Registro:

Referencias:

• Abel, R., Young, T., Farid, R., Berne, B.J., Friesner, R.A., Role of the activesite solvent in the thermodynamics of factor xa ligand binding (2008) J Am Chem Soc, 130, pp. 2817-2831
• Agostino, M., Jene, C., Boyle, T., Ramsland, P.A., Yuriev, E., Molecular docking of carbohydrate ligands to antibodies: Structural validation against crystal structures (2009) J Chem Inf Model, 49, pp. 2749-2760
• Agostino, M., Sandrin, M.S., Thompson, P.E., Yuriev, E., Ramsland, P.A., Identification of preferred carbohydrate binding modes in xenoreactive antibodies by combining conformational filters and binding site maps (2010) Glycobiology, 20, pp. 724-735
• Agostino, M., Yuriev, E., Ramsland, P.A., A computational approach for exploring carbohydrate recognition by lectins in innate immunity (2011) Front Immunol, 2, p. 23
• Ahmad, N., Gabius, H.J., Sabesan, S., Oscarson, S., Brewer, C.F., Thermodynamic binding studies of bivalent oligosaccharides to galectin-1, galectin-3, and the carbohydrate recognition domain of galectin-3 (2004) Glycobiology, 14, pp. 817-825
• Amzel, L.M., Structure-based drug design (1998) Curr Opin Biotechnol, 9, pp. 366-369
• Balzarini, J., Targeting the glycans of glycoproteins: A novel paradigm for antiviral therapy (2007) Nat Rev Microbiol, 5, pp. 583-597
• Banerji, S., Wright, A.J., Noble, M., Mahoney, D.J., Campbell, I.D., Day, A.J., Jackson, D.G., Structures of the cd44-hyaluronan complex provide insight into a fundamental carbohydrate-protein interaction (2007) Nat Struct Mol Biol, 14, pp. 234-239
• Barril, X., Javier Luque, F., Molecular simulation methods in drug discovery: A prospective outlook (2012) J Comput-Aided Mol des, 26, pp. 81-86
• Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F., Dinola, A., Haak, J.R., Molecular dynamics with coupling to an external bath (1984) J Chem Phys, 81, pp. 3684-3690
• Boraston, A.B., Ficko-Blean, E., Healey, M., Carbohydrate recognition by a large sialidase toxin from clostridium perfringens† (2007) Biochemistry, 46, pp. 11352-11360
• Brooijmans, N., Kuntz, I.D., Molecular recognition and docking algorithms (2003) Annu Rev Biophys Biomol Struct, 32, pp. 335-373
• Case, D.A., Cheatham Iii., T.E., Darden, T., Gohlke, H., Luo, R., Merz Jr., K.M., Onufriev, A., Woods, R.J., The amber biomolecular simulation programs (2005) J Comput Chem, 26, pp. 1668-1688
• Crocker, P.R., Paulson, J.C., Varki, A., Siglecs and their roles in the immune system (2007) Nat Rev Immunol, 7, pp. 255-266
• Crouch, E., McDonald, B., Smith, K., Cafarella, T., Seaton, B., Head, J., Contributions of phenylalanine 335 to ligand recognition by human surfactant protein d: Ring interactions with sp-d ligands (2006) J Biol Chem, 281, pp. 18008-18014
• Dam, T.K., Brewer, C.F., Lectins as pattern recognition molecules: The effects of epitope density in innate immunity (2010) Glycobiology, 20, pp. 270-279
• De Beer, S.B., Vermeulen, N.P., Oostenbrink, C., The role of water molecules in computational drug design (2010) Curr Top Med Chem, 10, pp. 55-66
• Di Lella, S., Marti, M.A., Alvarez, R.M., Estrin, D.A., Ricci, J.C., Characterization of the galectin-1 carbohydrate recognition domain in terms of solvent occupancy (2007) J Phys Chem B, 111, pp. 7360-7366
• Di Lella, S., Sundblad, V., Cerliani, J.P., Guardia, C.M., Estrin, D.A., Vasta, G.R., Rabinovich, G.A., When galectins recognize glycans: From biochemistry to physiology and back again (2011) Biochemistry, 50, pp. 7842-7857
• Drews, J., Drug discovery: A historical perspective (2000) Science, 287, pp. 1960-1964
• Echeverria, I., Amzel, L.M., Disaccharide binding to galectin-1: Free energy calculations and molecular recognition mechanism (2011) Biophys J, 100, pp. 2283-2292
• Englebienne, P., Moitessier, N., Docking ligands into flexible and solvated macromolecules. 5. Force-field-based prediction of binding affinities of ligands to proteins (2009) J Chem Inf Model, 49, pp. 2564-2571
• Ernst, B., Magnani, J.L., From carbohydrate leads to glycomimetic drugs (2009) Nat Rev Drug Discovery, 8, pp. 661-677
• Fadda, E., Woods, R.J., Molecular simulations of carbohydrates and protein-carbohydrate interactions: Motivation, issues and prospects (2010) Drug Discov Today, 15, pp. 596-609
• Feinberg, H., Mitchell, D.A., Drickamer, K., Weis, W.I., Structural basis for selective recognition of oligosaccharides by dc-sign and dc-signr (2001) Science, 294, pp. 2163-2166
• Feinberg, H., Taylor, M.E., Razi, N., McBride, R., Knirel, Y.A., Graham, S.A., Drickamer, K., Weis, W.I., Structural basis for langerin recognition of diverse pathogen and mammalian glycans through a single binding site (2011) J Mol Biol, 405, pp. 1027-1039
• Feliu, E., Oliva, B., How different from random are docking predictions when ranked by scoring functions? (2010) Proteins, 78, pp. 3376-3385
• Feng, L., Sun, H., Zhang, Y., Li, D.F., Wang, D.C., Structural insights into the recognition mechanism between an antitumor galectin AAL and the Thomsen-Friedenreich antigen (2010) FASEB J, 24, pp. 3861-3868
• Frank, M., Schloissnig, S., Bioinformatics and molecular modeling in glycobiology (2010) Cell Mol Life Sci, 67, pp. 2749-2772
• Friesner, R.A., Banks, J.L., Murphy, R.B., Halgren, T.A., Klicic, J.J., Mainz, D.T., Repasky, M.P., Perry, J.K., Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy (2004) J Med Chem, 47, pp. 1739-1749
• Gauto, D.F., Di Lella, S., Estrin, D.A., Monaco, H.L., Marti, M.A., Structural basis for ligand recognition in a mushroom lectin: Solvent structure as specificity predictor (2011) Carbohydr Res, 346, pp. 939-948
• Gauto, D.F., Di Lella, S., Guardia, C.M., Estrin, D.A., Marti, M.A., Carbohydrate-binding proteins: Dissecting ligand structures through solvent environment occupancy (2009) J Phys Chem B, 113, pp. 8717-8724
• Goodsell, D.S., Morris, G.M., Olson, A.J., Automated docking of flexible ligands: Applications of AutoDock (1996) J Mol Recognit, 9, pp. 1-5
• Guardia, C.M., Gauto, D.F., Di Lella, S., Rabinovich, G.A., Marti, M.A., Estrin, D.A., An integrated computational analysis of the structure, dynamics, and ligand binding interactions of the human galectin network (2011) J Chem Inf Model, 51, pp. 1918-1930
• Hirabayashi, J., Lectin-based structural glycomics: Glycoproteomics and glycan profiling (2004) Glycoconj J, 21, pp. 35-40
• Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., Simmerling, C., Comparison of multiple amber force fields and development of improved protein backbone parameters (2006) Proteins, 65, pp. 712-725
• Huey, R., Morris, G.M., Olson, A.J., Goodsell, D.S., A semiempirical free energy force field with charge-based desolvation (2007) J Comput Chem, 28, pp. 1145-1152
• Kadirvelraj, R., Foley, B.L., Dyekjaer, J.D., Woods, R.J., Involvement of water in carbohydrate-protein binding: Concanavalin a revisited (2008) J Am Chem Soc, 130, pp. 16933-16942
• Kerzmann, A., Fuhrmann, J., Kohlbacher, O., Neumann, D., Balldock/slick: A new method for protein-carbohydrate docking (2008) J Chem Inf Model, 48, pp. 1616-1625
• Kerzmann, A., Neumann, D., Kohlbacher, O., Slick-Scoring and energy functions for protein-carbohydrate interactions (2006) J Chem Inf Model, 46, pp. 1635-1642
• Lazaridis, T., Inhomogeneous fluid approach to solvation thermodynamics. 1. Theory (1998) J Phys Chem B, 102, pp. 3531-3541
• Lazaridis, T., Inhomogeneous fluid approach to solvation thermodynamics. 2. Applications to simple fluids (1998) J Phys Chem B, 102, pp. 3542-3550
• Leach, A.R., Shoichet, B.K., Peishoff, C.E., Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps (2006) J Med Chem, 49, pp. 5851-5855
• Leffler, H., Carlsson, S., Hedlund, M., Qian, Y., Poirier, F., Introduction to galectins (2004) Glycoconj J, 19, pp. 433-440
• Li, L., Chen, R., Weng, Z., Rdock: Refinement of rigid-body protein docking predictions (2003) Proteins, 53, pp. 693-707
• Li, Z., Lazaridis, T., Thermodynamic contributions of the ordered water molecule in hiv-1 protease (2003) J Am Chem Soc, 125, pp. 6636-6637
• Li, Z., Lazaridis, T., The effect of water displacement on binding thermodynamics: Concanavalin a (2005) J Phys Chem B, 109, pp. 662-670
• Loging, W., Rodriguez-Esteban, R., Hill, J., Freeman, T., Miglietta, J., Cheminformatic/bioinformatic analysis of large corporate databases: Application to drug repurposing (2012) Drug Discov Today Ther Strateg, 8, pp. 109-116
• Loris, R., Maes, D., Poortmans, F., Wyns, L., Bouckaert, J., A structure of the complex between concanavalin a and methyl-3,6-di-o-(alpha-d-mannopyranosyl)-alpha-d-mannopyranoside reveals two binding modes (1996) J Biol Chem, 271, pp. 30614-30618
• Luccarelli, J., Michel, J., Tirado-Rives, J., Jorgensen, W.L., Effects of water placement on predictions of binding affinities for p38α map kinase inhibitors (2010) J Chem Theory Comput, 6, pp. 3850-3856
• Michel, J., Tirado-Rives, J., Jorgensen, W.L., Energetics of displacing water molecules from protein binding sites: Consequences for ligand optimization (2009) J Am Chem Soc, 131, pp. 15403-15411
• Michel, J., Tirado-Rives, J., Jorgensen, W.L., Prediction of the water content in protein binding sites (2009) J Phys Chem B, 113, pp. 13337-13346
• Mishra, S.K., Adam, J., Wimmerova, M., Koca, J., In silico mutagenesis and docking study of ralstonia solanacearum rsl lectin: Performance of docking software to predict saccharide binding (2012) J Chem Inf Model, 52, pp. 1250-1261
• Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K., Olson, A.J., Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function (1998) J Comput Chem, 19, pp. 1639-1662
• 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 (1996) J Comput Aided Mol des, 10, pp. 293-304
• Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F., Belew, R.K., Goodsell, D.S., Olson, A.J., AutoDock4 and autodocktools4: Automated docking with selective receptor flexibility (2009) J Comput Chem, 30, pp. 2785-2791
• Moustakas, D.T., Lang, P.T., Pegg, S., Pettersen, E., Kuntz, I.D., Brooijmans, N., Rizzo, R.C., Development and validation of a modular, extensible docking program: Dock 5 (2006) J Comput Aided Mol des, 20, pp. 601-619
• Nurisso, A., Kozmon, S., Imberty, A., Comparison of docking methods for binding in calcium-dependent lectins and prediction of the carbohydrate binding mode to sea cucumber lectin cel-iii (2008) Mol Simul, 34, pp. 469-479
• Powlesland, A.S., Quintero-Martinez, A., Lim, P.G., Pipirou, Z., Taylor, M.E., Drickamer, K., Engineered carbohydrate-recognition domains for glycoproteomic analysis of cell surface glycosylation and ligands for glycan-binding receptors (2010) Methods Enzymol, 480, pp. 165-179
• Rabinovich, G.A., Galectin-1 as a potential cancer target (2005) Br J Cancer, 92, pp. 1188-1192
• Saraboji, K., Hakansson, M., Genheden, S., Diehl, C., Qvist, J., Weininger, U., Nilsson, U.J., Akke, M., The carbohydratebinding site in galectin-3 is preorganized to recognize a sugarlike framework of oxygens: Ultra-high-resolution structures and water dynamics (2012) Biochemistry, 51, pp. 296-306
• Seco, J., Luque, F.J., Barril, X., Binding site detection and druggability index from first principles (2009) J Med Chem, 52, pp. 2363-2371
• Seetharaman, J., Kanigsberg, A., Slaaby, R., Leffler, H., Barondes, S.H., Rini, J.M., X-ray crystal structure of the human galectin-3 carbohydrate recognition domain at 2.1 - A resolution (1998) J Biol Chem, 273, pp. 13047-13052
• Shoichet, B.K., McGovern, S.L., Wei, B., Irwin, J.J., Lead discovery using molecular docking (2002) Curr Opin Chem Biol, 6, pp. 439-446
• Taylor, M.E., Drickamer, K., Structural insights into what glycan arrays tell us about how glycan-binding proteins interact with their ligands (2009) Glycobiology, 19, pp. 1155-1162
• Taylor, R.D., Jewsbury, P.J., Essex, J.W., A review of protein-small molecule docking methods (2002) J Comput Aided Mol des, 16, pp. 151-166
• Trott, O., Olson, A.J., Autodock vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading (2010) J Comput Chem, 31, pp. 455-461
• Varki, A., Cummings, R., Esko, J., Freeze, H., Hart, G., Marth, J., (1999) Essentials of Glycobiology
• Von Der Lieth, C.W., Freire, A.A., Blank, D., Campbell, M.P., Ceroni, A., Damerell, D.R., Dell, A., Fogh, R., Eurocarbdb: An open-access platform for glycoinformatics (2011) Glycobiology, 21, pp. 493-502
• Von Schantz, L., Hakansson, M., Logan, D.T., Walse, B., Osterlin, J., Nordberg-Karlsson, E., Ohlin, M., Structural basis for carbohydratebinding specificity - A comparative assessment of two engineered carbohydrate-binding modules (2012) Glycobiology, 22, pp. 948-961
• Woods, R.J., Tessier, M.B., Computational glycoscience: Characterizing the spatial and temporal properties of glycans and glycan-protein complexes (2010) Curr Opin Struct Biol, 20, pp. 575-583
• Young, T., Abel, R., Kim, B., Berne, B.J., Friesner, R.A., Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding (2007) Proc Natl Acad Sci USA, 104, pp. 808-813

Citas:

---------- APA ----------

---------- CHICAGO ----------

---------- MLA ----------

---------- VANCOUVER ----------