Registro:

Referencias:

• Abel, R., Young, T., Farid, R., Berne, B.J., Friesner, R.A., Role of the active-site solvent in the thermodynamics of factor Xa ligand binding (2008) J Am Chem Soc., 130 (9), pp. 2817-2831
• Agostino, M., Jene, C., Boyle, T., Ramsland, P., Yuriev, E., Molecualr docking of carbohydrate ligands to antibodies: Structural validation against crystal structures (2009) J Chem Inf Model., 49, pp. 2749-2760
• Andres, D., Gohlke, U., Broeker, N.K., Schulze, S., Rabsch, W., Heinemann, U., Barbirz, S., An essential serotype recognition pocket on phage P22 tailspike protein forces Salmonella enterica serovar Paratyphi A O-antigen fragments to bind as nonsolution conformers (2013) Glycobiology., 23 (4), pp. 486-494
• Asensio, J.L., Cañada, F.J., Siebert, H.C., Laynez, J., Poveda, A., Nieto, P.M., Soedjanaamadja, U.M., Structural basis for chitin recognition by defense proteins: GlcNAc residues are bound in a multivalent fashion by extended binding sites in hevein domains (2000) Chem Biol., 7 (7), pp. 529-543
• Barillari, C., Duncan, A.L., Westwood, I.M., Blagg, J., Van Montfort, R.L.M., Analysis of water patterns in protein kinase binding sites (2011) Proteins., 79 (7), pp. 2109-2121
• Barillari, C., Taylor, J., Viner, R., Essex, J.W., Classification of water molecules in protein binding sites (2007) J Am Chem Soc., 129 (9), pp. 2577-2587
• Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., The Protein Data Bank. A computer-based archival file for macromolecular structures (1977) Eur Biochem/FEBS., 80 (2), pp. 319-324
• Beuming, T., Che, Y., Abel, R., Kim, B., Shanmugasundaram, V., Sherman, W., Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization (2012) Proteins., 80 (3), pp. 871-883
• Brooijmans, N., Kuntz, I.D., Molecular recognition and docking algorithms (2003) Annu Rev Biophy Biomol Struct., 32, pp. 335-373
• Chervenak, M.C., Toone, E.J., Calorimetric analysis of the binding of lectins with overlapping carbohydrate-binding ligand specificities (1995) Biochem., 34 (16), pp. 5685-5695
• Compagno, D., Jaworski, F.M., Gentilini, L., Contrufo, G., Gonzalez Perez, I., Elola, M.T., Pregi, N., Galectins: Major signaling modulators inside and outside the cell (2014) Curr Mol Med., 14 (5), pp. 630-651
• Crouch, E., Hartshorn, K., Horlacher, T., McDonald, B., Smith, K., Cafarella, T., Seaton, B., Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: Contributions of an extended site and residue 343 (2009) Biochem., 48 (15), pp. 3335-3345
• Dam, T.K., Brewer, C.F., Lectins as pattern recognition molecules: The effects of epitope density in innate immunity (2010) Glycobiology., 20 (3), pp. 270-279
• Di Lella, S., Martí, M.A., Alvarez, R.M.S., Estrin, D.A., Ricci, J.C.D., Characterization of the galectin-1 carbohydrate recognition domain in terms of solvent occupancy (2007) J Phys Chem B., 111 (25), pp. 7360-7366
• Di Lella, S., Martí, M.A., Croci, D.O., Guardia, C.M., Díaz-Ricci, J.C., Rabinovich, G.A., Caramelo, J.J., Linking the structure and thermal stability of beta-galactoside-binding protein galectin-1 to ligand binding and dimerization equilibria (2010) Biochemistry., 49 (35), pp. 7652-7658
• 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 Inform Model., 49 (11), pp. 2564-2571
• Fadda, E., Woods, R.J., Molecular simulations of carbohydrates and protein-carbohydrate interactions: Motivation, issues and prospects (2010) Drug Discov Today., 15 (15-16), pp. 596-609
• Forli, S., Olson, A.J., A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking (2012) J Med Chem., 55 (2), pp. 623-638
• Frank, M., Schloissnig, S., Bioinformatics and molecular modeling in glycobiology (2010) Cel Mol Life Sci., 67 (16), pp. 2749-2772
• Friesner, R.A., Banks, J.L., Murphy, R.B., Halgren, T.A., Klicic, J.J., Mainz, D.T., Repasky, M.P., Glide: A newapproach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy (2004) J Med Chem., 47 (7), pp. 1739-1749
• Gabius, H.-J., André, S., Jiménez-Barbero, J., Romero, A., Solís, D., From lectin structure to functional glycomics: Principles of the sugar code (2011) Trends Biochem Sci., 36 (6), pp. 298-313
• Garcia-Sosa, A.T., Hydration properties of ligands and drugs in protein binding sites: Tightly-bound, bridging water molecules and their effects and consequences on molecular design strategies (2013) J Chem Inform Model.
• García-Sosa, A.T., Mancera, R.L., Dean, P.M., WaterScore: A novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes (2003) J Mol Model., 9 (3), pp. 172-182
• Gauto, D.F., Di Lella, S., Estrin, D.A., Monaco, H.L., Martí, M.A., Structural basis for ligand recognition in a mushroom lectin: Solvent structure as specificity predictor (2011) Carbohy Res., 346 (7), pp. 939-948
• Gauto, D.F., Di Lella, S., Guardia, C.M., Estrin, D.A., Martí, M.A., Carbohydrate-binding proteins: Dissecting ligand structures through solvent environment occupancy (2009) J Phys Chem B., 113 (25), pp. 8717-8724
• Gauto, D.F., Petruk, A.A., Modenutti, C.P., Blanco, J.I., Di Lella, S., Martí, M.A., Solvent structure improves docking prediction in lectin-carbohydrate complexes (2013) Glycobiology., 23 (2), pp. 241-258
• Grant, O.C., Woods, R.J., Recent advances in employing molecular modelling to determine the specificity of glycan-binding proteins (2014) Curr Opin Struct Bio., 28 C, pp. 47-55
• Green, P.J., Reversible jump Markov chain Monte Carlo computation and Bayesian model determination (1995) Biometrika., 82 (4), pp. 711-732
• Guan, L., Hu, Y., Kaback, H.R., Aromatic stacking in the sugar binding site of the lactose permease (2003) Biochemistry., 42 (6), pp. 1377-1382
• Guardia, C.M., Gauto, D.F., Di Lella, S., Rabinovich, G.A., Martí, 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 Inform Model., 51 (8), pp. 1918-1930
• Hastings, J., De Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., Muthukrishnan, V., The ChEBI reference database and ontology for biologically relevant chemistry: Enhancements for 2013 (2013) Nucleic Acids Rese., 41, pp. D456-D463. , database issue
• Higgs, C., Beuming, T., Sherman, W., Hydration site thermodynamics explain SARs for triazolylpurines analogues binding to the A2A receptor (2010) ACS Med Chem Lett., 1 (4), pp. 160-164
• Huang, N., Schoichet, B.R., Exploiting ordered waters in molecular docking (2008) J Med Chem., 52, pp. 4862-4865
• Hummer, G., Molecular binding: Under water's influence (2010) Nat Chem., 2 (11), pp. 906-907
• Johal, A.R., Jarrell, H.C., Letts, J.A., Khieu, N.H., Landry, R.C., Jachymek, W., Yang, Q., The antigen-binding site of an N-propionylated polysialic acidspecific antibody protective against group B meningococci is consistent with extended epitopes (2013) Glycobio., 23 (8), pp. 946-954
• 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 (50), pp. 16933-16942
• Kerzmann, A., Fuhrmann, J., Kohlbacher, O., Neumann, D., BALLDock/ SLICK: A new method for protein-carbohydrate docking (2008) J Chem Inform Model., 48 (8), pp. 1616-1625
• Kumar, S., Frank, M., Schwartz-Albiez, R., Understanding the specificity of human Galectin-8C domain interactions with its glycan ligands based on molecular dynamics simulations (2013) PloS One., 8 (3), p. e59761
• Laughrey, Z.R., Kiehna, S.E., Riemen, A.J., Waters, M.L., Carbohydrate-pi interactions: What are they worth? (2008) J Am Chem Soc., 130 (44), pp. 14625-14633
• Lazaridis, T., Inhomogeneous fluid approach to solvation thermodynamics. 1 (1998) Theory. J Phys Chem B., 102 (18), pp. 3531-3541
• 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 (20), pp. 5851-5855
• Li, Z., Lazaridis, T., The effect of water displacement on binding thermodynamics: Concanavalin A (2005) J Phys Chem B., 109 (1), pp. 662-670
• Li, Z., Lazaridis, T., Thermodynamics of buried water clusters at a proteinligand binding interface (2006) J Phys Chem B., 110 (3), pp. 1464-1475
• Lie, M.A., Thomsen, R., Pedersen, C.N.S., Schiøtt, B., Christensen, M.H., Molecular docking with ligand attached water molecules (2011) J Chem Inform Model., 51 (4), pp. 909-917
• Lütteke, T., Frank, M., Von Der Lieth, C.-W., Carbohydrate structure suite(CSS): Analysis of carbohydrate 3D structures derived from the PDB (2005) Nucleic Acids Res., 33, pp. D242-D246. , database issue
• Maruyama, O., Heterodimeric protein complex identification by Naïve Bayes classifiers (2013) BMC Bioinform., 14, p. 347
• 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., 9 (9), pp. 15403-15411
• Mishra, S.K., Adam, J., Wimmerová, 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 Inform Model., 52 (5), 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 (14), pp. 1639-1662
• 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
• Nishio, M., Umezawa, Y., Fantini, J., Weiss, M.S., Chakrabarti, P., CH-? Hydrogen bonds in biological macromolecules (2014) Phy Chem Phys., 16 (25), pp. 12648-12683. , The Royal Society of Chemistry
• Nivedha, A.K., Makeneni, S., Foley, B.L., Tessier, M.B., Woods, R.J., Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff (2014) J Comput Chem., 35 (7), pp. 526-539
• Patil, A., Huard, D., Fonnesbeck, C.J., PyMC: Bayesian stochastic modelling in Python (2010) J Stat Software., 35 (4), pp. 1-81
• Ranzinger, R., Herget, S., Wetter, T., Von Der Lieth, C.-W., GlycomeDB-Integration of open-access carbohydrate structure databases (2008) BMC Bioinform., 9, p. 384
• Rarey, M., Kramer, B., Lengauer, T., The particle concept: Placing discrete water molecules during protein-ligand docking predictions (1999) Proteins., 34 (1), pp. 17-28
• Saraboji, K., Håkansson, M., Genheden, S., Diehl, C., Qvist, J., Weininger, U., Nilsson, U.J., The carbohydrate-binding site in galectin-3 is preorganized to recognize a sugarlike framework of oxygens: Ultrahigh-resolution structures and water dynamics (2012) Biochemistry., 51 (1), pp. 296-306
• Setny, P., Baron, R., McCammon, J., How can hydrophobic association be enthalpy driven? (2010) J Chem Theory Comput., 6 (9), pp. 2866-2871
• Sujatha, M.S., Sasidhar, Y.U., Balaji, P.V., Energetics of galactose-and glucose-aromatic amino acid interactions: Implications for binding in galactose-specific proteins (2004) Protein Sci Publ Protein Soc., 13 (9), pp. 2502-2514
• Taylor, R.D., Jewsbury, P.J., Essex, J.W., A review of protein-small molecule docking methods (2002) J Comput Aided Mol Des., 16 (3), pp. 151-166
• Terraneo, G., Potenza, D., Canales, A., Jiménez-Barbero, J., Baldridge, K.K., Bernardi, A., A simple model system for the study of carbohydrate-Aromatic interactions (2007) J Am Chem Soc., 129 (10), pp. 2890-2900
• Von Der Lieth, C.-W., Freire, A.A., Blank, D., Campbell, M.P., Ceroni, A., Damerell, D.R., Dell, A., EUROCarbDB: An open-access platform for glycoinformatics (2011) Glycobiology., 21 (4), pp. 493-502
• Von Schantz, L., Håkansson, 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 (7), pp. 948-961
• Wang, J.-C., Lin, J.-H., Chen, C.-M., Perryman, A.L., Olson, A.J., Robust scoring functions for protein-ligand interactions with quantum chemical charge models (2011) J Chem Inform Mode., 51 (10), pp. 2528-2537
• Yoshida, H., Teraoka, M., Nishi, N., Nakakita, S., Nakamura, T., Hirashima, M., Kamitori, S., X-ray structures of human galectin-9 C-terminal domain in complexes with a biantennary oligosaccharide and sialyllactose (2010) J Biol Chem., 285 (47), pp. 36969-36976
• Yuriev, E., Agostino, M., Ramsland, P.A., Challenges and advances in computational docking: 2009 in review (2009) J Recogn., 24 (2), pp. 149-164

Citas:

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

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

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

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