Publications
]
(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. Abstract
Download: yarov-yarovoy06A.pdf (3.13 MB)
(2006). ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.
Proteins. 65(3), 538-48. Abstract
Download: meiler06A.pdf (760.02 KB)
(2006). Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density.
PLoS computational biology. 2(10), e146. Abstract
Download: baker06B.pdf (945.92 KB)
(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. Abstract
Download: goobes06A.pdf (725.15 KB)
(2006). 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. Abstract
Download: dantas06A.pdf (1.15 MB)
(2007). Assessment of predictions submitted for the CASP7 domain prediction category.
Proteins. 69 Suppl 8, 137-51. Abstract
Download: tress07A.pdf (1.5 MB)
(2007). Conservation, variability and the modeling of active protein kinases.
PloS one. 2(10), e982. Abstract
Download: knight07A.pdf (2.64 MB)
(2007). Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.
Proteins. 69 Suppl 8, 118-28. Abstract
Download: das07B.pdf (808.02 KB)
(2007). Cooperative hydrogen bonding in amyloid formation.
Protein science. 16(4), 761-4. Abstract
Download: tsemekhman07A.pdf (260.96 KB)
(2007). Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology.
PLoS biology. 5(4), e76. Abstract
Download: malmström07A.pdf (592.42 KB)
(2007). RosettaDock in CAPRI rounds 6-12.
Proteins. 69(4), 758-63. Abstract
Download: wang07B.pdf (214.39 KB)
(2007). Prediction of structures of multidomain proteins from structures of the individual domains.
Protein science. 16(2), 165-75. Abstract
Download: wollacott07A.pdf (1.04 MB)
(2007). The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection.
Cell. 128(3), 613-24. Abstract
Download: watters07A.pdf (1.14 MB)
(2007). Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy.
The EMBO journal. 26(2), 481-93. Abstract
Download: shcherbata07A.pdf (916.91 KB)
(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. Abstract
Download: stankunas07A.pdf (579.3 KB)
(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. Abstract
Download: dantas07A.pdf (1.71 MB)
(2007). An alpha-helical burst in the src SH3 folding pathway.
Biochemistry. 46(17), 5072-82. Abstract
Download: li07A.pdf (493.42 KB)
(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. Abstract
Download: André07A.pdf (1.15 MB)
(2007). High-resolution structure prediction and the crystallographic phase problem.
Nature. 450(7167), 259-64. Abstract
Download: qian07A.pdf (1.73 MB)
(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. Abstract
Download: lengyel07A.pdf (454.13 KB)
(2007). Protein-protein docking with backbone flexibility.
Journal of molecular biology. 373(2), 503-19. Abstract
Download: wang07A.pdf (1.57 MB)
(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. Abstract
Download: barth07A.pdf (728.74 KB)
(2007). 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. Abstract
Download: das07A.pdf (1.29 MB)
(2007). A vast repertoire of Dscam binding specificities arises from modular interactions of variable Ig domains.
Cell. 130(6), 1134-45. Abstract
Download: wojtowicz07A.pdf (1.89 MB)
(2008). Advances in Rosetta Protein Structure Prediction on Massively Parallel Systems.
Journal of Research and Development . 52(1-2):7-17, Abstract
Download: raman08A.pdf (446.3 KB)
(2008). Macromolecular modeling with rosetta.
Annual review of biochemistry. 77, 363-82. Abstract
Download: das08A.pdf (1.13 MB)
(2008). Structural genomics of pathogenic protozoa: an overview.
Methods in molecular biology. 426, 497-513. Abstract
(2008). A new twist in TCR diversity revealed by a forbidden alphabeta TCR.
Journal of molecular biology. 375(5), 1306-19. Abstract
Download: mcbeth08A.pdf (5.02 MB)
(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. Abstract
Download: goobes08A.pdf (523.71 KB)
(2008). On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymes.
RNA. 14(7), 1284-9. Abstract
Download: cho08A.pdf (209.43 KB)
(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. Abstract
Download: keeble08A.pdf (1.25 MB)
(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. Abstract
Download: das08A.pdf (806.02 KB)
(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. Abstract
Download: shen08A.pdf (1.01 MB)
(2008). De novo computational design of retro-aldol enzymes.
Science. 319(5868), 1387-91. Abstract
Download: jiang08A.pdf (629.34 KB)
(2008). Ranking predicted protein structures with support vector regression.
Proteins. 71(3), 1175-82. Abstract
Download: qiu08A.pdf (320.82 KB)
(2008). Kemp elimination catalysts by computational enzyme design.
Nature. 453(7192), 190-5. Abstract
Download: röthlisberger08A.pdf (744.82 KB)
(2008). Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination.
Journal of the American Chemical Society. 130(47), 15907-15. Abstract
Download: alexandrova08A.pdf (4.49 MB)
(2008). Emergence of symmetry in homooligomeric biological assemblies.
Proceedings of the National Academy of Sciences of the United States of America. 105(42), 16148-52. Abstract
Download: andré08A.pdf (588.8 KB)
(2008). A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms.
Cell. 134(6), 1007-18. Abstract
Download: sawaya08A.pdf (6.42 MB)
(2009). 4e10 epitope-scaffolds mimic the antibody-bound epitope conformation and block neutralization by sera from rare HIV+ individuals.
Retrovirology. 6, Download: ban09A.pdf (130.41 KB)
(2009). Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8.
Proteins. 77 Suppl 9, 114-22. Abstract
Download: krieger09A.pdf (646.49 KB)
(2009). Structure prediction for CASP8 with all-atom refinement using Rosetta.
Proteins. 77 Suppl 9, 89-99. Abstract
Download: raman09A.pdf (500.47 KB)
(2009). Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.
Proteins. 75(1), 147-67. Abstract
Download: ramelot09A.pdf (790.67 KB)
(2009). A novel semi-biosynthetic route for artemisinin production using engineered substrate-promiscuous P450(BM3).
ACS chemical biology. 4(4), 261-7. Abstract
Download: dietrich09A.pdf (1.67 MB)
(2009). Comparative analysis of mutant tyrosine kinase chemical rescue.
Biochemistry. 48(15), 3378-86. Abstract
Download: muratore09A.pdf (318.66 KB)
(2009). The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3.
Molecular cell. 34(2), 234-49. Abstract
Download: zhu09A.pdf (4.15 MB)
(2009). Computation of conformational coupling in allosteric proteins.
PLoS computational biology. 5(8), e1000484. Abstract
Download: kidd09A.pdf (484.92 KB)
(2009). De novo protein structure generation from incomplete chemical shift assignments.
Journal of biomolecular NMR. 43(2), 63-78. Abstract
Download: shen09A.pdf (2.53 MB)
(2009). Prospects for de novo phasing with de novo protein models.
Acta crystallographica. 65(Pt 2), 169-75. Abstract
Download: das09B.pdf (713.43 KB)
(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. Abstract
Download: barth09A.pdf (596.08 KB)
(2009). Rationally designed integrin beta3 mutants stabilized in the high affinity conformation.
The Journal of biological chemistry. 284(6), 3917-24. Abstract
Download: luo09A.pdf (673.21 KB)
(2009). RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation.
Protein science. 18(1), 229-39. Abstract
Download: sheffler09A.pdf (503.42 KB)
(2009). RosettaLigand docking with full ligand and receptor flexibility.
Journal of molecular biology. 385(2), 381-92. Abstract
Download: davis09B.pdf (1.36 MB)
(2009). Assessment of the optimization of affinity and specificity at protein-DNA interfaces.
Nucleic acids research. 37(10), e73. Abstract
Download: ashworth09A.pdf (3.58 MB)
(2009). Motif-directed flexible backbone design of functional interactions.
Protein science. 18(6), 1293-305. Abstract
Download: havranek09A.pdf (753.33 KB)
(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. Abstract
Download: murphy09A.pdf (954.03 KB)
(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. Abstract
Download: spreter09A.pdf (2.37 MB)
(2009). Structure similarity measure with penalty for close non-equivalent residues.
Bioinformatics. 25(10), 1259-63. Abstract
Download: sadreyev09A.pdf (259.16 KB)
(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. Abstract
Download: das09A.pdf (1.57 MB)
(2009). Sampling bottlenecks in de novo protein structure prediction.
Journal of molecular biology. 393(1), 249-60. Abstract
Download: kim09A.pdf (1.12 MB)
(2009). Exploitation of binding energy for catalysis and design.
Nature. 461(7268), 1300-4. Abstract
Download: thyme09A.pdf (971.19 KB)
(2009). Blind docking of pharmaceutically relevant compounds using RosettaLigand.
Protein science. 18(9), 1998-2002. Abstract
Download: davis09A.pdf (261.62 KB)
(2009). CASD-NMR: critical assessment of automated structure determination by NMR.
Nature methods. 6(9), 625-6. Download: rosato09A.pdf (175.47 KB)
(2009). Refinement of protein structures into low-resolution density maps using rosetta.
Journal of molecular biology. 392(1), 181-90. Abstract
Download: dimaio09A.pdf (1.54 MB)
(2010). The Challenge of Designing Scientific Discovery Games.
Proceedings of the Fifth international Conference on the Foundations of Digital Games. Abstract
Download: cooper10A.pdf (1.19 MB)
(2010). Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System.
mBio. 1(3), Abstract
Download: sanowar10A.pdf (1.65 MB)
(2010). Atomic accuracy in predicting and designing noncanonical RNA structure.
Nature methods. 7(4), 291-4. Abstract
Download: das10A.pdf (1.13 MB)
(2010). An exciting but challenging road ahead for computational enzyme design.
Protein science. Download: baker10A.pdf (58.56 KB)
(2010). Predicting protein structures with a multiplayer online game.
Nature. 466(7307), 756-60. Abstract
Download: cooper10A.pdf (1.33 MB)
(2010). Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.
Journal of structural and functional genomics. 11(4), 223-32. Abstract
Download: tang10A.pdf (451.53 KB)
(2010). Computational design of orthogonal nucleoside kinases.
Chemical communications. 46(46), 8803-5. Abstract
Download: liu10A.pdf (1.22 MB)
(2010). Quantitative reactivity profiling predicts functional cysteines in proteomes.
Nature. 468(7325), 790-5. Abstract
Download: weerapana10A.pdf (608.01 KB)
(2010). NMR structure determination for larger proteins using backbone-only data.
Science. 327(5968), 1014-8. Abstract
Download: raman10A.pdf (2.02 MB)
(2010). Accurate automated protein NMR structure determination using unassigned NOESY data.
Journal of the American Chemical Society. 132(1), 202-7. Abstract
Download: raman10A.pdf (3.49 MB)
(2010). Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.
Science. 329(5989), 309-13. Abstract
Download: siegel10A.pdf (1.55 MB)
(2010). Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry.
Protein science. 19(3), 494-506. Abstract
Download: wang10A.pdf (571.91 KB)
(2010). Feature space resampling for protein conformational search.
Proteins. 78(6), 1583-93. Abstract
Download: blum10A.pdf (621.02 KB)
(2010). Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution.
Proteins. 78(14), 3056-62. Download: sampathkumar10A.pdf (2.78 MB)
(2010). Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping.
Journal of molecular biology. Abstract
Download: tyka10A.pdf (2.13 MB)
(2010). RosettaHoles2: a volumetric packing measure for protein structure refinement and validation.
Protein science. 19(10), 1991-5. Abstract
Download: sheffler10A.pdf (327.06 KB)