lewell, X. Q.1
Judd, D.2
Watson, S.3
Hann, M.4
-
53
-
-
34447305996
-
Structure and reaction based evaluation of synthetic accessibility
-
Boda, K., Seidel, T., and Gasteiger, J. (2007) Structure and reaction based evaluation of synthetic accessibility. J Comput Aided Mol Des 21, 311–25.
-
(2007)
J Comput Aided Mol Des
, vol.21
, pp. 311-325
-
-
Boda, K.1
Seidel, T.2
Gasteiger, J.3
-
54
-
-
65249148540
-
Route designer: a retrosynthetic analysis tool utilizing automated retrosynthetic rule generation
-
Law, J., Zsoldos, Z., Simon, A., Reid, D., Liu, Y., Khew, S. Y., Johnson, A. P., Major, S., Wade, R. A., and Ando, H. Y. (2009) Route designer: a retrosynthetic analysis tool utilizing automated retrosynthetic rule generation. J Chem Inf Model 49, 593–602.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 593-602
-
-
Law, J.1
Zsoldos, Z.2
Simon, A.3
Reid, D.4
Liu, Y.5
Khew, S. Y.6
Johnson, A. P.7
Major, S.8
Wade, R. A.9
Ando, H. Y.10
-
55
-
-
0037777697
-
SYNOPSIS: SYNthesize and OPtimize system in silico
-
Vinkers, H. M., de Jonge, M. R., Daeyaert, F. F., Heeres, J., Koymans, L. M., Lenthe, J. H., Lewi, P. J., Timmerman, H., Van Aken, K., and Janssen, P. A. (2003) SYNOPSIS: SYNthesize and OPtimize system in silico. J Med Chem 46, 2765–73.
-
(2003)
J Med Chem
, vol.46
, pp. 2765-2773
-
-
Vinkers, H. M.1
de Jonge, M. R.2
Daeyaert, F. F.3
Heeres, J.4
Koymans, L. M.5
Lenthe, J. H.6
Lewi, P. J.7
Timmerman, H.8
Van Aken, K.9
Janssen, P. A.10
-
56
-
-
85194795132
-
-
Symyx Technology Inc., 2440 Camino Ramon, Suite 300, San Ramon, CA 94583, USA.
-
Symyx Technology Inc., 2440 Camino Ramon, Suite 300, San Ramon, CA 94583, USA.
-
-
-
-
58
-
-
66249098082
-
Knowledge-based approach to de novo design using reaction vectors
-
Patel, H., Bodkin, M. J., Chen, B., and Gillet, V. J. (2009) Knowledge-based approach to de novo design using reaction vectors. J Chem Inf Model 49, 1163–84.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 1163-1184
-
-
Patel, H.1
Bodkin, M. J.2
Chen, B.3
Gillet, V. J.4
-
59
-
-
61949160999
-
Reaction-MQL: line notation for functional transformation
-
Reisen, F. H., Schneider, G., and Proschak, E. (2009) Reaction-MQL: line notation for functional transformation. J Chem Inf Model 49, 6–12.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 6-12
-
-
Reisen, F. H.1
Schneider, G.2
Proschak, E.3
-
60
-
-
37249009571
-
Kernel approach to molecular similarity based on iterative graph similarity
-
Rupp, M., Proschak, E., and Schneider, G. (2007) Kernel approach to molecular similarity based on iterative graph similarity. J Chem Inf Model 47, 2280–6.
-
(2007)
J Chem Inf Model
, vol.47
, pp. 2280-2286
-
-
Rupp, M.1
Proschak, E.2
Schneider, G.3
-
61
-
-
0030039619
-
The art and practice of structure-based drug design: a molecular modeling perspective
-
Bohacek R. S., McMartin C., and Guida W. C. (1996) The art and practice of structure-based drug design: a molecular modeling perspective. Med Res Rev 16, 3–50.
-
(1996)
Med Res Rev
, vol.16
, pp. 3-50
-
-
Bohacek, R. S.1
McMartin, C.2
Guida, W. C.3
-
62
-
-
34247250737
-
Chemical fragment spaces for de novo design
-
Mauser, H. and Stahl, M. (2007) Chemical fragment spaces for de novo design. J Chem Inf Model 47, 318–24.
-
(2007)
J Chem Inf Model
, vol.47
, pp. 318-324
-
-
Mauser, H.1
Stahl, M.2
-
63
-
-
1842411345
-
Energetic and entropic factors determining binding affinity in protein-ligand complexes
-
Klebe G. and Böhm H. J. (1997) Energetic and entropic factors determining binding affinity in protein-ligand complexes. J Recept Signal Transduct Res 17, 459–73.
-
(1997)
J Recept Signal Transduct Res
, vol.17
, pp. 459-473
-
-
Klebe, G.1
Böhm, H. J.2
-
64
-
-
61449150645
-
Additivity in the analysis and design of HIV protease inhibitors
-
Jorissen, R. N., Reddy, G. S., Ali, A., Altman, M. D., Chellappan, S., Anjum, S. G., Tidor, B., Schiffer, C. A., Rana, T. M., and Gilson, M. K. (2009) Additivity in the analysis and design of HIV protease inhibitors. J Med Chem 52,737–54.
-
(2009)
J Med Chem
, vol.52
, pp. 737-754
-
-
Jorissen, R. N.1
Reddy, G. S.2
Ali, A.3
Altman, M. D.4
Chellappan, S.5
Anjum, S. G.6
Tidor, B.7
Schiffer, C. A.8
Rana, T. M.9
Gilson, M. K.10
-
65
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
Rarey, M., Kramer, B., Lengauer, T., and Klebe, G. (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261, 470–89.
-
(1996)
J Mol Biol
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
66
-
-
0033598416
-
Prospective identification of biologically active structures by topomer shape similarity searching
-
Cramer, R. D., Poss, M. A., Hermsmeier, M. A., Caulfield, T. J., Kowala, M. C., and Valentine, M. T. (1999) Prospective identification of biologically active structures by topomer shape similarity searching. J Med Chem 42, 3919–33.
-
(1999)
J Med Chem
, vol.42
, pp. 3919-3933
-
-
Cramer, R. D.1
Poss, M. A.2
Hermsmeier, M. A.3
Caulfield, T. J.4
Kowala, M. C.5
Valentine, M. T.6
-
67
-
-
0034923575
-
Similarity searching in large combinatorial chemistry spaces
-
Rarey, M. and Stahl, M. (2001) Similarity searching in large combinatorial chemistry spaces. J Comput Aided Mol Des 15, 497–520.
-
(2001)
J Comput Aided Mol Des
, vol.15
, pp. 497-520
-
-
Rarey, M.1
Stahl, M.2
-
68
-
-
0032149905
-
Feature trees: a new molecular similarity measure based on tree matching
-
Rarey, M. and Dixon, S. (1998) Feature trees: a new molecular similarity measure based on tree matching. J Comput Aided Mol Des 12, 471–90.
-
(1998)
J Comput Aided Mol Des
, vol.12
, pp. 471-490
-
-
Rarey, M.1
Dixon, S.2
-
69
-
-
43049096782
-
Similarity searching and scaffold hopping in synthetically accessible combinatorial chemistry spaces
-
Boehm, M., Wu, T. Y., Claussen, H., and Lemmen, C. (2008) Similarity searching and scaffold hopping in synthetically accessible combinatorial chemistry spaces. J Med Chem 51, 2468–80.
-
(2008)
J Med Chem
, vol.51
, pp. 2468-2480
-
-
Boehm, M.1
Wu, T. Y.2
Claussen, H.3
Lemmen, C.4
-
70
-
-
65249124650
-
Searching fragment spaces with feature trees
-
Lessel, U., Wellenzohn, B., Lilienthal, M., and Claussen, H. (2009) Searching fragment spaces with feature trees. J Chem Inf Model 49, 270–9.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 270-279
-
-
Lessel, U.1
Wellenzohn, B.2
Lilienthal, M.3
Claussen, H.4
-
71
-
-
50849135173
-
Synthesis of de novo designed small-molecule inhibitors of bacterial RNA polymerase
-
Agarwal, A. K., Johnson, A. P., and Fishwick, C. W. (2008) Synthesis of de novo designed small-molecule inhibitors of bacterial RNA polymerase. Tetrahedron 64, 10049–54.
-
(2008)
Tetrahedron
, vol.64
, pp. 10049-10054
-
-
Agarwal, A. K.1
Johnson, A. P.2
Fishwick, C. W.3
-
72
-
-
60449100155
-
Design and synthesis of new hydroxyethylamines as inhibitors of D-alanyl-D-lactate ligase (VanA) and D-alanyl-D-alanine ligase (DdlB)
-
Sova, M., Cadez, G., Turk, S., Majce, V., Polanc, S., Batson, S., Lloyd, A. J., Roper, D. I., Fishwick, C. W., and Gobec, S. (2009) Design and synthesis of new hydroxyethylamines as inhibitors of D-alanyl-D-lactate ligase (VanA) and D-alanyl-D-alanine ligase (DdlB). Bioorg Med Chem Lett 19, 1376–9.
-
(2009)
Bioorg Med Chem Lett
, vol.19
, pp. 1376-1379
-
-
Sova, M.1
Cadez, G.2
Turk, S.3
Majce, V.4
Polanc, S.5
Batson, S.6
Lloyd, A. J.7
Roper, D. I.8
Fishwick, C. W.9
Gobec, S.10
-
73
-
-
67649934675
-
Structure-based de novo design and biochemical evaluation of novel Cdc25 phosphatase inhibitors
-
Park, H., Bahn, Y. J., and Ryu, S. E. (2009) Structure-based de novo design and biochemical evaluation of novel Cdc25 phosphatase inhibitors. Bioorg Med Chem Lett 19, 4330–4.
-
(2009)
Bioorg Med Chem Lett
, vol.19
, pp. 4330-4334
-
-
Park, H.1
Bahn, Y. J.2
Ryu, S. E.3
-
74
-
-
0000217414
-
LigBuilder: a multi-purpose program for structure-based drug design
-
Wang, R., Gao, Y., and Lai, L. (2000) LigBuilder: a multi-purpose program for structure-based drug design. J Mol Model 6, 498–516.
-
(2000)
J Mol Model
, vol.6
, pp. 498-516
-
-
Wang, R.1
Gao, Y.2
Lai, L.3
-
75
-
-
39049085817
-
The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNA
-
Sch€uller, A., Suhartono, M., Fechner, U., Tanrikulu, Y., Breitung, S., Scheffer, U., Göbel, M. W., and Schneider, G. (2008) The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNA. J Comput Aided Mol Des 22, 59–68.
-
(2008)
J Comput Aided Mol Des
, vol.22
, pp. 59-68
-
-
Sch€uller, A.1
Suhartono, M.2
Fechner, U.3
Tanrikulu, Y.4
Breitung, S.5
Scheffer, U.6
Göbel, M. W.7
Schneider, G.8
-
76
-
-
0033523672
-
“Scaffold-Hopping” by topological pharmacophore search: a contribution to virtual screening
-
Schneider, G., Neidhart, W., Giller, T., and Schmid, G. (1999) “Scaffold-Hopping” by topological pharmacophore search: a contribution to virtual screening. Angew Chem Int Ed 38, 2894–6.
-
(1999)
Angew Chem Int Ed
, vol.38
, pp. 2894-2896
-
-
Schneider, G.1
Neidhart, W.2
Giller, T.3
Schmid, G.4
-
77
-
-
42449095567
-
Recent developments in de novo design and scaffold hopping
-
Mauser, H. and Guba, W. (2008) Recent developments in de novo design and scaffold hopping. Curr Opin Drug Discovery Dev 11, 365–74.
-
(2008)
Curr Opin Drug Discovery Dev
, vol.11
, pp. 365-374
-
-
Mauser, H.1
Guba, W.2
-
78
-
-
33744827370
-
De novo ligand design to an ensemble of protein structures
-
Todorov, N. P., Buenemann, C. L., and Alberts, I. L. (2006) De novo ligand design to an ensemble of protein structures. Proteins: Struct, Funct, Bioinf 64, 43–59.
-
(2006)
Proteins: Struct, Funct, Bioinf
, vol.64
, pp. 43-59
-
-
Todorov, N. P.1
Buenemann, C. L.2
Alberts, I. L.3
-
79
-
-
27144484954
-
Receptor flexibility in de novo ligand design and docking
-
Alberts, I. L., Todorov, N. P., and Dean, P. M. (2005) Receptor flexibility in de novo ligand design and docking. J Med Chem 48, 6585–96.
-
(2005)
J Med Chem
, vol.48
, pp. 6585-6596
-
-
Alberts, I. L.1
Todorov, N. P.2
Dean, P. M.3
-
80
-
-
34247232594
-
Recore: a fast and versatile method for scaffold hopping based on small molecule crystal structure conformations
-
Maass, P., Schulz-Gasch, T., Stahl, M., and Rarey, M. (2007) Recore: a fast and versatile method for scaffold hopping based on small molecule crystal structure conformations. J Chem Inf Model 47, 390–9.
-
(2007)
J Chem Inf Model
, vol.47
, pp. 390-399
-
-
Maass, P.1
Schulz-Gasch, T.2
Stahl, M.3
Rarey, M.4
-
81
-
-
77953973777
-
Bioisosteric replacement of molecular scaffolds: fromnatural products to synthetic compounds
-
Grabowski, K., Proschak, E., Baringhaus, K., Rau, O., Schubert-Zsilaveczc, M., and Schneider, G. (2008) Bioisosteric replacement of molecular scaffolds: fromnatural products to synthetic compounds. Nat Prod Commun 3, 1355–60.
-
(2008)
Nat Prod Commun
, vol.3
, pp. 1355-1360
-
-
Grabowski, K.1
Proschak, E.2
Baringhaus, K.3
Rau, O.4
Schubert-Zsilaveczc, M.5
Schneider, G.6
-
82
-
-
45449111186
-
Concept of combinatorial de novo design of drug-like molecules by particle swarm optimization
-
Hartenfeller, M., Proschak, E., Sch€uller, A., and Schneider, G. (2008) Concept of combinatorial de novo design of drug-like molecules by particle swarm optimization. Chem Biol Drug Des 72, 16–26.
-
(2008)
Chem Biol Drug Des
, vol.72
, pp. 16-26
-
-
Hartenfeller, M.1
Proschak, E.2
Sch€uller, A.3
Schneider, G.4
|