Biochemical Profiling of Histone Binding Selectivity of the Yeast Bromodomain Family. Q. Zhang, S. Chakravarty, D. Ghersi, A.N. Plotnikov, R. Sanchez, and M.-M. Zhou. PLoS ONE, in press, 2010. EASYMIFs & SITEHOUND: a toolkit for the identification of ligand-binding sites in protein structures. D. Ghersi and R. Sanchez. Bioinformatics, 25, 3185-3186, 2009. [PDF] Role of bromodomains in regulating chromatin biology and gene transcription. R. Sanchez and M.-M. Zhou. Current Opinion in Drug Discovery & Development, 12, 659-665, 2009. Modern Homology Modeling of G-Protein Coupled Receptors: Which Structural Template to Use? J.C. Mobarec, R. Sanchez, and M. Filizola. J. Med. Chem., 52, 5207-5216, 2009. SITEHOUND-web: a server for ligand binding site identification in protein structures. M. Hernandez, D. Ghersi, and R. Sanchez. Nucleic Acids Research, 37, W413-W416, 2009. [PDF] [Server] Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites. D. Ghersi and R. Sanchez. Proteins, 74, 417-424, 2009. [PDF] Outcome of a workshop on applications of protein models in biomedical research. Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL Jr, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR Jr, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Structure, 17, 151-159, 2009. [PDF] Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure. S. Chakravarty, S. Godbole, B. Zhang, S. Berger, and R. Sanchez. BMC Structural Biology, 8:31, 2008. [PDF] Variable gap penalty for protein sequence-structure alignment. Madhusudhan M.S., M. Marti-Renom, R. Sanchez, and A. Sali. PEDS, 19, 129-33, 2006. Accuracy of structure-derived properties in simple comparative models of protein structure. S. Chakravarty, L. Wang, and R. Sanchez. Nucleic Acids Research, 33, 244-259, 2005. [PDF] Systematic analysis of added-value in simple comparative models of protein structure. S. Chakravarty and R. Sanchez. Structure, 12, 1461-1470, 2004. [PDF] Bacillus subtilis YhcR, a sugar non-specific, broad specificity endonuclease with a unique domain structure. I. Oussenko, R. Sanchez, and D. Bechhofer. J. Bacteriol., 186, 5376-5383, 2004 Vitamin C is a kinase inhibitor: Dehydroascobic acid inhibits IKK-beta. J.M. Carcamo, A. Pedraza, O. Borquez-Ojeda, B. Zhang, R. Sanchez, and D.W. Golde. Molecular and Cellular Biology, 24, 6645-6652, 2004 Structural mechanism of the bromodomain of the coactivator CBP in p53 transcriptional activation. S. Mujtaba, Y. He, L. Zeng, S. Yan, O. Plotnikova, Sachchidanand, R. Sanchez, N.J. Zeleznik-Le, Z. Ronai, M.-M. Zhou. Molecular Cell, 13, 251-263, 2004 The beta-gamma subunits of G proteins gate a K+ channel by pivoted bending of a transmembrane segment. T. Jin, L. Peng, T. Mirshahi, T. Rohacs, K.W. Chan, R. Sanchez, and D. Logothetis. Molecular Cell, 10, 469-481, 2002 Bacillus subtilis YhaM, a member of a new family of 3'-to-5' exonucleases in Gram-positive bacteria. I. Oussenko, R. Sanchez, and D. Bechhofer. J. Bacteriol., 184, 6250-6259, 2002 Structure, upstream promoter region, and functional domains of a mouse and human Mix paired-like homeobox gene. K. Sahr, D. Campos Dias, R. Sanchez, D. Chen, S. W. Chen, L. J. Gudas, and M. H. Baron. Gene, 291, 135-147, 2002 Statistical potentials for fold assessment. F. Melo, R. Sánchez, and A. Sali. Prot. Sci., 11, 430-448, 2002. Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. S. Gopal, M. Schroeder, U. Pieper, A. Sczyrba, G. Aytekin-Kurban, S. Bekiranov, E. J. Fajardo, N. Eswar, R. Sánchez, A. Sali, and T. Gaasterland. Nat. Genet., 27,337-340, 2001. Protein structure modeling for structural genomics. R. Sánchez, U. Pieper, F. Melo, N. Eswar, M.A. Martí-Renom, M.S. Madhusudhan, N. Mirkovic, and A. Sali. Nat. Struct. Biol., 7, 986-990, 2000. MODBASE, a database of annotated comparative protein structure models. R. Sánchez, U. Pieper, N. Mirkovic, P. I. W. de Bakker, E. Wittenstein, and A. Sali. Nucl. Acids Res., 28, 250-253, 2000. [PDF] Comparative protein structure modeling: Introduction and practical examples with MODELLER. R. Sánchez and A. Sali. In Protein Structure Prediction: Methods and Protocols, pp 97-129. D.M. Webster, editor, Humana Press, 2000. Comparative protein structure modeling. A. Fiser, R. Sánchez, F. Melo and A. Sali. In Computational Biochemistry and Biophysics. M. Watanabe, B. Roux, A. MacKerell, and O. Becker, editors, Marcel Dekker, 2000. Comparative protein structure modeling of genes and genomes. M. A. Martí-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, and A. Sali. Ann. Rev. Biophys. Biomolec. Struct., 29,291-325, 2000. lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS. J. M. Miwa, I. Ibanez-Tallon, G. W. Crabtree, R. Sánchez, A. Sali, L. W. Role and N. Heintz. Neuron, 23, 105-114, 1999. ModBase: A database of comparative protein structure models. R. Sánchez and A. Sali. Bioinformatics, 15, 1060-1061, 1999. Comparative protein structure modeling in genomics. R. Sánchez and A. Sali. J. Comput. Phys., 151, 388-401, 1999. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. R. Sánchez and A. Sali. Proc. Natl. Acad. Sci. USA, 95, 13597-13602, 1998. [PDF] Prediction of bendability and curvature in genomic DNA. A. Gabrielian, K. Vlahovicek, M.G. Munteanu, M.M. Gromiha, I. Brukner, R. Sánchez, and S. Pongor. In Structure, Motion, Interaction and Expression of Biological Molecules, pp117-131. R.H. Sarma and M.H. Sarma, editors, Adenine Press, 1998. Homology protein structure modeling. R. Sánchez, A. Ya. Badretdinov, E. Feyfant and A. Sali. Trans. Amer. Cryst. Assoc., 32, 81-91, 1997. Evaluation of comparative protein structure modeling by MODELLER-3. R. Sánchez and A. Sali. Proteins, Suppl. 1, 50-58, 1997. Advances in comparative protein-structure modelling. R. Sánchez and A. Sali. Current Opinion in Structural Biology, 7, 206-214, 1997. Mammalian cell expression of dimeric small immune proteins. E. Li, A. Pedraza, M. Bestagno, S. Mancardi, R. Sánchez, and O. Burrone. Protein Engineering, 10, 731-736, 1997. Molecular characterisation of the Entamoeba histolytica enolase encoding gene and modelling of the predicted protein. M.E. Hidalgo, R. Sánchez, D.G. Pérez, M.A. Rodríguez, J. García, and E. Orozco. FEMS Microbiology Letters, 148, 123-129, 1997. Comparative protein structure modeling as an optimization problem. R. Sánchez, A. Sali. Journal of Molecular Structure (Theochem), 398, 489-496, 1997. Ligand specificity of brain lipid-binding protein. L. Xu, R. Sánchez , A. Sali, N. Heintz. Journal of Biological Chemistry, 271, 24711-24719, 1996. [PDF] Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data. I. Brukner, R. Sánchez, D. Suck, S. Pongor. J. Biomol. Structure and Dynamics 13, 309-317, 1995. Rationally designed helix-turn-helix proteins and their conformational changes upon DNA-binding. P. Percipalle, A. Simoncsits, S. Zahariev, C. Guarnaccia, R. Sánchez, S. Pongor. EMBO Journal 14, 3200-3205, 1995. Sequence-dependent DNA bending as revealed by DNase I : Bending Parameters for trinucleotides. I. Brukner, R. Sánchez, D. Suck, S. Pongor. EMBO Journal 14, 1812-1818, 1995. Isolation and structure of a novel alpha-amylase inhibitor from Amaranthus hypocondriacus. A. Chagolla, A. Patthy, R. Sáchez, A. Blanco and S. Pongor. in Peptides 1994, ed. Maia H.L.S., ESCOM, Netherlands, pp. 431-432, 1995. Substrate specificity of CDC2 kinase from human HeLa cells as determined with synthetic peptides and molecular modeling. J. Zhang, R. Sánchez, S. Wang, A. Tossi, C. Guarnaccia, S. Zahariev and S. Pongor. Archives of Biochemistry and Biophysics 315, 415-424, 1994. A novel alpha-amylase inhibitor from amaranth (Amaranthus hypocondriacus) seeds. A. Chagolla, A. Blanco, A. Patthy, R. Sánchez and S. Pongor. Journal of Biological Chemistry 269, 23675-23680, 1994. Effect of five irreversible inhibitors on beta-lactamase from Shigella flexneri UCSF-129. M. Campos, M. Alarcón, H. González, R. Sánchez. Microbios 76, 171-179, 1993. Induction of beta-lactamase from Shigella flexneri UCSF-129: purification by affinity chromatography and some properties. M. Campos, H. González, M. Alarcón, R. Sánchez. Microbios 69,171-179, 1992.