-
1
-
-
33644861784
-
Diversity in medicinal chemistry space
-
Gorse, A. D. Diversity in medicinal chemistry space Curr. Top. Med. Chem. 2006, 6, 3-18
-
(2006)
Curr. Top. Med. Chem.
, vol.6
, pp. 3-18
-
-
Gorse, A.D.1
-
2
-
-
78650352933
-
Quo vadis, virtual screening? A comprehensive survey of prospective applications
-
Ripphausen, P.; Nisius, B.; Peltason, L.; Bajorath, J. Quo vadis, virtual screening? A comprehensive survey of prospective applications J. Med. Chem. 2010, 53, 8461-8467
-
(2010)
J. Med. Chem.
, vol.53
, pp. 8461-8467
-
-
Ripphausen, P.1
Nisius, B.2
Peltason, L.3
Bajorath, J.4
-
3
-
-
34548288600
-
Virtual screening in drug discovery - A computational perspective
-
Reddy, A. S.; Pati, S. P.; Kumar, P. P.; Pradeep, H. N.; Sastry, G. N. Virtual screening in drug discovery-a computational perspective Curr. Protein. Pept. Sci. 2007, 8, 329-351
-
(2007)
Curr. Protein. Pept. Sci.
, vol.8
, pp. 329-351
-
-
Reddy, A.S.1
Pati, S.P.2
Kumar, P.P.3
Pradeep, H.N.4
Sastry, G.N.5
-
4
-
-
61949166066
-
How similar are similarity searching methods? A principal component analysis of molecular descriptor space
-
Bender, A.; Jenkins, J. L.; Scheiber, J.; Sukuru, S. C. K.; Glick, M.; Davies, J. W. How similar are similarity searching methods? A principal component analysis of molecular descriptor space J. Chem. Inf. Model. 2009, 49, 108-119
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 108-119
-
-
Bender, A.1
Jenkins, J.L.2
Scheiber, J.3
Sukuru, S.C.K.4
Glick, M.5
Davies, J.W.6
-
5
-
-
0037068532
-
Do structurally similar molecules have similar biological activity?
-
Martin, Y. C.; Kofron, J. L.; Traphagen, L. M. Do structurally similar molecules have similar biological activity? J. Med. Chem. 2002, 45, 4350-4358
-
(2002)
J. Med. Chem.
, vol.45
, pp. 4350-4358
-
-
Martin, Y.C.1
Kofron, J.L.2
Traphagen, L.M.3
-
6
-
-
0029783934
-
Neighborhood behavior: A useful concept for validation of "molecular diversity" descriptors
-
Patterson, D. E.; Cramer, R. D.; Ferguson, A. M.; Clark, R. D.; Weinberger, L. E. Neighborhood behavior: A useful concept for validation of "molecular diversity" descriptors J. Med. Chem. 1996, 39, 3049-3059
-
(1996)
J. Med. Chem.
, vol.39
, pp. 3049-3059
-
-
Patterson, D.E.1
Cramer, R.D.2
Ferguson, A.M.3
Clark, R.D.4
Weinberger, L.E.5
-
7
-
-
10344230435
-
Molecular similarity: A key technique in molecular informatics
-
Bender, A.; Glen, R. C. Molecular similarity: A key technique in molecular informatics Org. Biomol. Chem. 2004, 2, 3204-3218
-
(2004)
Org. Biomol. Chem.
, vol.2
, pp. 3204-3218
-
-
Bender, A.1
Glen, R.C.2
-
8
-
-
1042265247
-
Approaches to measure chemical similarity - A review
-
Nikolova, N.; Jaworska, J. Approaches to measure chemical similarity-A review Qsar. Comb. Sci. 2004, 22, 1006-1026
-
(2004)
Qsar. Comb. Sci.
, vol.22
, pp. 1006-1026
-
-
Nikolova, N.1
Jaworska, J.2
-
9
-
-
0037008160
-
Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
-
Gohlke, H.; Klebe, G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors Angew. Chem., Int. Ed. 2002, 41, 2645-2676
-
(2002)
Angew. Chem., Int. Ed.
, vol.41
, pp. 2645-2676
-
-
Gohlke, H.1
Klebe, G.2
-
10
-
-
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
-
11
-
-
0030598347
-
Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking
-
Meyer, M.; Wilson, P.; Schomburg, D. Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking J. Mol. Biol. 1996, 264, 199-210
-
(1996)
J. Mol. Biol.
, vol.264
, pp. 199-210
-
-
Meyer, M.1
Wilson, P.2
Schomburg, D.3
-
12
-
-
0038457635
-
Shape and similarity: Two aspects of molecular recognition
-
Amovilli, C. Shape and similarity: Two aspects of molecular recognition J. Mol. Struct.-THEOCHEM 1991, 227, 1-9
-
(1991)
J. Mol. Struct.-THEOCHEM
, vol.227
, pp. 1-9
-
-
Amovilli, C.1
-
13
-
-
84863097556
-
The good, the bad and the twisted: A survey of ligand geometry in protein crystal structures
-
Liebeschuetz, J.; Hennemann, J.; Olsson, T.; Groom, C. R. The good, the bad and the twisted: A survey of ligand geometry in protein crystal structures J. Comput.-Aided Mol. Des. 2012, 26, 169-183
-
(2012)
J. Comput.-Aided Mol. Des.
, vol.26
, pp. 169-183
-
-
Liebeschuetz, J.1
Hennemann, J.2
Olsson, T.3
Groom, C.R.4
-
14
-
-
1642492947
-
Molecular shape, dimensions, and shape selective catalysis
-
Tasi, G.; Palinko, I.; Molnar, A.; Hannus, I. Molecular shape, dimensions, and shape selective catalysis J. Mol. Struct.-THEOCHEM 2003, 666, 69-77
-
(2003)
J. Mol. Struct.-THEOCHEM
, vol.666
, pp. 69-77
-
-
Tasi, G.1
Palinko, I.2
Molnar, A.3
Hannus, I.4
-
15
-
-
77952716960
-
Molecular shape and medicinal chemistry: A perspective
-
Nicholls, A.; McGaughey, G. B.; Sheridan, R. P.; Good, A. C.; Warren, G.; Mathieu, M.; Muchmore, S. W.; Brown, S. P.; Grant, J. A.; Haigh, J. A.; Nevins, N.; Jain, A. N.; Kelley, B. Molecular shape and medicinal chemistry: A perspective J. Med. Chem. 2010, 53, 3862-3886
-
(2010)
J. Med. Chem.
, vol.53
, pp. 3862-3886
-
-
Nicholls, A.1
McGaughey, G.B.2
Sheridan, R.P.3
Good, A.C.4
Warren, G.5
Mathieu, M.6
Muchmore, S.W.7
Brown, S.P.8
Grant, J.A.9
Haigh, J.A.10
Nevins, N.11
Jain, A.N.12
Kelley, B.13
-
16
-
-
0029902763
-
Computational methods for biomolecular docking
-
Lengauer, T.; Rarey, M. Computational methods for biomolecular docking Curr. Opin. Struct. Biol. 1996, 6, 402-406
-
(1996)
Curr. Opin. Struct. Biol.
, vol.6
, pp. 402-406
-
-
Lengauer, T.1
Rarey, M.2
-
17
-
-
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
-
18
-
-
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
-
19
-
-
8844263008
-
Docking and scoring in virtual screening for drug discovery: Methods and applications
-
Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: Methods and applications Nat. Rev. Drug Discovery 2004, 3, 935-949
-
(2004)
Nat. Rev. Drug Discovery
, vol.3
, pp. 935-949
-
-
Kitchen, D.B.1
Decornez, H.2
Furr, J.R.3
Bajorath, J.4
-
20
-
-
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
-
21
-
-
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. F.; 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.F.8
Cornell, W.D.9
-
22
-
-
42149089443
-
Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligand-receptor docking
-
Perez-Nueno, V. I.; Ritchie, D. W.; Rabal, O.; Pascual, R.; Borrell, J. I.; Teixido, J. Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligand-receptor docking J. Chem. Inf. Model. 2008, 48, 509-533
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 509-533
-
-
Perez-Nueno, V.I.1
Ritchie, D.W.2
Rabal, O.3
Pascual, R.4
Borrell, J.I.5
Teixido, J.6
-
23
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
Warren, G. L.; Andrews, C. W.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A critical assessment of docking programs and scoring functions J. Med. Chem. 2006, 49, 5912-5931
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.M.3
Clarke, B.4
Lalonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
24
-
-
67650077384
-
Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins?
-
Englebienne, P.; Moitessier, N. Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins? J. Chem. Inf. Model. 2009, 49, 1568-1580
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1568-1580
-
-
Englebienne, P.1
Moitessier, N.2
-
25
-
-
84857451391
-
The errors of our ways: Taking account of error in computer-aided drug design to build confidence intervals for our next 25 years
-
Stouch, T. R. The errors of our ways: Taking account of error in computer-aided drug design to build confidence intervals for our next 25 years J. Comput.-Aided Mol. Des. 2012, 26, 125-134
-
(2012)
J. Comput.-Aided Mol. Des.
, vol.26
, pp. 125-134
-
-
Stouch, T.R.1
-
26
-
-
34547260921
-
Ultrafast shape recognition to search compound databases for similar molecular shapes
-
Ballester, P. J.; Richards, W. G. Ultrafast shape recognition to search compound databases for similar molecular shapes J. Comput. Chem. 2007, 28, 1711-1723
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 1711-1723
-
-
Ballester, P.J.1
Richards, W.G.2
-
27
-
-
61449202735
-
Ultrafast shape recognition: Evaluating a new ligand-based virtual screening technology
-
Ballester, P. J.; Finn, P. W.; Richards, W. G. Ultrafast shape recognition: Evaluating a new ligand-based virtual screening technology J. Mol. Graphics Modell. 2009, 27, 836-845
-
(2009)
J. Mol. Graphics Modell.
, vol.27
, pp. 836-845
-
-
Ballester, P.J.1
Finn, P.W.2
Richards, W.G.3
-
28
-
-
78650643212
-
Ultrafast shape recognition: Method and applications
-
Ballester, P. J. Ultrafast shape recognition: method and applications Future Med. Chem. 2011, 3, 65-78
-
(2011)
Future Med. Chem.
, vol.3
, pp. 65-78
-
-
Ballester, P.J.1
-
29
-
-
0001109246
-
A fast method of molecular shape comparison: A simple application of Gaussian descriptor of molecular shape
-
Grant, J. A.; Gallardo, M. A.; Pickup, B. T. A fast method of molecular shape comparison: A simple application of Gaussian descriptor of molecular shape J. Comput. Chem. 1996, 17, 1653-1666
-
(1996)
J. Comput. Chem.
, vol.17
, pp. 1653-1666
-
-
Grant, J.A.1
Gallardo, M.A.2
Pickup, B.T.3
-
30
-
-
84883225607
-
-
version 2.2; OpenEye Scientific Software: Santa Fe, NM.
-
ROCS, version 2.2; OpenEye Scientific Software: Santa Fe, NM, 2006.
-
(2006)
ROCS
-
-
-
31
-
-
40649089098
-
An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison
-
Mak, L.; Grandison, S.; Morris, R. J. An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison J. Mol. Graphics Modell. 2008, 26, 1035-1045
-
(2008)
J. Mol. Graphics Modell.
, vol.26
, pp. 1035-1045
-
-
Mak, L.1
Grandison, S.2
Morris, R.J.3
-
32
-
-
19544389524
-
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
-
Morris, R. J.; Najmanovich, R. J.; Kahraman, A.; Thornton, J. M. Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons Bioinformatics 2005, 21, 2347-2355
-
(2005)
Bioinformatics
, vol.21
, pp. 2347-2355
-
-
Morris, R.J.1
Najmanovich, R.J.2
Kahraman, A.3
Thornton, J.M.4
-
33
-
-
65549151866
-
Spherical-harmonic decomposition for molecular recognition in electron-density maps
-
DiMaio, F. P.; Soni, A. B.; Phillips, G. N.; Shavlik, J. W. Spherical-harmonic decomposition for molecular recognition in electron-density maps Int. J. Data Min. Bioin. 2009, 3, 205-227
-
(2009)
Int. J. Data Min. Bioin.
, vol.3
, pp. 205-227
-
-
Dimaio, F.P.1
Soni, A.B.2
Phillips, G.N.3
Shavlik, J.W.4
-
34
-
-
35248839331
-
Toward high throughput 3D virtual screening using spherical harmonic surface representations
-
Mavridis, L.; Hudson, B. D.; Ritchie, D. W. Toward high throughput 3D virtual screening using spherical harmonic surface representations J. Chem. Inf. Model. 2007, 47, 1787-1796
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 1787-1796
-
-
Mavridis, L.1
Hudson, B.D.2
Ritchie, D.W.3
-
35
-
-
84861234741
-
A novel, customizable and optimizable parameter method using spherical harmonics for molecular shape similarity comparisons
-
Cai, C.; Gong, J.; Liu, X.; Jiang, H.; Gao, D.; Li, H. A novel, customizable and optimizable parameter method using spherical harmonics for molecular shape similarity comparisons J. Mol. Model. 2012, 18, 1597-1610
-
(2012)
J. Mol. Model.
, vol.18
, pp. 1597-1610
-
-
Cai, C.1
Gong, J.2
Liu, X.3
Jiang, H.4
Gao, D.5
Li, H.6
-
36
-
-
0342424187
-
Fast prediction and visualization of protein binding pockets with PASS
-
Brady, G. P.; Stouten, P. F. W. 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.1
Stouten, P.F.W.2
-
37
-
-
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
-
38
-
-
84883250075
-
-
A Directory of Useful Decoys. (accessed Jun 13).
-
A Directory of Useful Decoys. http://dud.docking.org/ (accessed Jun 13, 2010).
-
(2010)
-
-
-
39
-
-
74049133612
-
Optimal assignment methods for ligand-based virtual screening
-
Article 14 (accessed Apr 30, 2013)
-
Jahn, A.; Hinselmann, G.; Fechner, N.; Zell, A. Optimal assignment methods for ligand-based virtual screening J. Cheminf. 2013, 1 Article 14 http://www.jcheminf.com/content/1/1/14 (accessed Apr 30, 2013)
-
(2013)
J. Cheminf.
, vol.1
-
-
Jahn, A.1
Hinselmann, G.2
Fechner, N.3
Zell, A.4
-
40
-
-
41349122416
-
Optimization of CAMD techniques 3. Virtual screening enrichment studies: A help or hindrance in tool selection?
-
Good, A. C.; Oprea, T. I. Optimization of CAMD techniques 3. Virtual screening enrichment studies: A help or hindrance in tool selection? J. Comput.-Aided Mol. Des. 2008, 22, 169-178
-
(2008)
J. Comput.-Aided Mol. Des.
, vol.22
, pp. 169-178
-
-
Good, A.C.1
Oprea, T.I.2
-
41
-
-
0037434582
-
Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine
-
Jain, A. N. Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine J. Med. Chem. 2003, 46, 499-511
-
(2003)
J. Med. Chem.
, vol.46
, pp. 499-511
-
-
Jain, A.N.1
-
42
-
-
33747818007
-
CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
-
Dundas, J.; Ouyang, Z.; Tseng, J.; Binkowski, A.; Turpaz, Y.; Liang, J. CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues Nucleic Acids Res. 2006, 34, W116-W118
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Dundas, J.1
Ouyang, Z.2
Tseng, J.3
Binkowski, A.4
Turpaz, Y.5
Liang, J.6
-
43
-
-
33646855259
-
-
version 7.5; Accelrys: San Diego, CA.
-
Pipeline Pilot, version 7.5; Accelrys: San Diego, CA, 2008.
-
(2008)
Pipeline Pilot
-
-
-
44
-
-
0000747830
-
A Gaussian description of molecular shape
-
Grant, J. A.; Pickup, B. T. A Gaussian description of molecular shape J. Phys. Chem. 1995, 99, 3503-3510
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 3503-3510
-
-
Grant, J.A.1
Pickup, B.T.2
-
45
-
-
0001458213
-
The utilisation of Gaussian functions for the rapid evaluation of molecular similarity
-
Good, A. C.; Hodgkin, E. E.; Richards, W. G. The utilisation of Gaussian functions for the rapid evaluation of molecular similarity J. Chem. Inf. Comput. Sci. 1992, 32, 188-191
-
(1992)
J. Chem. Inf. Comput. Sci.
, vol.32
, pp. 188-191
-
-
Good, A.C.1
Hodgkin, E.E.2
Richards, W.G.3
-
46
-
-
30844443282
-
Molecular similarity and diversity in chemoinformatics: From theory to applications
-
Maldonado, A. G.; Doucet, J. P.; Petitjean, M.; Fan, B. T. Molecular similarity and diversity in chemoinformatics: From theory to applications Mol. Diversity 2006, 10, 39-79
-
(2006)
Mol. Diversity
, vol.10
, pp. 39-79
-
-
Maldonado, A.G.1
Doucet, J.P.2
Petitjean, M.3
Fan, B.T.4
-
47
-
-
80054905079
-
Rapid shape-based ligand alignment and virtual screening method based on atom/feature-pair similarities and volume overlap scoring
-
Sastry, G. M.; Dixon, S. L.; Sherman, W. Rapid shape-based ligand alignment and virtual screening method based on atom/feature-pair similarities and volume overlap scoring J. Chem. Inf. Model. 2011, 51, 2455-2466
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 2455-2466
-
-
Sastry, G.M.1
Dixon, S.L.2
Sherman, W.3
-
48
-
-
77649220192
-
Current trends in ligand-based virtual screening: Molecular representations, data mining methods, new application areas, and performance evaluation
-
Geppert, H.; Vogt, M.; Bajorath, J. Current trends in ligand-based virtual screening: Molecular representations, data mining methods, new application areas, and performance evaluation J. Chem. Inf. Model. 2010, 50, 205-216
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 205-216
-
-
Geppert, H.1
Vogt, M.2
Bajorath, J.3
-
49
-
-
41349093326
-
What do we know and when do we know it?
-
Nicholls, A. What do we know and when do we know it? J. Comput.-Aided Mol. Des. 2008, 22, 239-255
-
(2008)
J. Comput.-Aided Mol. Des.
, vol.22
, pp. 239-255
-
-
Nicholls, A.1
-
50
-
-
33646023117
-
An introduction to ROC analysis
-
Fawcett, T. An introduction to ROC analysis Pattern Recog. Lett. 2006, 27, 861-874
-
(2006)
Pattern Recog. Lett.
, vol.27
, pp. 861-874
-
-
Fawcett, T.1
-
52
-
-
34247272948
-
Evaluating virtual screening methods: Good and bad metrics for the "early recognition" problem
-
Truchon, J. F.; Bayly, C. I. Evaluating virtual screening methods: Good and bad metrics for the "early recognition" problem J. Chem. Inf. Model. 2007, 47, 488-508
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 488-508
-
-
Truchon, J.F.1
Bayly, C.I.2
-
53
-
-
41349106585
-
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes?
-
Kirchmair, J.; Markt, P.; Distinto, S.; Wolber, G.; Langer, T. Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - what can we learn from earlier mistakes? J. Comput.-Aided Mol. Des. 2008, 22, 213-228
-
(2008)
J. Comput.-Aided Mol. Des.
, vol.22
, pp. 213-228
-
-
Kirchmair, J.1
Markt, P.2
Distinto, S.3
Wolber, G.4
Langer, T.5
-
54
-
-
41349106542
-
Recommendations for evaluation of computational methods
-
Jain, A. N.; Nicholls, A. Recommendations for evaluation of computational methods J. Comput.-Aided Mol. Des. 2008, 22, 133-139
-
(2008)
J. Comput.-Aided Mol. Des.
, vol.22
, pp. 133-139
-
-
Jain, A.N.1
Nicholls, A.2
-
55
-
-
66249144110
-
Better than random? The chemotype enrichment problem
-
Mackey, M. D.; Melville, J. L. Better than random? The chemotype enrichment problem J. Chem. Inf. Model. 2009, 49, 1154-1162
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1154-1162
-
-
Mackey, M.D.1
Melville, J.L.2
-
56
-
-
78650681756
-
How different are two chemical structures?
-
Marques, J. M. C.; Llanio-Trujillo, J. L.; Abreu, P. E.; Pereira, F. B. How different are two chemical structures? J. Chem. Inf. Model. 2010, 50, 2129-2140
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 2129-2140
-
-
Marques, J.M.C.1
Llanio-Trujillo, J.L.2
Abreu, P.E.3
Pereira, F.B.4
-
57
-
-
34250851446
-
Mathematical correction for fingerprint similarity measures to improve chemical retrieval
-
Swamidass, S. J.; Baldi, P. Mathematical correction for fingerprint similarity measures to improve chemical retrieval J. Chem. Inf. Model. 2007, 47, 952-964
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 952-964
-
-
Swamidass, S.J.1
Baldi, P.2
-
58
-
-
0036429879
-
Rapid evaluation of molecular shape similarity index using pairwise calculation of the nearest atomic distances
-
Kotani, T.; Higashiura, K. Rapid evaluation of molecular shape similarity index using pairwise calculation of the nearest atomic distances J. Chem. Inf. Comput. Sci. 2002, 42, 58-63
-
(2002)
J. Chem. Inf. Comput. Sci.
, vol.42
, pp. 58-63
-
-
Kotani, T.1
Higashiura, K.2
-
59
-
-
20444388307
-
Small molecule shape-fingerprints
-
Haigh, J. A.; Pickup, B. T.; Grant, J. A.; Nicholls, A. Small molecule shape-fingerprints J. Chem. Inf. Model. 2005, 45, 673-684
-
(2005)
J. Chem. Inf. Model.
, vol.45
, pp. 673-684
-
-
Haigh, J.A.1
Pickup, B.T.2
Grant, J.A.3
Nicholls, A.4
-
60
-
-
66249123260
-
APIF: A new interaction fingerprint based on atom pairs and its application to virtual screening
-
Perez-Nueno, V. I.; Rabal, O.; Borrell, J. I.; Teixido, J. APIF: A new interaction fingerprint based on atom pairs and its application to virtual screening J. Chem. Inf. Model. 2009, 49, 1245-1260
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1245-1260
-
-
Perez-Nueno, V.I.1
Rabal, O.2
Borrell, J.I.3
Teixido, J.4
-
61
-
-
77954080572
-
Comparative evaluation of 3D virtual ligand screening methods: Impact of the molecular alignment on enrichment
-
Giganti, D.; Guillemain, H.; Spadoni, J. L.; Nilges, M.; Zagury, J. F.; Montes, M. Comparative evaluation of 3D virtual ligand screening methods: Impact of the molecular alignment on enrichment J. Chem. Inf. Model. 2010, 50, 992-1004
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 992-1004
-
-
Giganti, D.1
Guillemain, H.2
Spadoni, J.L.3
Nilges, M.4
Zagury, J.F.5
Montes, M.6
-
62
-
-
0035025191
-
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
-
Ewing, T. J. A.; Makino, S.; Skillman, A. G.; Kuntz, I. D. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases J. Comput.-Aided Mol. Des. 2001, 15, 411-428
-
(2001)
J. Comput.-Aided Mol. Des.
, vol.15
, pp. 411-428
-
-
Ewing, T.J.A.1
Makino, S.2
Skillman, A.G.3
Kuntz, I.D.4
-
63
-
-
0029197510
-
Time-efficient docking of flexible ligands into active sites of proteins
-
Rarey, M.; Kramer, B.; Lengauer, T. Time-efficient docking of flexible ligands into active sites of proteins Proc. Int. Conf. Intell. Syst. Mol. Biol. 1995, 3, 300-308
-
(1995)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.3
, pp. 300-308
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
-
64
-
-
0033137131
-
Prediction of the binding energy for small molecules, peptides and proteins
-
Schapira, M.; Totrov, M.; Abagyan, R. Prediction of the binding energy for small molecules, peptides and proteins J. Mol. Recognit. 1999, 12, 177-190
-
(1999)
J. Mol. Recognit.
, vol.12
, pp. 177-190
-
-
Schapira, M.1
Totrov, M.2
Abagyan, R.3
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