-
1
-
-
84866241579
-
Early phase drug discovery: Cheminformatics and computational techniques in identifying lead series
-
Duffy, B. C.; Zhu, L.; Decornez, H.; Kitchen, D. B. Early phase drug discovery: Cheminformatics and computational techniques in identifying lead series Bioorg. Med. Chem. 2012, 20, 5324-5342
-
(2012)
Bioorg. Med. Chem.
, vol.20
, pp. 5324-5342
-
-
Duffy, B.C.1
Zhu, L.2
Decornez, H.3
Kitchen, D.B.4
-
2
-
-
0032632418
-
Molecular diversity and representativity in chemical databases
-
Bayada, D. M.; Hamersma, H.; van Geerestein, V. J. Molecular diversity and representativity in chemical databases J. Chem. Inf. Comput. Sci. 1999, 39, 1-10
-
(1999)
J. Chem. Inf. Comput. Sci.
, vol.39
, pp. 1-10
-
-
Bayada, D.M.1
Hamersma, H.2
Van Geerestein, V.J.3
-
4
-
-
33645265985
-
Clustering methods and their uses in computational chemistry
-
Lipkowitz, K. B. Boyd, D. B.
-
Downs, G. M.; Barnard, J. M. Clustering methods and their uses in computational chemistry. In Reviews in Computational Chemistry, Lipkowitz, K. B.; Boyd, D. B., Eds.; 2002; Vol. 18, pp 1-40.
-
(2002)
Reviews in Computational Chemistry
, vol.18
, pp. 1-40
-
-
Downs, G.M.1
Barnard, J.M.2
-
5
-
-
84944178665
-
Hierarchical grouping to optimize an objective function
-
Ward, J. H. Hierarchical grouping to optimize an objective function J. Am. Stat. Assoc. 1963, 58, 236
-
(1963)
J. Am. Stat. Assoc.
, vol.58
, pp. 236
-
-
Ward, J.H.1
-
7
-
-
0020787001
-
An improved algorithm for hierarchical-clustering using strong components
-
Tarjan, R. E. An improved algorithm for hierarchical-clustering using strong components Inform. Process. Lett. 1983, 17, 37-41
-
(1983)
Inform. Process. Lett.
, vol.17
, pp. 37-41
-
-
Tarjan, R.E.1
-
8
-
-
84884960411
-
Clustering compound data: Asymmetric clustering of chemical datasets
-
Lavine, B. K.
-
MacCuish, N. E.; MacCuish, J. D. Clustering compound data: Asymmetric clustering of chemical datasets. In Chemometrics and Chemoinformatics, Lavine, B. K., Ed.; 2005; Vol. 894, pp 157-171.
-
(2005)
Chemometrics and Chemoinformatics
, vol.894
, pp. 157-171
-
-
Maccuish, N.E.1
Maccuish, J.D.2
-
9
-
-
0348047467
-
A new multi-domain clustering algorithm for lead discovery that exploits ties in proximities
-
Dusseldorf, Germany, Aug 27-Sep 1, 2000; Holtje, H. D. Sippl, W. Eds
-
Nicolaou, C. A.; MacCuish, J. D.; Tamura, S. Y. A new multi-domain clustering algorithm for lead discovery that exploits ties in proximities. In Rational approaches to drug design, Proceedings of the 13th European Symposium on Quantitative Structure-Activity Relationships, Dusseldorf, Germany, Aug 27-Sep 1, 2000; Holtje, H. D.; Sippl, W., Eds; 2001; p 486-495.
-
(2001)
Rational Approaches to Drug Design, Proceedings of the 13th European Symposium on Quantitative Structure-Activity Relationships
, pp. 486-495
-
-
Nicolaou, C.A.1
Maccuish, J.D.2
Tamura, S.Y.3
-
10
-
-
84899013108
-
On spectral clustering: Analysis and an algorithm
-
Dietterich, T. G. Becker, S. Ghahramani, Z. MIT Press: Vol
-
Ng, A. Y.; Jordan, M. I.; Weiss, Y. On spectral clustering: analysis and an algorithm. In Advances in Neural Information Processing Systems; Dietterich, T. G.; Becker, S.; Ghahramani, Z., Eds.; MIT Press: 2002; Vol. 14, pp 849-856.
-
(2002)
Advances in Neural Information Processing Systems
, vol.14
, pp. 849-856
-
-
Ng, A.Y.1
Jordan, M.I.2
Weiss, Y.3
-
11
-
-
0028961335
-
SCOP - A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A. G.; Brenner, S. E.; Hubbard, T.; Chothia, C. SCOP-A structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 1995, 247, 536-540
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
12
-
-
33645523636
-
Spectral clustering of protein sequences
-
Paccanaro, A.; Casbon, J. A.; Saqi, M. A. S. Spectral clustering of protein sequences Nucleic Acids Res. 2006, 34, 1571-1580
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 1571-1580
-
-
Paccanaro, A.1
Casbon, J.A.2
Saqi, M.A.S.3
-
13
-
-
77950430912
-
SCPS: A fast implementation of a spectral method for detecting protein families on a genome-wide scale
-
Nepusz, T.; Sasidharan, R.; Paccanaro, A. SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale BMC Bioinformatics 2010, 11, 120
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 120
-
-
Nepusz, T.1
Sasidharan, R.2
Paccanaro, A.3
-
14
-
-
78650863624
-
Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms
-
Sgourakis, N. G.; Merced-Serrano, M.; Boutsidis, C.; Drineas, P.; Du, Z.; Wang, C.; Garcia, A. E. Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms J. Mol. Biol. 2011, 405, 570-583
-
(2011)
J. Mol. Biol.
, vol.405
, pp. 570-583
-
-
Sgourakis, N.G.1
Merced-Serrano, M.2
Boutsidis, C.3
Drineas, P.4
Du, Z.5
Wang, C.6
Garcia, A.E.7
-
15
-
-
84880490740
-
SC(3): Triple spectral clustering-based consensus clustering framework for class discovery from cancer gene expression profiles
-
Zhiwen, Y.; Le, L.; You, J.; Hau-San, W.; Guoqiang, H. SC(3): Triple spectral clustering-based consensus clustering framework for class discovery from cancer gene expression profiles IEEE/ACM Trans. Comput. Biol. Bioinf. 2012, 9, 1751-1765
-
(2012)
IEEE/ACM Trans. Comput. Biol. Bioinf.
, vol.9
, pp. 1751-1765
-
-
Zhiwen, Y.1
Le, L.2
You, J.3
Hau-San, W.4
Guoqiang, H.5
-
16
-
-
35248839332
-
Development of a spectral clustering method for the analysis of molecular data sets
-
Brewer, M. L. Development of a spectral clustering method for the analysis of molecular data sets J. Chem. Inf. Model. 2007, 47, 1727-1733
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 1727-1733
-
-
Brewer, M.L.1
-
17
-
-
0032121920
-
Quantitative measures of change based on feature organization: Eigenvalues and eigenvectors
-
Sarkar, S.; Boyer, K. L. Quantitative measures of change based on feature organization: Eigenvalues and eigenvectors Comput. Vis.Image Und. 1998, 71, 110-136
-
(1998)
Comput. Vis.Image Und.
, vol.71
, pp. 110-136
-
-
Sarkar, S.1
Boyer, K.L.2
-
18
-
-
58549110871
-
Discovery of novel inhibitors of Trypanosoma cruzi trans-sialidase from in silico screening
-
Neres, J.; Brewer, M. L.; Ratier, L.; Botti, H.; Buschiazzo, A.; Edwards, P. N.; Mortenson, P. N.; Charlton, M. H.; Alzari, P. M.; Frasch, A. C.; Bryce, R. A.; Douglas, K. T. Discovery of novel inhibitors of Trypanosoma cruzi trans-sialidase from in silico screening Bioorg. Med. Chem. Lett. 2009, 19, 589-596
-
(2009)
Bioorg. Med. Chem. Lett.
, vol.19
, pp. 589-596
-
-
Neres, J.1
Brewer, M.L.2
Ratier, L.3
Botti, H.4
Buschiazzo, A.5
Edwards, P.N.6
Mortenson, P.N.7
Charlton, M.H.8
Alzari, P.M.9
Frasch, A.C.10
Bryce, R.A.11
Douglas, K.T.12
-
19
-
-
84878186205
-
Fighting obesity with a sugar-based library: Discovery of novel MCH-1R antagonists by a new computational-VAST approach for exploration of GPCR binding sites
-
Heifetz, A.; Barker, O.; Verquin, G.; Wimmer, N.; Meutermans, W.; Pal, S.; Law, R. J.; Whittaker, M. Fighting obesity with a sugar-based library: discovery of novel MCH-1R antagonists by a new computational-VAST approach for exploration of GPCR binding sites J. Chem. Inf. Model. 2013, 53, 1084-1099
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 1084-1099
-
-
Heifetz, A.1
Barker, O.2
Verquin, G.3
Wimmer, N.4
Meutermans, W.5
Pal, S.6
Law, R.J.7
Whittaker, M.8
-
20
-
-
67649491053
-
Picking up the pieces with FBDD or FADD: Invest early for future success
-
Whittaker, M. Picking up the pieces with FBDD or FADD: invest early for future success Drug Discovery Today 2009, 14, 623-624
-
(2009)
Drug Discovery Today
, vol.14
, pp. 623-624
-
-
Whittaker, M.1
-
21
-
-
0000094594
-
An iteration method for the solution of the eigenvalue problem of linear differential and integral operators
-
Lanczos, C. An iteration method for the solution of the eigenvalue problem of linear differential and integral operators J. Res. Natl. Bur. Stand. 1950, 45, 255-282
-
(1950)
J. Res. Natl. Bur. Stand.
, vol.45
, pp. 255-282
-
-
Lanczos, C.1
-
24
-
-
0003474751
-
-
Cambridge University Press: Cambridge, MA
-
Press, W.; Teukolsky, S.; Vetterling, W.; Flannery, B. Numerical recipes: the art of scientific computing; Cambridge University Press: Cambridge, MA, 2007.
-
(2007)
Numerical Recipes: The Art of Scientific Computing
-
-
Press, W.1
Teukolsky, S.2
Vetterling, W.3
Flannery, B.4
-
25
-
-
0003668665
-
-
Society for Industrial and Applied Mathematics: Philadelphia, PA
-
Parlett, B. N. The symmetric eigenvalue problem; Society for Industrial and Applied Mathematics: Philadelphia, PA, 1998.
-
(1998)
The Symmetric Eigenvalue Problem
-
-
Parlett, B.N.1
-
27
-
-
0004203940
-
-
3 rd ed. Wellesley-Cambridge Press: Wellesley MA
-
Strang, G. Introduction to Linear Algebra, 3 rd ed.; Wellesley-Cambridge Press: Wellesley MA, 2003.
-
(2003)
Introduction to Linear Algebra
-
-
Strang, G.1
-
29
-
-
84919669621
-
-
(accessed Sep 30)
-
CERN COLT Matrix Package. http://acs.lbl.gov/software/colt (accessed Sep 30, 2014).
-
(2014)
CERN COLT Matrix Package
-
-
-
30
-
-
0003603793
-
-
University of Tennessee, CS-93-194
-
Berry, M.; Do, T.; OBrien, G.; Krishna, V.; Varadhan, S. SVDPACKC users guide; University of Tennessee, 1993; CS-93-194.
-
(1993)
SVDPACKC Users Guide
-
-
Berry, M.1
Do, T.2
Obrien, G.3
Krishna, V.4
Varadhan, S.5
-
32
-
-
84862192766
-
ChEMBL: A large-scale bioactivity database for drug discovery
-
Gaulton, A.; Bellis, L. J.; Bento, A. P.; Chambers, J.; Davies, M.; Hersey, A.; Light, Y.; McGlinchey, S.; Michalovich, D.; Al-Lazikani, B.; Overington, J. P. ChEMBL: a large-scale bioactivity database for drug discovery Nucleic Acids Res. 2012, 40, D1100-D1107
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 1100-D1107
-
-
Gaulton, A.1
Bellis, L.J.2
Bento, A.P.3
Chambers, J.4
Davies, M.5
Hersey, A.6
Light, Y.7
McGlinchey, S.8
Michalovich, D.9
Al-Lazikani, B.10
Overington, J.P.11
-
33
-
-
33646855259
-
-
version 7.5; Accelrys: San Diego, CA
-
Pipeline Pilot, version 7.5; Accelrys: San Diego, CA, 2010.
-
(2010)
Pipeline Pilot
-
-
-
34
-
-
0036827075
-
Reoptimization of MDL keys for use in drug discovery
-
Durant, J. L.; Leland, B. A.; Henry, D. R.; Nourse, J. G. Reoptimization of MDL keys for use in drug discovery J. Chem. Inf. Comput. Sci. 2002, 42, 1273-1280
-
(2002)
J. Chem. Inf. Comput. Sci.
, vol.42
, pp. 1273-1280
-
-
Durant, J.L.1
Leland, B.A.2
Henry, D.R.3
Nourse, J.G.4
-
35
-
-
84872194892
-
Fast rule-based bioactivity prediction using associative classification mining
-
Yu, P.; Wild, D. J. Fast rule-based bioactivity prediction using associative classification mining J. Cheminformatics 2012, 4 29
-
(2012)
J. Cheminformatics
, vol.4
, pp. 29
-
-
Yu, P.1
Wild, D.J.2
-
36
-
-
10244222365
-
Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
-
Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures Org. Biomol. Chem. 2004, 2, 3256-3266
-
(2004)
Org. Biomol. Chem.
, vol.2
, pp. 3256-3266
-
-
Hert, J.1
Willett, P.2
Wilton, D.J.3
Acklin, P.4
Azzaoui, K.5
Jacoby, E.6
Schuffenhauer, A.7
-
37
-
-
79953656228
-
Effectiveness of 2D fingerprints for scaffold hopping
-
Gardiner, E. J.; Holliday, J. D.; ODowd, C.; Willett, P. Effectiveness of 2D fingerprints for scaffold hopping Future Med. Chem. 2011, 3, 405-414
-
(2011)
Future Med. Chem.
, vol.3
, pp. 405-414
-
-
Gardiner, E.J.1
Holliday, J.D.2
Odowd, C.3
Willett, P.4
-
38
-
-
70349319569
-
Clustering files of chemical structures using the Szekely-Rizzo generalization of Wards method
-
Varin, T.; Bureau, R.; Mueller, C.; Willett, P. Clustering files of chemical structures using the Szekely-Rizzo generalization of Wards method J. Mol. Graphics Modell. 2009, 28, 187-195
-
(2009)
J. Mol. Graphics Modell.
, vol.28
, pp. 187-195
-
-
Varin, T.1
Bureau, R.2
Mueller, C.3
Willett, P.4
-
39
-
-
34250815328
-
-
Digital Chemistry: Sheffield, UK
-
BCI Software; Digital Chemistry: Sheffield, UK, 2010.
-
(2010)
BCI Software
-
-
-
40
-
-
84919634652
-
-
Daylight Chemical Information Systems: Aliso Viejo, CA
-
Daylight Software; Daylight Chemical Information Systems: Aliso Viejo, CA, 2010.
-
(2010)
Daylight Software
-
-
-
41
-
-
77952772341
-
Extended-Connectivity Fingerprints
-
Rogers, D.; Hahn, M. Extended-Connectivity Fingerprints J. Chem. Inf. Model. 2010, 50, 742-754
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 742-754
-
-
Rogers, D.1
Hahn, M.2
-
42
-
-
84919669620
-
-
Symyx Technologies Inc
-
MDL software; Symyx Technologies Inc.
-
MDL Software
-
-
-
43
-
-
84919673988
-
-
Tripos L.P. St. Louis, MO
-
Unity 4.4; Tripos L.P.: St. Louis, MO, 2003.
-
(2003)
Unity 4.4
-
-
-
44
-
-
53249137874
-
3D Pharmacophore, hierarchical methods, and 5-HT(4) receptor binding data
-
Varin, T.; Saettel, N.; Villain, J.; Lesnard, A.; Dauphin, F.; Bureau, R.; Rault, S. 3D Pharmacophore, hierarchical methods, and 5-HT(4) receptor binding data J. Enzyme Inhib. Med. Chem. 2008, 23, 593-603
-
(2008)
J. Enzyme Inhib. Med. Chem.
, vol.23
, pp. 593-603
-
-
Varin, T.1
Saettel, N.2
Villain, J.3
Lesnard, A.4
Dauphin, F.5
Bureau, R.6
Rault, S.7
-
45
-
-
0029831680
-
An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
-
Kelley, L.; Gardner, S.; Sutcliffe, M. An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies Protein Eng. Des. Sel. 1996, 9, 1063-1065
-
(1996)
Protein Eng. Des. Sel.
, vol.9
, pp. 1063-1065
-
-
Kelley, L.1
Gardner, S.2
Sutcliffe, M.3
-
46
-
-
0001288470
-
Accuracy and effectiveness of the Lanczos algorithm for the symmetric eigenproblem
-
Paige, C. C. Accuracy and effectiveness of the Lanczos algorithm for the symmetric eigenproblem Linear Algebra Appl. 1980, 34, 235-258
-
(1980)
Linear Algebra Appl.
, vol.34
, pp. 235-258
-
-
Paige, C.C.1
-
48
-
-
0003911273
-
-
Symyx Technologies Inc
-
MDL Drug Data Report; Symyx Technologies Inc.: 2006.
-
(2006)
MDL Drug Data Report
-
-
-
50
-
-
0037835585
-
Analysis and display of the size dependence of chemical similarity coefficients
-
Holliday, J. D.; Salim, N.; Whittle, M.; Willett, P. Analysis and display of the size dependence of chemical similarity coefficients J. Chem. Inf. Comput. Sci. 2003, 43, 819-828
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.43
, pp. 819-828
-
-
Holliday, J.D.1
Salim, N.2
Whittle, M.3
Willett, P.4
-
51
-
-
84880520518
-
Do not hesitate to use Tversky-and other hints for successful active analogue searches with feature count descriptors
-
Horvath, D.; Marcou, G.; Varnek, A. Do not hesitate to use Tversky-and other hints for successful active analogue searches with feature count descriptors J. Chem. Inf. Model. 2013, 53, 1543-1562
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 1543-1562
-
-
Horvath, D.1
Marcou, G.2
Varnek, A.3
-
52
-
-
46849089254
-
Recent developments in fragment-based drug discovery
-
Congreve, M.; Chessari, G.; Tisi, D.; Woodhead, A. J. Recent developments in fragment-based drug discovery J. Med. Chem. 2008, 51, 3661-3680
-
(2008)
J. Med. Chem.
, vol.51
, pp. 3661-3680
-
-
Congreve, M.1
Chessari, G.2
Tisi, D.3
Woodhead, A.J.4
-
53
-
-
85170282443
-
A density-based algorithm for discovering clusters in large spatial databases with noise
-
Portland, Oregon, USA; Simoudis, E. Han, J. Fayyad, U. M. AAAI Press: Portland, Oregon, USA
-
Ester, M.; Kriegel, H.-P.; Sander, J. A density-based algorithm for discovering clusters in large spatial databases with noise. In KDD-96, Portland, Oregon, USA; Simoudis, E.; Han, J.; Fayyad, U. M., Eds.; AAAI Press: Portland, Oregon, USA, 1996; pp 226-231.
-
(1996)
KDD-96
, pp. 226-231
-
-
Ester, M.1
Kriegel, H.-P.2
Sander, J.3
-
54
-
-
70449848686
-
Ieee Singular Value Decomposition on GPU using CUDA
-
Rome, Italy, May 23-29; IEEE: New York, Vols
-
Lahabar, S.; Narayanan, P. J. Ieee Singular Value Decomposition on GPU using CUDA. In Proceedings IEEE International Symposium on Parallel & Distributed Processing, Rome, Italy, May 23-29; IEEE: New York, 2009; Vols. 1-5, pp 840-849.
-
(2009)
Proceedings IEEE International Symposium on Parallel & Distributed Processing
, vol.15
, pp. 840-849
-
-
Lahabar, S.1
Narayanan, P.J.2
-
55
-
-
0023453329
-
Silhouettes - A graphical aid to the interpretation and validation of cluster-analysis
-
Rousseeuw, P. J. Silhouettes-a graphical aid to the interpretation and validation of cluster-analysis J. Comput. Appl. Math. 1987, 20, 53-65
-
(1987)
J. Comput. Appl. Math.
, vol.20
, pp. 53-65
-
-
Rousseeuw, P.J.1
|