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Advances in Rosetta Protein Structure Prediction on Massively Parallel Systems. Journal of Research and Development . 52(1-2):7-17,(2008).
Structure similarity measure with penalty for close non-equivalent residues. Bioinformatics. 25(10), 1259-63.(2009).
Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein science. 12(10), 2262-72.(2003).
Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution. Proteins. 78(14), 3056-62.(2010).
Evaluation of structural and evolutionary contributions to deleterious mutation prediction. Journal of molecular biology. 322(4), 891-901.(2002).
Recapitulation of protein family divergence using flexible backbone protein design. Journal of molecular biology. 346(2), 631-44.(2005).
Kinetics of folding of the IgG binding domain of peptostreptococcal protein L.. Biochemistry. 36(11), 3373-82.(1997).
Structural transitions in the protein L denatured state ensemble. Biochemistry. 38(48), 15927-35.(1999).
Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability. Proceedings of the National Academy of Sciences of the United States of America. 94(20), 10636-40.(1997).
Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. Journal of molecular biology. 338(3), 573-83.(2004).
Low free energy cost of very long loop insertions in proteins. Protein science. 12(2), 197-206.(2003).
Ageneral expressionforbimolecularassociationrates withorientational constraints. Physical Chemistry B.(2002).
Protein Structure Determination from Pseudocontact Shifts Using ROSETTA. Journal of molecular biology.(2012).
Protein structure prediction in 2002.. Current opinion in structural biology. 12(3), 348-54.(2002).
Progress in modeling of protein structures and interactions. Science. 310(5748), 638-42.(2005).
Conserved residue clustering and protein structure prediction. Proteins. 52(2), 225-35.(2003).
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings. Journal of the American Chemical Society.(2011).
Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy. The EMBO journal. 26(2), 481-93.(2007).
RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation. Protein science. 18(1), 229-39.(2009).
RosettaHoles2: a volumetric packing measure for protein structure refinement and validation. Protein science. 19(10), 1991-5.(2010).
Consistent blind protein structure generation from NMR chemical shift data. Proceedings of the National Academy of Sciences of the United States of America. 105(12), 4685-90.(2008).
De novo protein structure generation from incomplete chemical shift assignments. Journal of biomolecular NMR. 43(2), 63-78.(2009).
Clustering of low-energy conformations near the native structures of small proteins. Proceedings of the National Academy of Sciences of the United States of America. 95(19), 11158-62.(1998).
Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science. 329(5989), 309-13.(2010).
Prospects for ab initio protein structural genomics. Journal of molecular biology. 306(5), 1191-9.(2001).
Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins. Suppl 3, 171-6.(1999).
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. Journal of molecular biology. 268(1), 209-25.(1997).
Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion. The Journal of biological chemistry. 281(8), 5042-9.(2006).
Recapitulation and design of protein binding peptide structures and sequences. Journal of molecular biology. 357(3), 917-27.(2006).
Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging. PLoS biology. 4(6), e148.(2006).
A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system. Nature structural & molecular biology. 16(5), 468-76.(2009).
Rescue of degradation-prone mutants of the FK506-rapamycin binding (FRB) protein with chemical ligands. Chembiochem : a European journal of chemical biology. 8(10), 1162-9.(2007).
Mining endonuclease cleavage determinants in genomic sequence data.. The Journal of biological chemistry. 286(37), 32617-27.(2011).