-
1
-
-
84986518987
-
Molecular docking using shape descriptors
-
Shoichet, B. K.; Bodian, D. L.; Kuntz, I. D. Molecular docking using shape descriptors J. Comput. Chem. 1992, 13, 380-397
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 380-397
-
-
Shoichet, B.K.1
Bodian, D.L.2
Kuntz, I.D.3
-
2
-
-
0031565730
-
Modelling protein docking using shape complementarity, electrostatics and biochemical information
-
Gabb, H. A.; Jackson, R. M.; Sternberg, M. J. Modelling protein docking using shape complementarity, electrostatics and biochemical information J. Mol. Biol. 1997, 272, 106-120
-
(1997)
J. Mol. Biol.
, vol.272
, pp. 106-120
-
-
Gabb, H.A.1
Jackson, R.M.2
Sternberg, M.J.3
-
3
-
-
14944348527
-
A shape-based 3-d scaffold hopping method and its application to a bacterial protein-protein interaction
-
Rush, T. S., III; Grant, J. A.; Mosyak, L.; Nicholls, A. A shape-based 3-d scaffold hopping method and its application to a bacterial protein-protein interaction J. Med. Chem. 2005, 48, 1489-1495
-
(2005)
J. Med. Chem.
, vol.48
, pp. 1489-1495
-
-
Iii, S.R.T.1
Grant, J.A.2
Mosyak, L.3
Nicholls, A.4
-
4
-
-
33846212271
-
Comparison of shape-matching and docking as virtual screening tools
-
Hawkins, P. C. D.; Skillman, A. G.; Nicholls, A. Comparison of shape-matching and docking as virtual screening tools J. Med. Chem. 2007, 50, 74-82
-
(2007)
J. Med. Chem.
, vol.50
, pp. 74-82
-
-
Hawkins, P.C.D.1
Skillman, A.G.2
Nicholls, A.3
-
5
-
-
84871606438
-
-
Version 4.9; Daylight Chemical Information Systems, Inc.: Aliso Viejo, CA
-
Daylight, Version 4.9; Daylight Chemical Information Systems, Inc.: Aliso Viejo, CA, 2008.
-
(2008)
Daylight
-
-
-
6
-
-
34547673017
-
Comparison of topological, shape, and docking methods in virtual screening
-
McGaughey, G. B.; Sheridan, R. P.; Bayly, C. I.; Culberson, J. C.; Kreatsoulas, C.; Lindsley, S.; Maiorov, V.; Truchon, J.; Cornell, W. D. Comparison of topological, shape, and docking methods in virtual screening J. Chem. Inf. Model. 2007, 47, 1504-1519
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 1504-1519
-
-
McGaughey, G.B.1
Sheridan, R.P.2
Bayly, C.I.3
Culberson, J.C.4
Kreatsoulas, C.5
Lindsley, S.6
Maiorov, V.7
Truchon, J.8
Cornell, W.D.9
-
7
-
-
5444258174
-
Comparison of 2D similarity and 3D superposition. Application to searching a conformational drug database
-
Thimm, M.; Goede, A.; Hougardy, S.; Preissner, R. Comparison of 2D similarity and 3D superposition. Application to searching a conformational drug database J. Chem. Inf. Comput. Sci. 2004, 44, 1816-1822
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 1816-1822
-
-
Thimm, M.1
Goede, A.2
Hougardy, S.3
Preissner, R.4
-
8
-
-
77249106566
-
Three-dimensional pharmacophore methods in drug discovery
-
Leach, A. R.; Gillet, V. J.; Lewis, R. A.; Taylor, R. Three-dimensional pharmacophore methods in drug discovery J. Med. Chem. 2010, 53, 539-558
-
(2010)
J. Med. Chem.
, vol.53
, pp. 539-558
-
-
Leach, A.R.1
Gillet, V.J.2
Lewis, R.A.3
Taylor, R.4
-
9
-
-
74949101324
-
Pharmacophore-based virtual screening versus docking-based virtual screening: A benchmark comparison against eight targets
-
Chen, Z.; Li, H.; Zhang, Q.; Bao, X.; Yu, K.; Luo, X.; Zhu, W.; Jiang, H. Pharmacophore-based virtual screening versus docking-based virtual screening: A benchmark comparison against eight targets Acta Pharmacol. Sin. 2009, 30, 1694-1708
-
(2009)
Acta Pharmacol. Sin.
, vol.30
, pp. 1694-1708
-
-
Chen, Z.1
Li, H.2
Zhang, Q.3
Bao, X.4
Yu, K.5
Luo, X.6
Zhu, W.7
Jiang, H.8
-
10
-
-
65249142225
-
Comparison of ligand- and structure-based virtual screening on the DUD data set
-
von Korff, M.; Freyss, J.; Sander, T. Comparison of ligand- and structure-based virtual screening on the DUD data set J. Chem. Inf. Model. 2009, 49, 209-231
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 209-231
-
-
Von Korff, M.1
Freyss, J.2
Sander, T.3
-
11
-
-
77954054470
-
-
Version 2.4.2; OpenEye Scientific Software: Santa Fe, NM
-
ROCS, Version 2.4.2; OpenEye Scientific Software: Santa Fe, NM, 2009.
-
(2009)
ROCS
-
-
-
12
-
-
65249167560
-
Shaep: Molecular overlay based on shape and electrostatic potential
-
Vainio, M. J.; Puranen, J. S.; Johnson, M. S. Shaep: molecular overlay based on shape and electrostatic potential J. Chem. Inf. Model. 2009, 49, 492-502
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 492-502
-
-
Vainio, M.J.1
Puranen, J.S.2
Johnson, M.S.3
-
13
-
-
0030203710
-
Distributed automated docking of flexible ligands to proteins: Parallel applications of autodock 2.4
-
Morris, G. M.; Goodsell, D. S.; Huey, R.; Olson, A. J. Distributed automated docking of flexible ligands to proteins: Parallel applications of autodock 2.4 J. Comput.-Aided Mol. Des. 1996, 10, 293-304
-
(1996)
J. Comput.-Aided Mol. Des.
, vol.10
, pp. 293-304
-
-
Morris, G.M.1
Goodsell, D.S.2
Huey, R.3
Olson, A.J.4
-
14
-
-
77954052728
-
-
Version 5.5; Schrödinger, LLC: New York
-
Glide, Version 5.5; Schrödinger, LLC: New York, 2009.
-
(2009)
Glide
-
-
-
15
-
-
0041919542
-
Improved protein-ligand docking using gold
-
Verdonk, M. L.; Cole, J. C.; Hartshorn, M. J.; Murray, C. W.; Taylor, R. D. Improved protein-ligand docking using gold Proteins 2003, 52, 609-623
-
(2003)
Proteins
, vol.52
, pp. 609-623
-
-
Verdonk, M.L.1
Cole, J.C.2
Hartshorn, M.J.3
Murray, C.W.4
Taylor, R.D.5
-
16
-
-
0346665839
-
Gaussian docking functions
-
McGann, M. R.; Almond, H. R.; Nicholls, A.; Grant, J. A.; Brown, F. K. Gaussian docking functions Biopolymers 2003, 68, 76-90
-
(2003)
Biopolymers
, vol.68
, pp. 76-90
-
-
McGann, M.R.1
Almond, H.R.2
Nicholls, A.3
Grant, J.A.4
Brown, F.K.5
-
17
-
-
44949173950
-
Assessment of scaffold hopping efficiency by use of molecular interaction fingerprints
-
Venhorst, J.; Núñez, S.; Terpstra, J. W.; Kruse, C. G. Assessment of scaffold hopping efficiency by use of molecular interaction fingerprints J. Med. Chem. 2008, 51, 3222-3229
-
(2008)
J. Med. Chem.
, vol.51
, pp. 3222-3229
-
-
Venhorst, J.1
Núñez, S.2
Terpstra, J.W.3
Kruse, C.G.4
-
18
-
-
0028158936
-
Ligand docking to proteins with discrete side-chain flexibility
-
Leach, A. R. Ligand docking to proteins with discrete side-chain flexibility J. Mol. Biol. 1994, 235, 345-356
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 345-356
-
-
Leach, A.R.1
-
19
-
-
0031581852
-
Molecular docking to ensembles of protein structures
-
Knegtel, R. M.; Kuntz, I. D.; Oshiro, C. M. Molecular docking to ensembles of protein structures J. Mol. Biol. 1997, 266, 424-440
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 424-440
-
-
Knegtel, R.M.1
Kuntz, I.D.2
Oshiro, C.M.3
-
20
-
-
0033135477
-
Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation
-
Mangoni, M.; Roccatano, D.; Di Nola, A. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation Proteins 1999, 35, 153-162
-
(1999)
Proteins
, vol.35
, pp. 153-162
-
-
Mangoni, M.1
Roccatano, D.2
Di Nola, A.3
-
21
-
-
21644473891
-
Representing receptor flexibility in ligand docking through relevant normal modes
-
Cavasotto, C. N.; Kovacs, J. A.; Abagyan, R. A. Representing receptor flexibility in ligand docking through relevant normal modes J. Am. Chem. Soc. 2005, 127, 9632-9640
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 9632-9640
-
-
Cavasotto, C.N.1
Kovacs, J.A.2
Abagyan, R.A.3
-
22
-
-
33750991346
-
Benchmarking sets for molecular docking
-
Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking sets for molecular docking J. Med. Chem. 2006, 49, 6789-6801
-
(2006)
J. Med. Chem.
, vol.49
, pp. 6789-6801
-
-
Huang, N.1
Shoichet, B.K.2
Irwin, J.J.3
-
23
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
24
-
-
33748538349
-
Automatic atom type and bond type perception in molecular mechanical calculations
-
Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations J. Mol. Graphics Modell. 2006, 25, 247-260
-
(2006)
J. Mol. Graphics Modell.
, vol.25
, pp. 247-260
-
-
Wang, J.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
25
-
-
77954059553
-
-
Version 2.1; Schrödinger, LLC: New York
-
ConfGen, Version 2.1; Schrödinger, LLC: New York, 2009.
-
(2009)
ConfGen
-
-
-
26
-
-
0342424187
-
Fast prediction and visualization of protein binding pockets with pass
-
Brady, G. P. J.; Stouten, P. F. Fast prediction and visualization of protein binding pockets with pass J. Comput.-Aided Mol. Des. 2000, 14, 383-401
-
(2000)
J. Comput.-Aided Mol. Des.
, vol.14
, pp. 383-401
-
-
Brady, G.P.J.1
Stouten, P.F.2
-
27
-
-
0027995683
-
Detection, delineation, measurement and display of cavities in macromolecular structures
-
Kleywegt, G. J.; Jones, T. A. Detection, delineation, measurement and display of cavities in macromolecular structures Acta Crystallogr., Sect. D: Biol. Crystallogr. 1994, 50, 178-185
-
(1994)
Acta Crystallogr., Sect. D: Biol. Crystallogr.
, vol.50
, pp. 178-185
-
-
Kleywegt, G.J.1
Jones, T.A.2
-
28
-
-
19944426826
-
Bodil: A molecular modeling environment for structure-function analysis and drug design
-
Lehtonen, J. V.; Still, D.; Rantanen, V.; Ekholm, J.; Björklund, D.; Iftikhar, Z.; Huhtala, M.; Repo, S.; Jussila, A.; Jaakkola, J.; Pentikäinen, O.; Nyrönen, T.; Salminen, T.; Gyllenberg, M.; Johnson, M. S. Bodil: a molecular modeling environment for structure-function analysis and drug design J. Comput.-Aided Mol. Des. 2004, 18, 401-419
-
(2004)
J. Comput.-Aided Mol. Des.
, vol.18
, pp. 401-419
-
-
Lehtonen, J.V.1
Still, D.2
Rantanen, V.3
Ekholm, J.4
Björklund, D.5
Iftikhar, Z.6
Huhtala, M.7
Repo, S.8
Jussila, A.9
Jaakkola, J.10
Pentikäinen, O.11
Nyrönen, T.12
Salminen, T.13
Gyllenberg, M.14
Johnson, M.S.15
-
29
-
-
27344436659
-
Scalable molecular dynamics with namd
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. Scalable molecular dynamics with namd J. Comput. Chem. 2005, 26, 1781-1802
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kalé, L.9
Schulten, K.10
-
30
-
-
72149121816
-
Exploring kainate receptor pharmacology using molecular dynamics simulations
-
Postila, P. A.; Swanson, G. T.; Pentikäinen, O. T. Exploring kainate receptor pharmacology using molecular dynamics simulations Neuropharmacology 2010, 58, 515-527
-
(2010)
Neuropharmacology
, vol.58
, pp. 515-527
-
-
Postila, P.A.1
Swanson, G.T.2
Pentikäinen, O.T.3
-
31
-
-
13844312649
-
ZINC - A free database of commercially available compounds for virtual screening
-
Irwin, J. J.; Shoichet, B. K. ZINC - A free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 2005, 45, 177-182
-
(2005)
J. Chem. Inf. Model.
, vol.45
, pp. 177-182
-
-
Irwin, J.J.1
Shoichet, B.K.2
-
32
-
-
77954039266
-
-
Version 9.0; Schrödinger, LLC: New York
-
Maestro, Version 9.0; Schrödinger, LLC: New York, 2009.
-
(2009)
Maestro
-
-
-
33
-
-
0020083498
-
The meaning and use of the area under a receiver operating characteristic (ROC) curve
-
Hanley, J. A.; McNeil, B. J. The meaning and use of the area under a receiver operating characteristic (ROC) curve Radiology 1982, 143, 29-36
-
(1982)
Radiology
, vol.143
, pp. 29-36
-
-
Hanley, J.A.1
McNeil, B.J.2
-
34
-
-
0026244229
-
Molscript: A program to produce both detailed and schematic plots of protein structures
-
Kraulis, P. J. Molscript: A program to produce both detailed and schematic plots of protein structures J. Appl. Crystallogr. 1991, 24, 946-950
-
(1991)
J. Appl. Crystallogr.
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
35
-
-
0030815133
-
Raster3d: Photorealistic molecular graphics
-
Merritt, E. A.; Bacon, D. J. Raster3d: Photorealistic molecular graphics Methods Enzymol. 1997, 277, 505-524
-
(1997)
Methods Enzymol.
, vol.277
, pp. 505-524
-
-
Merritt, E.A.1
Bacon, D.J.2
-
36
-
-
0034521981
-
Calculating structures and free energies of complex molecules combining molecular mechanics and continuum models
-
Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. Calculating structures and free energies of complex molecules combining molecular mechanics and continuum models Acc. Chem. Res. 2000, 33, 889-897
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham, T.E.15
-
37
-
-
44449165575
-
Novel approach to structure-based pharmacophore search using computational geometry and shape matching techniques
-
Ebalunode, J. O.; Ouyang, Z.; Liang, J.; Zheng, W. Novel approach to structure-based pharmacophore search using computational geometry and shape matching techniques J. Chem. Inf. Model. 2008, 48, 889-901
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 889-901
-
-
Ebalunode, J.O.1
Ouyang, Z.2
Liang, J.3
Zheng, W.4
-
38
-
-
72949097266
-
Improving virtual screening performance against conformational variations of receptors by shape matching with ligand binding pocket
-
Lee, H. S.; Lee, C. S.; Kim, J. S.; Kim, D. H.; Choe, H. Improving virtual screening performance against conformational variations of receptors by shape matching with ligand binding pocket J. Chem. Inf. Model. 2009, 49, 2419-2428
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 2419-2428
-
-
Lee, H.S.1
Lee, C.S.2
Kim, J.S.3
Kim, D.H.4
Choe, H.5
|