|
[1]
|
Weber, A., Casini, A., Heine, A., Kuhn, D., Supuran, C.T., Scozzafava, A. and Klebe, G. (2004) Unexpected Nanomolar Inhibition of Carbonic Anhydrase by COX-2-Selective Celecoxib: New Pharmacological Opportunities Due to Related Binding Site Recognition. Journal of Medicinal Chemistry, 47, 550-557.
http://dx.doi.org/10.1021/jm030912m
|
|
|
[2]
|
Arrowsmith, J. and Miller, P. (2013) Phase II and Phase III attrition rates 2011-2012. Nature Reviews Drug Discovery, 12, 568-568.
http://dx.doi.org/10.1038/nrd4090
|
|
|
[3]
|
Giacomini, K.M., Krauss, R.M., Roden, D.M., Eichelbaum, M. and Hayden, M.R. (2007) When Good Drugs Go Bad. Nature, 446, 975-977.
http://dx.doi.org/10.1038/446975a
|
|
|
[4]
|
Pearson, H. (2006) The Bitterest Pill. Nature, 444, 532-533.
http://dx.doi.org/10.1038/444532a
|
|
|
[5]
|
Haupt, V.J., Daminelli, S. and Schroeder, M. (2013) Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key. PLoS ONE, 8, e65894.
http://dx.doi.org/10.1371/journal.pone.0065894
|
|
|
[6]
|
Sturm, N., Desaphy, J., Quinn, R.J., Rognan, D. and Kellenberger, E. (2012) Structural Insights into the Molecular Basis of the Ligand Promiscuity. Journal of Chemical Information and Modeling, 52, 2410-2421.
http://dx.doi.org/10.1021/ci300196g
|
|
|
[7]
|
Hendlich, M., Rippmann, F. and Barnickel, G. (1997) LIGSITE: Automatic and Efficient Detection of Potential Small Molecule-Binding Sites in Proteins. Journal of Molecular Graphics and Modelling, 15, 359-363.
http://dx.doi.org/10.1016/S1093-3263(98)00002-3
|
|
|
[8]
|
Laurie, A.T.R. and Jackson, R.M. (2005) Q-Site Finder: An Energy-Based Method for the Prediction of Protein-Ligand Binding Sites. Bioinformatics, 21, 1908-1916.
http://dx.doi.org/10.1093/bioinformatics/bti315
|
|
|
[9]
|
Schmitt, S., Kuhn, D. and Klebe, G. (2002) A New Method to Detect Related Function among Proteins Independent of Sequence and Fold Homology. Journal of Molecular Biology, 323, 387-406.
http://dx.doi.org/10.1016/S0022-2836(02)00811-2
|
|
|
[10]
|
Halgren, T. (2007) New Method for Fast and Accurate Binding-Site Identification and Analysis. Chemical Biology & Drug Design, 69, 146-148.
http://dx.doi.org/10.1111/j.1747-0285.2007.00483.x
|
|
|
[11]
|
Jalencas, X. and Mestres, J. (2013) Identification of Similar Binding Sites to Detect Distant Polypharmacology. Molecular Informatics, 32, 976-990.
http://dx.doi.org/10.1002/minf.201300082
|
|
|
[12]
|
Perot, S., Sperandio, O., Miteva, M.A., Camproux, A.C. and Villoutreix, B.O. (2010) Druggable Pockets and Binding Site Centric Chemical Space: A Paradigm Shift in Drug Discovery. Drug Discovery Today, 15, 656-667.
http://dx.doi.org/10.1016/j.drudis.2010.05.015
|
|
|
[13]
|
Rosen, M., Lin, S.L., Wolfson, H. and Nussinov, R. (1998) Molecular Shape Comparisons in Searches for Active Sites and Functional Similarity. Protein Engineering, Design and Selection, 11, 263-277.
http://dx.doi.org/10.1093/protein/11.4.263
|
|
|
[14]
|
Kupas, K., Ultsch, A. and Klebe, G. (2008) Large Scale Analysis of Protein-Binding Cavities Using Self-Organizing Maps and Wavelet-Based Surface Patches to Describe Functional Properties, Selectivity Discrimination, and Putative Cross-Reactivity. Proteins: Structure, Function, and Bioinformatics, 71, 1288-1306.
http://dx.doi.org/10.1002/prot.21823
|
|
|
[15]
|
Kalliokoski, T., Olsson, T.S.G. and Vulpetti, A. (2013) Subpocket Analysis Method for Fragment-Based Drug Discovery. Journal of Chemical Information and Modeling, 53, 131-141.
http://dx.doi.org/10.1021/ci300523r
|
|
|
[16]
|
Xiong, B., Wu, J., Burk, D.L., Xue, M.Z., Jiang, H.L. and Shen, J.K. (2010) BSSF: A Fingerprint Based Ultrafast Binding Site Similarity Search and Function Analysis Server. BMC Bioinformatics, 11, 47.
http://dx.doi.org/10.1186/1471-2105-11-47
|
|
|
[17]
|
Feldman, H.J. and Labute, P. (2010) Pocket Similarity: Are Alpha Carbons Enough? Journal of Chemical Information and Modeling, 50, 1466-1475.
http://dx.doi.org/10.1021/ci100210c
|
|
|
[18]
|
Powers, R., Copeland, J.C., Germer, K., Mercier, K.A., Ramanathan, V. and Revesz, P. (2006) Comparison of Protein Active Site Structures for Functional Annotation of Proteins and Drug Design. Proteins: Structure, Function, and Bioinformatics, 65, 124-135.
http://dx.doi.org/10.1002/prot.21092
|
|
|
[19]
|
Minai, R., Matsuo, Y., Onuki, H. and Hirota, H. (2008) Method for Comparing the Structures of Protein Ligand-Binding Sites and Application for Predicting Protein-Drug Interactions. Proteins: Structure, Function, and Bioinformatics, 72, 367-381.
http://dx.doi.org/10.1002/prot.21933
|
|
|
[20]
|
Wallace, A.C., Borkakoti, N. and Thornton, J.M. (1997) TESS: A Geometric Hashing Algorithm for Deriving 3D Coordinate Templates for Searching Structural Databases. Application to Enzyme Active Sites. Protein Science, 6, 2308-2323.
http://dx.doi.org/10.1002/pro.5560061104
|
|
|
[21]
|
Artymiuk, P.J., Poirrette, A.R., Grindley, H.M., Rice, D.W. and Willett, P. (1994) A Graph-Theoretic Approach to the Identification of 3-Dimensional Patterns of Amino-Acid Side-Chains in Protein Structures. Journal of Molecular Biology, 243, 327-344.
http://dx.doi.org/10.1006/jmbi.1994.1657
|
|
|
[22]
|
Jackson, J.E. (1991) A User’s Guide to Principal Component Analysis. John Wiley & Sons, Hoboken.
http://dx.doi.org/10.1002/0471725331
|
|
|
[23]
|
Kastenholz, M.A., Pastor, M., Cruciani, G., Haaksma, E.E.J. and Fox, T. (2000) GRID/CPCA: A New Computational Tool to Design Selective Ligands. Journal of Medicinal Chemistry, 43, 3033-3044.
http://dx.doi.org/10.1021/jm000934y
|
|
|
[24]
|
Andersson, C.D., Chen, B.Y. and Linusson, A. (2010) Mapping of Ligand-Binding Cavities in Proteins. Proteins: Structure, Function, and Bioinformatics, 78, 1408-1422.
|
|
|
[25]
|
Desdouits, N., Nilges, M. and Blondel, A. (2015) Principal Component Analysis Reveals Correlation of Cavities Evolution and Functional Motions in Proteins. Journal of Molecular Graphics and Modelling, 55, 13-24.
http://dx.doi.org/10.1016/j.jmgm.2014.10.011
|
|
|
[26]
|
Bylesjo, M., Rantalainen, M., Cloarec, O., Nicholson, J.K., Holmes, E. and Trygg, J. (2006) OPLS Discriminant Analysis: Combining the Strengths of PLS-DA and SIMCA Classification. Journal of Chemometrics, 20, 341-351.
http://dx.doi.org/10.1002/cem.1006
|
|
|
[27]
|
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Research, 28, 235-242.
http://dx.doi.org/10.1093/nar/28.1.235
|
|
|
[28]
|
Prasad, S., Cantwell, A.M., Bush, L.A., Shih, P., Xu, H. and Di Cera, E. (2004) Residue Asp-189 Controls both Substrate Binding and the Monovalent Cation Specificity of Thrombin. The Journal of Biological Chemistry, 279, 10103-10108.
http://dx.doi.org/10.1074/jbc.M312614200
|
|
|
[29]
|
Wold, S., Esbensen, K. and Geladi, P. (1987) Principal Component Analysis. Chemometrics and Intelligent Laboratory Systems, 2, 37-52.
http://dx.doi.org/10.1016/0169-7439(87)80084-9
|
|
|
[30]
|
Trygg, J. and Wold, S. (2002) Orthogonal Projections to Latent Structures (O-PLS). Journal of Chemometrics, 16, 119-128.
http://dx.doi.org/10.1002/cem.695
|
|
|
[31]
|
Pozzi, N., Chen, Z.W., Zapata, F., Pelc, L.A., Barranco-Medina, S. and Di Cera, E. (2011) Crystal Structures of Prethrombin-2 Reveal Alternative Conformations under Identical Solution Conditions and the Mechanism of Zymogen Activation. Biochemistry, 50, 10195-10202.
http://dx.doi.org/10.1021/bi2015019
|
|
|
[32]
|
Johnson, D.J.D., Adams, T.E., Li, W. and Huntington, J.A. (2005) Crystal Structure of Wild-Type Human Thrombin in the Na+-Free State. Biochemical Journal, 392, 21-28.
http://dx.doi.org/10.1042/BJ20051217
|
|
|
[33]
|
Eigenbrot, C., Kirchhofer, D., Dennis, M.S., Santell, L., Lazarus, R.A., Stamos, J. and Ultsch, M.H. (2001) The Factor VII Zymogen Structure Reveals Reregistration of Beta Strands during Activation. Structure, 9, 627-636.
http://dx.doi.org/10.1016/S0969-2126(01)00624-4
|
|
|
[34]
|
Gandhi, P.S., Page, M.J., Chen, Z.W., Bush-Pelc, L. and Di Cera, E. (2009) Mechanism of the Anticoagulant Activity of Thrombin Mutant W215A/E217A. The Journal of Biological Chemistry, 284, 24098-24105.
http://dx.doi.org/10.1074/jbc.m109.025403
|
|
|
[35]
|
Katayama, K., Ericsson, L.H., Enfield, D.L., Walsh, K.A., Neurath, H., Davie, E.W. and Titani, K. (1979) Comparison of Amino-Acid Sequence of Bovine Coagulation Factor-IX (Christmas Factor) with That of Other Vitamin K-Dependent Plasma-Proteins. Proceedings of the National Academy of Sciences of the United States of America, 76, 4990-4994.
http://dx.doi.org/10.1073/pnas.76.10.4990
|
|
|
[36]
|
Brandstetter, H., Bauer, M., Huber, R., Lollar, P. and Bode, W. (1995) X-Ray Structure of Clotting Factor IXa: Active-Site and Module Structure Related to Xase Activity and Hemophilia B. Proceedings of the National Academy of Sciences of the United States of America, 92, 9796-9800.
http://dx.doi.org/10.1073/pnas.92.21.9796
|
|
|
[37]
|
Shirk, R.A. and Vlasuk, G.P. (2007) Inhibitors of Factor VIIa/Tissue Factor. Arteriosclerosis, Thrombosis, and Vascular Biology, 27, 1895-1900.
http://dx.doi.org/10.1161/ATVBAHA.107.148304
|
|
|
[38]
|
Kortagere, S., Ekins, S. and Welsh, W.J. (2008) Halogenated Ligands and Their Interactions with Amino Acids: Implications for Structure-Activity and Structure-Toxicity Relationships. Journal of Molecular Graphics and Modelling, 27, 170-177.
http://dx.doi.org/10.1016/j.jmgm.2008.04.001
|
|