-
1
-
-
0023751431
-
Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins
-
Cramer, R. D.; Patterson, D. E.; Bunce, J. D. Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins J. Am. Chem. Soc. 1988, 110, 5959-5967
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 5959-5967
-
-
Cramer, R.D.1
Patterson, D.E.2
Bunce, J.D.3
-
2
-
-
0034065350
-
Computational methods for the structural alignment of molecules
-
DOI 10.1023/A:1008194019144
-
Lemmen, C.; Langauer, T. Computational Methods for the Structural Alignment of Molecules J. Comput.-Aided Mol. Des. 2000, 14, 215-232 (Pubitemid 30175941)
-
(2000)
Journal of Computer-Aided Molecular Design
, vol.14
, Issue.3
, pp. 215-232
-
-
Lemmen, C.1
Lengauer, T.2
-
3
-
-
73349132036
-
Multiobjective Optimization of Pharmacophore Hypotheses: Bias Toward Low-Energy Conformations
-
Gardiner, E. J.; Cosgrove, D. A.; Taylor, R.; Gillet, V. J. Multiobjective Optimization of Pharmacophore Hypotheses: Bias Toward Low-Energy Conformations J. Chem. Inf. Model. 2009, 49, 2761-2773
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 2761-2773
-
-
Gardiner, E.J.1
Cosgrove, D.A.2
Taylor, R.3
Gillet, V.J.4
-
4
-
-
69549103257
-
Flexible Alignment of Small Molecules Using the Penalty Method
-
Shin, W.; Hyun, S. A.; Chae, C. H.; Chon, J. K. Flexible Alignment of Small Molecules Using the Penalty Method J. Chem. Inf. Model. 2009, 49, 1879-1888
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1879-1888
-
-
Shin, W.1
Hyun, S.A.2
Chae, C.H.3
Chon, J.K.4
-
5
-
-
52049125711
-
Pharao: Pharmacophore Alignment and Optimization
-
Taminau, J.; Thijs, G.; de Winter, H. Pharao: Pharmacophore Alignment and Optimization J. Mol. Graphics Modell. 2008, 27, 161-169
-
(2008)
J. Mol. Graphics Modell.
, vol.27
, pp. 161-169
-
-
Taminau, J.1
Thijs, G.2
De Winter, H.3
-
6
-
-
37649005977
-
Shapelets: Possibilities and Limitations of Shape-Based Virtual Screening
-
Proschak, E.; Rupp, M.; Derksen, S.; Schneider, G. Shapelets: Possibilities and Limitations of Shape-Based Virtual Screening J. Comput. Chem. 2008, 29, 108-114
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 108-114
-
-
Proschak, E.1
Rupp, M.2
Derksen, S.3
Schneider, G.4
-
7
-
-
34250801603
-
QUASI: A Novel Method for Simultaneous Superposition of Multiple Flexible Ligands and Virtual Screening Using Partial Similarity
-
Todorov, N. P.; Alberts, I. L.; de Esch, I. J. P.; Dean, P. M. QUASI: A Novel Method for Simultaneous Superposition of Multiple Flexible Ligands and Virtual Screening Using Partial Similarity J. Chem. Inf. Model. 2007, 47, 1007-1020
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 1007-1020
-
-
Todorov, N.P.1
Alberts, I.L.2
De Esch, I.J.P.3
Dean, P.M.4
-
8
-
-
34247208044
-
Graph-based Molecular Alignment (GMA)
-
DOI 10.1021/ci600387r
-
Marialke, J.; Körner, R.; Tietze, S.; Apostolakis, J. Graph-Based Molecular Alignment (GMA) J. Chem. Inf. Model. 2007, 47, 591-601 (Pubitemid 46615960)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.2
, pp. 591-601
-
-
Marialke, J.1
Korner, R.2
Tietze, S.3
Apostolakis, J.4
-
9
-
-
33947599081
-
Efficient overlay of small organic molecules using 3D pharmacophores
-
DOI 10.1007/s10822-006-9078-7, Advances in Phatmacophores and 3-D Screening
-
Wolber, G.; Dornhofer, A. A.; Langer, T. Efficient Overlay of Small Organic Molecules Using 3D Pharmacophores J. Comput.-Aided Mol. Des. 2006, 20, 773-788 (Pubitemid 46476946)
-
(2006)
Journal of Computer-Aided Molecular Design
, vol.20
, Issue.12
, pp. 773-788
-
-
Wolber, G.1
Dornhofer, A.A.2
Langer, T.3
-
10
-
-
34249022980
-
GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D
-
DOI 10.1007/s10822-006-9082-y
-
Richmond, N. J.; Abrams, C. A.; Wolohan, P. R. N.; Abrahamian, E.; Willett, P.; Clark, R. D. GALAHAD: 1. Pharmacophore Identification by Hypermolecular Alignment of Ligands in 3D J. Comput.-Aided Mol. Des. 2006, 20, 567-587 (Pubitemid 44823892)
-
(2006)
Journal of Computer-Aided Molecular Design
, vol.20
, Issue.9
, pp. 567-587
-
-
Richmond, N.J.1
Abrams, C.A.2
Wolohan, P.R.N.3
Abrahamian, E.4
Willett, P.5
Clark, R.D.6
-
11
-
-
33646227896
-
Molecular Field Extrema as Descriptors of Biological Activity: Definition and Validation
-
Cheeseright, T.; Mackey, M.; Rose, S.; Vinter, A. Molecular Field Extrema as Descriptors of Biological Activity: Definition and Validation J. Chem. Inf. Model. 2006, 46, 665-676
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 665-676
-
-
Cheeseright, T.1
MacKey, M.2
Rose, S.3
Vinter, A.4
-
13
-
-
33748250857
-
BRUTUS: Optimization of a grid-based similarity function for rigid-body molecular superposition. II. Description and characterization
-
DOI 10.1007/s10822-006-9052-4
-
Rönkkö, T.; Tervo, A. J.; Parkkinen, J.; Poso, A. BRUTUS: Optimization of a Grid-Based Similarity Function for Rigid-Body Molecular Superposition. II. Description and Characterization J. Comput.-Aided Mol. Des. 2006, 20, 227-236 (Pubitemid 44317515)
-
(2006)
Journal of Computer-Aided Molecular Design
, vol.20
, Issue.4
, pp. 227-236
-
-
Rokko, T.1
Tervo, A.J.2
Parkkinen, J.3
Poso, A.4
-
14
-
-
33745427398
-
PharmID: Pharmacophore identification using gibbs sampling
-
DOI 10.1021/ci050427v
-
Feng, J.; Sanil, A.; Young, S. S. PharmID: Pharmacophore Identification Using Gibbs Sampling J. Chem. Inf. Model 2006, 46, 1352-1359 (Pubitemid 43999178)
-
(2006)
Journal of Chemical Information and Modeling
, vol.46
, Issue.3
, pp. 1352-1359
-
-
Feng, J.1
Sanil, A.2
Stanley Young, S.3
-
15
-
-
14944348527
-
A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction
-
DOI 10.1021/jm040163o
-
Rush, T. S.; 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 (Pubitemid 40364556)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.5
, pp. 1489-1495
-
-
Rush III, T.S.1
Grant, J.A.2
Mosyak, L.3
Nicholls, A.4
-
16
-
-
0035837073
-
Flexible alignment of small molecules
-
DOI 10.1021/jm0002634
-
Labute, P.; Williams, C.; Feher, M.; Sourial, E.; Schmidt, J. M. Flexible Alignment of Small Molecules J. Med. Chem. 2001, 44, 1483-1490 (Pubitemid 32852192)
-
(2001)
Journal of Medicinal Chemistry
, vol.44
, Issue.10
, pp. 1483-1490
-
-
Labute, P.1
Williams, C.2
-
17
-
-
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 (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, 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
-
18
-
-
0033965404
-
A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors. 2. The relationship between alignment solutions obtained from conformationally rigid and flexible matching
-
DOI 10.1023/A:1008168228728
-
Mestres, J.; Rohrer, D. C.; Maggiora, G. M. A Molecular-Field-Based Similarity Study of Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors. 2. The Relationship Between Alignment Solutions Obtained from Conformationally Rigid and Flexible Matching J. Comput.-Aided Mol. Des. 2000, 14, 39-51 (Pubitemid 30103821)
-
(2000)
Journal of Computer-Aided Molecular Design
, vol.14
, Issue.1
, pp. 39-51
-
-
Mestres, J.1
Rohrer, D.C.2
Maggiora, G.M.3
-
19
-
-
0033529045
-
SQ: A Program for Rapidly Producing Pharmacophorically Relevent Molecular Superpositions
-
Miller, M. D.; Sheridan, R. P.; Kearsley, S. K. SQ: A Program for Rapidly Producing Pharmacophorically Relevent Molecular Superpositions J. Med. Chem. 1999, 42, 1505-1514
-
(1999)
J. Med. Chem.
, vol.42
, pp. 1505-1514
-
-
Miller, M.D.1
Sheridan, R.P.2
Kearsley, S.K.3
-
20
-
-
44949267284
-
An Alternative Method for the Alignment of Molecular Structures: Maximizing Electrostatic and Steric Overlap
-
Kearsley, S. K.; Smith, G. M. An Alternative Method for the Alignment of Molecular Structures: Maximizing Electrostatic and Steric Overlap Tetrahedron Comput. Methodol. 1990, 3, 615-633
-
(1990)
Tetrahedron Comput. Methodol.
, vol.3
, pp. 615-633
-
-
Kearsley, S.K.1
Smith, G.M.2
-
21
-
-
0029320502
-
Flexible Matching of Test Ligands to a 3D Pharmacophore Using a Molecular Superposition Force Field: Comparison of Predicted and Experimental Conformations of Inhibitors of Three Enzymes
-
McMartin, C.; Bohacek, R. S. Flexible Matching of Test Ligands to a 3D Pharmacophore Using a Molecular Superposition Force Field: Comparison of Predicted and Experimental Conformations of Inhibitors of Three Enzymes J. Comput.-Aided Mol. Des. 1995, 9, 237-250
-
(1995)
J. Comput.-Aided Mol. Des.
, vol.9
, pp. 237-250
-
-
McMartin, C.1
Bohacek, R.S.2
-
22
-
-
77957230161
-
-
Chemical Computing Group: Montreal, Quebec, Canada
-
MOE; Chemical Computing Group: Montreal, Quebec, Canada, 2009.
-
(2009)
MOE
-
-
-
23
-
-
33750290951
-
Geometric accuracy of three-dimensional molecular overlays
-
DOI 10.1021/ci060134h
-
Chen, Q.; Higgs, R. E.; Vieth, M. Geometric Accuracy of Three-Dimensional Molecular Overlays J. Chem. Inf. Model. 2006, 46, 1996-2002 (Pubitemid 44625971)
-
(2006)
Journal of Chemical Information and Modeling
, vol.46
, Issue.5
, pp. 1996-2002
-
-
Chen, Q.1
Higgs, R.E.2
Vieth, M.3
-
24
-
-
2942708194
-
SURFCOMP: A Novel Graph-Based Approach to Molecular Surface Comparison
-
Hofbauer, C.; Lohninger, H.; Aszódi, A. SURFCOMP: A Novel Graph-Based Approach to Molecular Surface Comparison J. Chem. Inf. Comput. Sci. 2004, 44, 837-847
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 837-847
-
-
Hofbauer, C.1
Lohninger, H.2
Aszódi, A.3
-
25
-
-
0033921932
-
A Novel Method of Aligning Molecules by Local Surface Shape Similarity
-
Cosgrove, D. A.; Bayada, D. M.; Johnson, A. P. A Novel Method of Aligning Molecules by Local Surface Shape Similarity J. Comput.-Aided Mol. Des. 2000, 14, 573-591
-
(2000)
J. Comput.-Aided Mol. Des.
, vol.14
, pp. 573-591
-
-
Cosgrove, D.A.1
Bayada, D.M.2
Johnson, A.P.3
-
26
-
-
77957231844
-
-
OpenEye Scientific Software: Santa Fe, NM
-
ROCS; OpenEye Scientific Software: Santa Fe, NM, 2005.
-
(2005)
ROCS
-
-
-
27
-
-
0032488013
-
FLEXS: A method for fast flexible ligand superposition
-
DOI 10.1021/jm981037l
-
Lemmen, C.; Lengauer, T.; Klebe, G. FLEXS: A Method for Fast Flexible Ligand Superposition J. Med. Chem. 1998, 41, 4502-4520 (Pubitemid 28516449)
-
(1998)
Journal of Medicinal Chemistry
, vol.41
, Issue.23
, pp. 4502-4520
-
-
Lemmen, C.1
Lengauer, T.2
Klebe, G.3
-
28
-
-
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
-
29
-
-
17144385534
-
Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4
-
DOI 10.1021/jm049092j
-
Triballeau, N.; Acher, F.; Brabet, I.; Pin, J.-P.; Bertrand, H.-O. Virtual Screening Workflow Development Guided by the "Receiver Operating Characteristic" Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4 J. Med. Chem. 2005, 48, 2534-2547 (Pubitemid 40520517)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.7
, pp. 2534-2547
-
-
Triballeau, N.1
Acher, F.2
Brabet, I.3
Pin, J.-P.4
Bertrand, H.-O.5
-
30
-
-
0001242234
-
MMFF VII. Characterization of MMFF94, MMFF94s, and Other Widely Available Force Fields for Conformational Energies and for Intermolecular-interaction Energies and Geometries
-
Halgren, T. A. MMFF VII. Characterization of MMFF94, MMFF94s, and Other Widely Available Force Fields for Conformational Energies and for Intermolecular-interaction Energies and Geometries J. Comput. Chem. 1999, 20, 730-748
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 730-748
-
-
Halgren, T.A.1
-
31
-
-
56149110450
-
Towards More Accurate Pharmacophore Modeling: Multicomplex-Based Comprehensive Pharmacophore Map and Most-Frequent-Feature Pharmacophore Model of CDK2
-
Zou, J.; Xie, H.-Z.; Yang, S.-Y.; Chen, J.-J.; Ren, J.-X.; Wei, Y.-Q. Towards More Accurate Pharmacophore Modeling: Multicomplex-Based Comprehensive Pharmacophore Map and Most-Frequent-Feature Pharmacophore Model of CDK2 J. Mol. Graphics Modell. 2008, 27, 430-438
-
(2008)
J. Mol. Graphics Modell.
, vol.27
, pp. 430-438
-
-
Zou, J.1
Xie, H.-Z.2
Yang, S.-Y.3
Chen, J.-J.4
Ren, J.-X.5
Wei, Y.-Q.6
-
32
-
-
0024454604
-
Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses
-
Badger, J.; Minor, I.; Oliveira, M. A.; Smith, T. J.; Rossmann, M. G. Structural Analysis of Antiviral Agents that Interact with the Capsid of Human Rhinoviruses Proteins 1989, 6, 1-19 (Pubitemid 19263658)
-
(1989)
Proteins: Structure, Function and Genetics
, vol.6
, Issue.1
, pp. 1-19
-
-
Badger, J.1
Minor, I.2
Oliveira, M.A.3
Smith, T.J.4
Rossmann, M.G.5
|