Found 388 results
Sampling bottlenecks in de novo protein structure prediction. Journal of molecular biology. 393(1), 249-60.(2009).
Simultaneous prediction of protein folding and docking at high resolution. Proceedings of the National Academy of Sciences of the United States of America. 106(45), 18978-83.(2009).
Structure similarity measure with penalty for close non-equivalent residues. Bioinformatics. 25(10), 1259-63.(2009).
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).
Alteration of enzyme specificity by computational loop remodeling and design. Proceedings of the National Academy of Sciences of the United States of America. 106(23), 9215-20.(2009).
Assessment of the optimization of affinity and specificity at protein-DNA interfaces. Nucleic acids research. 37(10), e73.(2009).
Motif-directed flexible backbone design of functional interactions. Protein science. 18(6), 1293-305.(2009).
RosettaLigand docking with full ligand and receptor flexibility. Journal of molecular biology. 385(2), 381-92.(2009).
RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation. Protein science. 18(1), 229-39.(2009).
Rationally designed integrin beta3 mutants stabilized in the high affinity conformation. The Journal of biological chemistry. 284(6), 3917-24.(2009).
Prediction of membrane protein structures with complex topologies using limited constraints. Proceedings of the National Academy of Sciences of the United States of America. 106(5), 1409-14.(2009).
De novo protein structure generation from incomplete chemical shift assignments. Journal of biomolecular NMR. 43(2), 63-78.(2009).
Prospects for de novo phasing with de novo protein models. Acta crystallographica. 65(Pt 2), 169-75.(2009).
Computation of conformational coupling in allosteric proteins. PLoS computational biology. 5(8), e1000484.(2009).
The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3. Molecular cell. 34(2), 234-49.(2009).
Comparative analysis of mutant tyrosine kinase chemical rescue. Biochemistry. 48(15), 3378-86.(2009).
A novel semi-biosynthetic route for artemisinin production using engineered substrate-promiscuous P450(BM3). ACS chemical biology. 4(4), 261-7.(2009).
Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins. 75(1), 147-67.(2009).
Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins. 77 Suppl 9, 89-99.(2009).
Emergence of symmetry in homooligomeric biological assemblies. Proceedings of the National Academy of Sciences of the United States of America. 105(42), 16148-52.(2008).
Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination. Journal of the American Chemical Society. 130(47), 15907-15.(2008).
Kemp elimination catalysts by computational enzyme design. Nature. 453(7192), 190-5.(2008).
Ranking predicted protein structures with support vector regression. Proteins. 71(3), 1175-82.(2008).
De novo computational design of retro-aldol enzymes. Science. 319(5868), 1387-91.(2008).
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).
Structural inference of native and partially folded RNA by high-throughput contact mapping. Proceedings of the National Academy of Sciences of the United States of America. 105(11), 4144-9.(2008).
Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases. Journal of molecular biology. 379(4), 745-59.(2008).
The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite. Magnetic resonance in chemistry. 45(S1), S32-S47.(2008).
A new twist in TCR diversity revealed by a forbidden alphabeta TCR. Journal of molecular biology. 375(5), 1306-19.(2008).
Macromolecular modeling with rosetta. Annual review of biochemistry. 77, 363-82.(2008).
Structural genomics of pathogenic protozoa: an overview. Methods in molecular biology. 426, 497-513.(2008).
Advances in Rosetta Protein Structure Prediction on Massively Parallel Systems. Journal of Research and Development . 52(1-2):7-17,(2008).
Automated de novo prediction of native-like RNA tertiary structures. Proceedings of the National Academy of Sciences of the United States of America. 104(37), 14664-9.(2007).
Toward high-resolution prediction and design of transmembrane helical protein structures. Proceedings of the National Academy of Sciences of the United States of America. 104(40), 15682-7.(2007).
Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity. The Journal of biological chemistry. 282(42), 30658-66.(2007).
Protein-protein docking with backbone flexibility. Journal of molecular biology. 373(2), 503-19.(2007).
High-resolution structure prediction and the crystallographic phase problem. Nature. 450(7167), 259-64.(2007).
Prediction of the structure of symmetrical protein assemblies. Proceedings of the National Academy of Sciences of the United States of America. 104(45), 17656-61.(2007).
A putative Src homology 3 domain binding motif but not the C-terminal dystrophin WW domain binding motif is required for dystroglycan function in cellular polarity in Drosophila.. The Journal of biological chemistry. 282(20), 15159-69.(2007).
An alpha-helical burst in the src SH3 folding pathway. Biochemistry. 46(17), 5072-82.(2007).
High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. Journal of molecular biology. 366(4), 1209-21.(2007).
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).
Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy. The EMBO journal. 26(2), 481-93.(2007).
Prediction of structures of multidomain proteins from structures of the individual domains. Protein science. 16(2), 165-75.(2007).
RosettaDock in CAPRI rounds 6-12. Proteins. 69(4), 758-63.(2007).
Cooperative hydrogen bonding in amyloid formation. Protein science. 16(4), 761-4.(2007).
Assessment of predictions submitted for the CASP7 domain prediction category. Proteins. 69 Suppl 8, 137-51.(2007).
Conservation, variability and the modeling of active protein kinases. PloS one. 2(10), e982.(2007).
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins. 69 Suppl 8, 118-28.(2007).
Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. Journal of molecular biology. 362(5), 1004-24.(2006).
Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals. Proceedings of the National Academy of Sciences of the United States of America. 103(44), 16083-8.(2006).
Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density. PLoS computational biology. 2(10), e146.(2006).
ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins. 65(3), 538-48.(2006).
Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels. Proceedings of the National Academy of Sciences of the United States of America. 103(19), 7292-7.(2006).
Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs. Chemistry & biology. 13(5), 521-30.(2006).
High-resolution structural validation of the computational redesign of human U1A protein. Structure. 14(5), 847-56.(2006).
Recapitulation and design of protein binding peptide structures and sequences. Journal of molecular biology. 357(3), 917-27.(2006).
Prediction and design of macromolecular structures and interactions. Philosophical transactions of the Royal Society of London. 361(1467), 459-63.(2006).
Electron density redistribution accounts for half the cooperativity of alpha helix formation. The journal of physical chemistry. B. 110(10), 4503-5.(2006).
The 3D profile method for identifying fibril-forming segments of proteins. Proceedings of the National Academy of Sciences of the United States of America. 103(11), 4074-8.(2006).
Multipass membrane protein structure prediction using Rosetta. Proteins. 62(4), 1010-25.(2006).
Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major. Acta crystallographica. Section F, Structural biology and crystallization communications. 62(Pt 3), 175-9.(2006).
Computational redesign of endonuclease DNA binding and cleavage specificity. Nature. 441(7093), 656-9.(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).
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).
New algorithms and an in silico benchmark for computational enzyme design. Protein science : a publication of the Protein Society. 15(12), 2785-94.(2006).
Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. Journal of molecular biology. 361(1), 195-208.(2006).
Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proceedings of the National Academy of Sciences of the United States of America. 103(14), 5361-6.(2006).
Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic acids research. 34(17), e112.(2006).
Toward high-resolution de novo structure prediction for small proteins. Science. 309(5742), 1868-71.(2005).
Progress in modeling of protein structures and interactions. Science. 310(5748), 638-42.(2005).
A model of anthrax toxin lethal factor bound to protective antigen. Proceedings of the National Academy of Sciences of the United States of America. 102(45), 16409-14.(2005).