-
2
-
-
0037262054
-
Ligand-protein docking: Cancer research at the interface between biology and chemistry
-
Glen, R. C.; Allen, S. C. Ligand-Protein Docking: Cancer Research at the Interface between Biology and Chemistry. Curr. Med. Chem. 2003, 10, 767-782.
-
(2003)
Curr. Med. Chem.
, vol.10
, pp. 767-782
-
-
Glen, R.C.1
Allen, S.C.2
-
3
-
-
0036520840
-
A review of protein-small molecule docking methods
-
Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. A Review of Protein-Small Molecule Docking Methods. J. Comput.-Aided. Mol. Des. 2002, 16, 151-166.
-
(2002)
J. Comput.-Aided. Mol. Des.
, vol.16
, pp. 151-166
-
-
Taylor, R.D.1
Jewsbury, P.J.2
Essex, J.W.3
-
4
-
-
0001650642
-
A good ligand is hard to find: Automated docking methods
-
Blaney, J. M.; Dixon, J. S. A Good Ligand is Hard to Find: Automated Docking Methods. Perp. Drug Discuss. Des. 1993, 1, 301-319.
-
(1993)
Perp. Drug Discuss. Des.
, vol.1
, pp. 301-319
-
-
Blaney, J.M.1
Dixon, J.S.2
-
5
-
-
0037107887
-
Structure-based virtual screening: An overview
-
Lyne, P. Structure-Based Virtual Screening: An Overview. Drug Discuss. Today. 2002, 7, 1047-1055.
-
(2002)
Drug Discuss. Today
, vol.7
, pp. 1047-1055
-
-
Lyne, P.1
-
7
-
-
3242688618
-
A validation study on the practical use of automated de novo design
-
Stahl, M.; Todorov, N. P.; James, T.; Mauser, H.; Boehm, H.-J.; Dean, P. M. A Validation Study on the Practical Use of Automated de novo Design. J. Comput.-Aided Mol. Des. 2002, 16, 459-478.
-
(2002)
J. Comput.-Aided Mol. Des.
, vol.16
, pp. 459-478
-
-
Stahl, M.1
Todorov, N.P.2
James, T.3
Mauser, H.4
Boehm, H.-J.5
Dean, P.M.6
-
8
-
-
0028493139
-
Current methods for site-directed structure generation
-
Lewis, R. A.; Leach, A. R. Current Methods for Site-Directed Structure Generation. J. Comput.-Aided Mol. Des. 1994, 8, 467-475.
-
(1994)
J. Comput.-Aided Mol. Des.
, vol.8
, pp. 467-475
-
-
Lewis, R.A.1
Leach, A.R.2
-
9
-
-
0035966871
-
Detailed analysis of scoring functions for virtual screening
-
Stahl, M.; Rarey, M. Detailed Analysis of Scoring Functions for Virtual Screening. J. Med. Chem. 2001, 44, 1035-1042.
-
(2001)
J. Med. Chem.
, vol.44
, pp. 1035-1042
-
-
Stahl, M.1
Rarey, M.2
-
10
-
-
0346962971
-
Structural interaction fingerprint (SIFt): A novel method for analysing three-dimensional proteinLigand binding interactions
-
Deng, Z.; Chuaqui, C.; Singh, J. Structural Interaction Fingerprint (SIFt): A Novel Method for Analysing Three-Dimensional ProteinLigand Binding Interactions. J. Med. Chem. 2004, 47, 337-344.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 337-344
-
-
Deng, Z.1
Chuaqui, C.2
Singh, J.3
-
11
-
-
2942519283
-
Assessment of multiple binding modes in ligand-protein docking
-
Källblad, P.; Mancera, R. L.; Todorov, N. P. Assessment of Multiple Binding Modes in Ligand-Protein Docking. J. Med. Chem. 2004, 47, 3334-3337.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 3334-3337
-
-
Källblad, P.1
Mancera, R.L.2
Todorov, N.P.3
-
12
-
-
33845379303
-
Atom pairs as molecular features in structure-activity studies: Definition and applications
-
Carhart, R. E.; Smith, D. H.; Venkataraghava, R. Atom Pairs as Molecular Features in Structure-Activity Studies: Definition and Applications. J. Chem. Inf. Comput. Sci. 1985, 25, 64-73.
-
(1985)
J. Chem. Inf. Comput. Sci.
, vol.25
, pp. 64-73
-
-
Carhart, R.E.1
Smith, D.H.2
Venkataraghava, R.3
-
13
-
-
0002728955
-
Implementation of nearest neighbour searching in an online chemical structure search system
-
Willett, P.; Winterman, V.; Bawden, D. Implementation of Nearest Neighbour Searching in an Online Chemical Structure Search System. J. Chem. Inf. Comput. Sci. 1986, 26, 36-41.
-
(1986)
J. Chem. Inf. Comput. Sci.
, vol.26
, pp. 36-41
-
-
Willett, P.1
Winterman, V.2
Bawden, D.3
-
14
-
-
33751392562
-
Molecular substructure similarity searching: Efficient retrieval in two-dimensional structure databases
-
Hagadone, T. R. Molecular Substructure Similarity Searching: Efficient Retrieval in Two-Dimensional Structure Databases. J. Chem. Inf. Comput. Sci. 1992, 32, 515-521.
-
(1992)
J. Chem. Inf. Comput. Sci.
, vol.32
, pp. 515-521
-
-
Hagadone, T.R.1
-
15
-
-
0036827080
-
Performance of similarity measures in 2D fragment-based similarity searching: Comparison of structural descriptors and similarity coefficients
-
Chen, X.; Reynolds, C. H. Performance of Similarity Measures in 2D Fragment-Based Similarity Searching: Comparison of Structural Descriptors and Similarity Coefficients. J. Chem. Inf. Comput. Sci. 2002, 42, 1407-1414.
-
(2002)
J. Chem. Inf. Comput. Sci.
, vol.42
, pp. 1407-1414
-
-
Chen, X.1
Reynolds, C.H.2
-
16
-
-
33751390853
-
Similarity searching on CAS registry substances. 1. Global molecular property and generic atom triangle geometric searching
-
Fisanick, W.; Cross, K. P.; Rusinko, A. Similarity Searching on CAS Registry Substances. 1. Global Molecular Property and Generic Atom Triangle Geometric Searching. J. Chem. Inf. Comput. Sci. 1992, 32, 664-674.
-
(1992)
J. Chem. Inf. Comput. Sci.
, vol.32
, pp. 664-674
-
-
Fisanick, W.1
Cross, K.P.2
Rusinko, A.3
-
17
-
-
0028496956
-
Similarity searching and clustering of chemical-structure databases using molecular property data
-
1994
-
Downs, G. M.; Willet, P.; Fisanick, W. 1994 Similarity Searching and Clustering of Chemical-Structure Databases Using Molecular Property Data. J. Chem. Inf. Comput. Sci. 1994, 34, 1094-1102.
-
(1994)
J. Chem. Inf. Comput. Sci.
, vol.34
, pp. 1094-1102
-
-
Downs, G.M.1
Willet, P.2
Fisanick, W.3
-
18
-
-
0001577643
-
Chemical similarity using physiochemical property descriptors
-
Kearsley, S. K.; Sallamack, S.; Fluder, E. M.; Andose, J. D.; Mosley, R. T.; Sheriden, R. P. Chemical Similarity Using Physiochemical Property Descriptors. J. Chem. Inf. Comput. Sci. 1996, 36, 118-127.
-
(1996)
J. Chem. Inf. Comput. Sci.
, vol.36
, pp. 118-127
-
-
Kearsley, S.K.1
Sallamack, S.2
Fluder, E.M.3
Andose, J.D.4
Mosley, R.T.5
Sheriden, R.P.6
-
19
-
-
0000132991
-
Similarity searching in files of three-dimensional chemical structures: Flexible field-based searching of molecular electrostatic potentials
-
Thorner, D. A.; Wild, D. J.; Willet, P.; Wright, P. M. Similarity Searching in Files of Three-Dimensional Chemical Structures: Flexible Field-Based Searching of Molecular Electrostatic Potentials. J. Chem. Inf. Comput. Sci. 1996, 36, 900-908.
-
(1996)
J. Chem. Inf. Comput. Sci.
, vol.36
, pp. 900-908
-
-
Thorner, D.A.1
Wild, D.J.2
Willet, P.3
Wright, P.M.4
-
20
-
-
0023981806
-
Determining structural similarity of chemicals using graph-theoretic indices
-
Basak, S. C.; Magnuson, V. R.; Niemi, G. J.; Regal, R. R. Determining Structural Similarity of Chemicals Using Graph-Theoretic Indices. Discrete. Appl. Math. 1988, 19, 17-44.
-
(1988)
Discrete. Appl. Math.
, vol.19
, pp. 17-44
-
-
Basak, S.C.1
Magnuson, V.R.2
Niemi, G.J.3
Regal, R.R.4
-
21
-
-
0031133147
-
Similarity measures for rational set selection and analysis of combinatorial libraries: The diverse property-derived (DPD) approach
-
Lewis, R. A.; Mason, J. S.; McLay, I. M. Similarity Measures for Rational Set Selection and Analysis of Combinatorial Libraries: The Diverse Property-Derived (DPD) Approach. J. Chem. Inf. Comput. Sci. 1997, 37, 559-614.
-
(1997)
J. Chem. Inf. Comput. Sci.
, vol.37
, pp. 559-614
-
-
Lewis, R.A.1
Mason, J.S.2
McLay, I.M.3
-
22
-
-
0342645323
-
Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection
-
Brown, R. D.; Martin, Y. C. Use of Structure-Activity Data to Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection. J. Chem. Inf. Comput. Sci. 1996, 36, 572-584.
-
(1996)
J. Chem. Inf. Comput. Sci.
, vol.36
, pp. 572-584
-
-
Brown, R.D.1
Martin, Y.C.2
-
23
-
-
5344244908
-
Chemical similarity searching
-
Willet, P. Chemical Similarity Searching. J. Chem. Inf. Comput. Sci. 1998, 38, 983-996.
-
(1998)
J. Chem. Inf. Comput. Sci.
, vol.38
, pp. 983-996
-
-
Willet, P.1
-
24
-
-
0037835585
-
Analysis and display of the size dependence of chemical similarity coefficients
-
Holliday, J. D.; Salim, N.; Whittle, M.; Willet, 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
Willet, P.4
-
25
-
-
0037362042
-
Evaluation of similarity measures for searching the dictionary of natural products database
-
Whittle, M.; Willet, P.; Klaffke, W.; van-Noort, P. Evaluation of Similarity Measures For Searching the Dictionary of Natural Products Database. J. Chem. Inf. Comput. Sci. 2003, 43, 449-457.
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.43
, pp. 449-457
-
-
Whittle, M.1
Willet, P.2
Klaffke, W.3
Van-Noort, P.4
-
26
-
-
0031226772
-
Empirical scoring functions: I. The development of a fast empirical scoring f1unction to estimate the binding affinity of ligands in receptor complexes
-
Eldridge, M.; Murray, C. W.; Auton, T. A.; Paolini, G. V.; Lee, R. P. Empirical Scoring Functions: I. The Development of a Fast Empirical Scoring Function to Estimate the Binding Affinity of Ligands in Receptor Complexes. J. Comput.-Aided Mol. Des. 1997, 11, 425-445.
-
(1997)
J. Comput.-Aided Mol. Des.
, vol.11
, pp. 425-445
-
-
Eldridge, M.1
Murray, C.W.2
Auton, T.A.3
Paolini, G.V.4
Lee, R.P.5
-
27
-
-
0033545622
-
A general fast scoring function for protein-ligand interactions: A simplified potential approach
-
Muegge, I.; Martin, Y. C. A General Fast Scoring Function for Protein-Ligand Interactions: A Simplified Potential Approach. J. Med. Chem. 1999, 42, 791-804.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 791-804
-
-
Muegge, I.1
Martin, Y.C.2
-
28
-
-
0344465830
-
A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein
-
Kelly, M. D.; Mancera, R. L. A New Method For Estimating the Importance of Hydrogen-Bonding Groups in the Binding Site of a Protein. J. Comput.-Aided Mol. Des. 2003, 17, 401-414.
-
(2003)
J. Comput.-Aided Mol. Des.
, vol.17
, pp. 401-414
-
-
Kelly, M.D.1
Mancera, R.L.2
-
29
-
-
0031261930
-
IsoStar: A library of information about nonbonded interactions
-
Bruno, I. J.; Cole, J. C.; Lommerse, J. P. M.; Rowland, R. S.; Taylor, R.; Verdonk, M. L. IsoStar: A Library of Information about Nonbonded Interactions. J. Comput.-Aided Mol. Des. 1997, 11, 525-537.
-
(1997)
J. Comput.-Aided Mol. Des.
, vol.11
, pp. 525-537
-
-
Bruno, I.J.1
Cole, J.C.2
Lommerse, J.P.M.3
Rowland, R.S.4
Taylor, R.5
Verdonk, M.L.6
-
30
-
-
0028454828
-
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
-
Bohm, H.-J. 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. 1994, 8, 243-256.
-
(1994)
J. Comput.-Aided Mol. Des.
, vol.8
, pp. 243-256
-
-
Bohm, H.-J.1
-
31
-
-
0000825481
-
A statistical method for evaluating systematic relationships
-
Sokal, R. R.; Michener. C. D. A Statistical Method for Evaluating Systematic Relationships. Univ. Kans. Sci. Bull. 1958, 38, 1409-1438
-
(1958)
Univ. Kans. Sci. Bull.
, vol.38
, pp. 1409-1438
-
-
Sokal, R.R.1
Michener, C.D.2
-
32
-
-
0038300317
-
Algorithms for computational solvent mapping of proteins
-
Kortvelyesi, T.; Dennis, S.; Silberstein, M.; Brown, L.; Vajda, S. Algorithms for Computational Solvent Mapping of Proteins. Proteins: Struct., Fund., Genet. 2003, 51, 340-351.
-
(2003)
Proteins: Struct., Fund., Genet.
, vol.51
, pp. 340-351
-
-
Kortvelyesi, T.1
Dennis, S.2
Silberstein, M.3
Brown, L.4
Vajda, S.5
-
33
-
-
10044239085
-
An elementary mathematical theory of classification and prediction
-
Tanimoto, T. T. An Elementary Mathematical Theory of Classification and Prediction. IBM Internal Report; 1958.
-
(1958)
IBM Internal Report
-
-
Tanimoto, T.T.1
-
34
-
-
0036567220
-
A modification of the jaccard-tanimoto similarity index for diverse selection of chemical compounds using binary strings
-
Fligner, M. A.; Verducci, J. S.; Blower, P. E. A Modification of the Jaccard-Tanimoto Similarity Index for Diverse Selection of Chemical Compounds Using Binary Strings. Technometrics 2002, 0, 1-10.
-
(2002)
Technometrics
, vol.0
, pp. 1-10
-
-
Fligner, M.A.1
Verducci, J.S.2
Blower, P.E.3
-
35
-
-
84944178665
-
Hierarchical grouping to optimise an objective function
-
Ward, J. H. Hierarchical Grouping to Optimise an Objective Function. J. Am. Stat. Assoc. 1963, 58, 236-244.
-
(1963)
J. Am. Stat. Assoc.
, vol.58
, pp. 236-244
-
-
Ward, J.H.1
-
36
-
-
0000930268
-
Hierarchical grouping methods and stopping rules: An evaluation
-
Mojena, R. Hierarchical Grouping Methods and Stopping Rules: An Evaluation. Comput. J. 1977, 20, 359-363.
-
(1977)
Comput. J.
, vol.20
, pp. 359-363
-
-
Mojena, R.1
-
37
-
-
1942454773
-
Ligand-protein docking using a quantum stochastic tunneling optimization method
-
Mancera, R. L.; Källblad, P.; Todorov, N. P. Ligand-Protein Docking Using A Quantum Stochastic Tunneling Optimization Method. J. Comput, Chem. 2004, 25, 858-864.
-
(2004)
J. Comput, Chem.
, vol.25
, pp. 858-864
-
-
Mancera, R.L.1
Källblad, P.2
Todorov, N.P.3
-
38
-
-
0013133162
-
A new test set for validating predictions of protein-ligand interaction
-
Nissink, J. W.; Murray, C.; Hartshorn, M.; Verdonk, M. L.; Cole, J. C.; Taylor, R. A New Test Set for Validating Predictions of Protein-Ligand Interaction. Proteins 2002, 49, 457-471.
-
(2002)
Proteins
, vol.49
, pp. 457-471
-
-
Nissink, J.W.1
Murray, C.2
Hartshorn, M.3
Verdonk, M.L.4
Cole, J.C.5
Taylor, R.6
-
39
-
-
0032111471
-
A branch-and-bound method for optimal atom-type assignment in de novo ligand design
-
Todorov, N. P.; Dean, P. M. A Branch-And-Bound Method for Optimal Atom-Type Assignment in de novo Ligand Design. J. Comput.-Aided Mol. Des. 1998, 12, 335-349.
-
(1998)
J. Comput.-Aided Mol. Des.
, vol.12
, pp. 335-349
-
-
Todorov, N.P.1
Dean, P.M.2
-
40
-
-
0031088353
-
Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design
-
Todorov, N. P.; Dean, P. M. Evaluation of a Method for Controlling Molecular Scaffold Diversity in de novo Ligand Design. J. Comput.Aided Mol. Des. 1997, 11, 175-192.
-
(1997)
J. Comput.Aided Mol. Des.
, vol.11
, pp. 175-192
-
-
Todorov, N.P.1
Dean, P.M.2
-
41
-
-
0000947082
-
Anthrax toxin edema factor: A bacterial adenylate cycalse that increases cyclic AMP concentrations eukaryotic cells
-
Leppla, S. H. Anthrax Toxin Edema Factor: A Bacterial Adenylate Cycalse that Increases Cyclic AMP Concentrations Eukaryotic Cells. Proc. Natl. Acad. Sci. U.S.A. 1982, 79, 3162-3166.
-
(1982)
Proc. Natl. Acad. Sci. U.S.A.
, vol.79
, pp. 3162-3166
-
-
Leppla, S.H.1
-
42
-
-
0021930758
-
Effects of anthrax toxin components on human neutrophils
-
O'Brien, J.; Friedlander, A.; Dreier, T.; Ezzell, J.; Leppla, S. Effects of Anthrax Toxin Components on Human Neutrophils. Infect. Immun. 1985,47, 306-310.
-
(1985)
Infect. Immun.
, vol.47
, pp. 306-310
-
-
O'Brien, J.1
Friedlander, A.2
Dreier, T.3
Ezzell, J.4
Leppla, S.5
-
43
-
-
10044248119
-
Proteolytic inactivation of MAP-kinase-kinase by anthrax lethal factor
-
Duesbery, N. S.; Webb, C. P.; Leppla, S. H.; Gordon, V. M.; Kumpel, K. R.; Copeland, T. D., Ahn, N. G., Oskarsson, M. K., Fukasawa, K., Paull, K. D., Woude, V. Proteolytic Inactivation of MAP-Kinase-Kinase by Anthrax Lethal Factor. Infect. Immun. 1985, 47, 306-310.
-
(1985)
Infect. Immun.
, vol.47
, pp. 306-310
-
-
Duesbery, N.S.1
Webb, C.P.2
Leppla, S.H.3
Gordon, V.M.4
Kumpel, K.R.5
Copeland, T.D.6
Ahn, N.G.7
Oskarsson, M.K.8
Fukasawa, K.9
Paull, K.D.10
Woude, V.11
-
44
-
-
0032755353
-
Anthrax lethal factor cleaves MKK3 in macrophages and inhibits the LPS/IFNgamma-induced release of NO and TNFalpha
-
Pellizzari, R.; Guidi-Rontani, C.; Vitale, G.; Mock, M.; Montecucco, C. Anthrax Lethal Factor Cleaves MKK3 in Macrophages and Inhibits the LPS/IFNgamma-induced Release of NO and TNFalpha. FEES Lett. 1999, 462, 199-204.
-
(1999)
FEES Lett.
, vol.462
, pp. 199-204
-
-
Pellizzari, R.1
Guidi-Rontani, C.2
Vitale, G.3
Mock, M.4
Montecucco, C.5
-
45
-
-
0022891493
-
Macrophages are sensitive to anthrax lethal toxin through an acid-dependent process
-
Friedlander, A. M. Macrophages are Sensitive to Anthrax Lethal Toxin Through an Acid-Dependent Process. J. Biol. Chem. 261, 7123-7126.
-
J. Biol. Chem.
, vol.261
, pp. 7123-7126
-
-
Friedlander, A.M.1
-
46
-
-
0031052342
-
Crystal structure of the anthrax toxin protective antigen
-
Petosa, C.; Collier, R. J.; Klimpel, K. R.; Leppla, S. H.; Liddington, R. C. Crystal Structure of the Anthrax Toxin Protective Antigen. Nature 1997, 385, 833-838.
-
(1997)
Nature
, vol.385
, pp. 833-838
-
-
Petosa, C.1
Collier, R.J.2
Klimpel, K.R.3
Leppla, S.H.4
Liddington, R.C.5
-
47
-
-
0037493019
-
Structure-based inhibitor discovery against adenylyl cyclase toxins from pathogenic bacteria that cause anthrax and whooping cough
-
Soelaiman, S.; Wei, B. Q.; Bergson, P.; Lee, Y.-S.; Shen, Y.; Mrksich, M.; Schoichet, B. K.; Tang, W.-J. Structure-Based Inhibitor Discovery Against Adenylyl Cyclase Toxins from Pathogenic Bacteria That Cause Anthrax and Whooping Cough. J. Biol. Chem. 2003, 278, 25990-25997.
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 25990-25997
-
-
Soelaiman, S.1
Wei, B.Q.2
Bergson, P.3
Lee, Y.-S.4
Shen, Y.5
Mrksich, M.6
Schoichet, B.K.7
Tang, W.-J.8
-
48
-
-
0037165139
-
Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin
-
Drum, C. L.; Yan, S.-Z.; Bard, J.; Shen, Y.-Q.; Lu, D.; Soelaiman, S.; Grabarek, Z.; Bohm, A.; Tang, W.-J. Structural Basis for the Activation of Anthrax Adenylyl Cyclase Exotoxin by Calmodulin. Nature 2002, 415, 396-402.
-
(2002)
Nature
, vol.415
, pp. 396-402
-
-
Drum, C.L.1
Yan, S.-Z.2
Bard, J.3
Shen, Y.-Q.4
Lu, D.5
Soelaiman, S.6
Grabarek, Z.7
Bohm, A.8
Tang, W.-J.9
|