Roland Bonneau

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Rosetta ab initio protein structure predictions in CASP4 were considerably more consistent and more accurate than previous ab initio structure predictions. Large segments were correctly predicted (>50 residues superimposed within an RMSD of 6.5 A) for 16 of the 21 domains under 300 residues for which models were submitted. Models with the global fold(More)
To generate structures consistent with both the local and nonlocal interactions responsible for protein stability, 3 and 9 residue fragments of known structures with local sequences similar to the target sequence were assembled into complete tertiary structures using a Monte Carlo simulated annealing procedure (Simons et al., J Mol Biol 1997; 268:209-225).(More)
Considerable recent progress has been made in the field of ab initio protein structure prediction, as witnessed by the third Critical Assessment of Structure Prediction (CASP3). In spite of this progress, much work remains, for the field has yet to produce consistently reliable ab initio structure prediction protocols. In this work, we review the features(More)
This study explores the use of multiple sequence alignment (MSA) information and global measures of hydrophobic core formation for improving the Rosetta ab initio protein structure prediction method. The most effective use of the MSA information is achieved by carrying out independent folding simulations for a subset of the homologous sequences in the MSA(More)
Ab initio protein structure prediction methods have improved dramatically in the past several years. Because these methods require only the sequence of the protein of interest, they are potentially applicable to the open reading frames in the many organisms whose sequences have been and will be determined. Ab initio methods cannot currently produce models(More)
Procedures for the generation and collection of transient UV-visible absorbance data are briefly reviewed. Problems associated with signal generation (scattered light, inhomogeneous distribution of transients, instability of pulsed light sources), signal detection (averaging, filtering), and signal analysis in kinetic and spectrographic flash photolysis are(More)
It was found that the anomalous fluorescence quenching in methanol (as compared to other solvents) of 9-trimethylsilylanthracene (2) is accompanied by a chemical reaction leading to anthracene. This ipso substitution is due to a hydrogen bonding formation in the excited singlet state preceding the carbon-silicon bond cleavage. The mechanism was studied(More)
The photoreactivity of methoxy-p-benzoquinone (MQ) and methoxyhydroquinone (MHQ) in dilute solution (10(-4)-10(-3) M) was studied using continuous irradiation and laser flash photolysis (LFP). The quinone irradiated in degassed tetrahydrofuran (THF) gives MHQ and an adduct with the solvent. Only the formation of hydroquinone is observed in ethanol, and(More)