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Publications 2008
A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis.
Nucleic Acids Res.36:4894-901
Abstract
G. Rodrigo, J. Carrera, K.J. Prather, and A. Jaramillo.
DESHARKY : Automatic design of metabolic pathways for optimal cell growth. Bioinformatics Advance Access published on
September 5, 2008. DOI:10.1093/bioinformatics/btn471.
P. Agudelo-Romero, P. Carbonell, F. de la Iglesia, J. Carrera, G. Rodrigo, A. Jaramillo, M.A. Pérez-Amador and S.F. Elena. Changes in the gene expression profile of Arabidopsis
thaliana after infection with Tobacco etch virus. Virology Journal 2008, 5:92.
DOI:10.1186/1743-422X-5-92
Daniele Sciretti, Pierpaolo Bruscolini, Alessandro Pelizzola, Marco Pretti and Alfonso Jaramillo.
Computational protein design with side-chain conformational entropy. Proteins
2008. DOI : 10.1002/prot.22145.
M. Suarez, P. Tortosa, J. Carrera and A. Jaramillo.
Pareto Optimization in Computational
Protein Design with Multiple Objectives. J. Comp. Chem 2008. DOI : 10.1002/jcc.20981
Suarez M., Tortosa P., Jaramillo A. PROTDES : CHARMM toolbox for computational protein design Systems and Synthetic Biology, 2008, 2, 105-113.
G. Rodrigo, J. Carrera and A. Jaramillo.
In silico evolution of the oscillatory response under light-dark cycles. Biochimie. 2008, 90(6):888-97. DOI : 10.1016/j.biochi.2008.02.012
J. Noirel, S.Y. Ow, G. Sanguinetti, A. Jaramillo and P.C. Wright.
Automated extraction of meaningful pathways from quantitative proteomics data. Briefings in Functional Genomics
and Proteomics 2008 Mar ;7(2):136-46. DOI : 10.1093/bfgp/eln011
Thompson D, Lazennec C, Plateau P, Simonson T.
Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations.
Proteins (2008) 71, 1450-1460.
Grigoras I, Lazard M, Plateau P, Blanquet S.
Functional characterization of the Saccharomyces cerevisiae ABC-transporter Yor1p overexpressed in plasma membranes.
Biochim. Biophys. Acta. (2008) 1778, 68-78
A. Aleksandrov, L. Schuldt, W. Hinrichs & T. Simonson T
repressor induction by tetracycline : a molecular dynamics, continuum electrostatics, and crystallographic study.
(2008) Journal of Molecular Biology, 378, 896-910.
A. Aleksandrov & T. Simonson
Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site.
(2008) Journal of the American Chemical Society, 130, 1114-1115.
J. Noirel & T. Simonson
Neutral evolution of proteins : the superfunnel in sequence space and its relation to mutational robustness.
(2008) Journal of Chemical Physics, 129, 185104-185112.
G. Launay & T. Simonson
Homology modelling of protein-protein complexes : a simple method and its possibilities and limitations.
(2008) BMC Bioinformatics, 9, 427-443.
M. Schmidt am Busch, A. Lopes, N. Amara, C. Bathelt & T. Simonson
Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.
(2008) BMC Bioinformatics, 9, 148-163.
M. Schmidt am Busch, A. Lopes, D. Mignon & T. Simonson
Computational protein design : software implementation, parameter optimization, and performance of a simple method.
(2008) Journal of Computational Chemistry, 29, 1092-1102.
T. Simonson
Dielectric relaxation in proteins : the computational perspective.
(2008) Photosynthesis Research, 97, 21-32
D. Thompson, C. Lazennec, P. Plateau & T. Simonson
Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations.
(2008) Proteins, 71, 1450-1460.
