Publications
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(2012). Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope.
Journal of molecular biology. 415(1), 175-92. Abstract
Download: azoitei12A.pdf (1.79 MB)
(2012). Structure of the Ultra-High-Affinity Colicin E2 DNase-Im2 Complex.
Journal of molecular biology. Abstract
Download: wojdyla12A.pdf (2.09 MB)
(2012). An engineered microbial platform for direct biofuel production from brown macroalgae.
Science. 335(6066), 308-13. Abstract
Download: wargacki12A.pdf (1.41 MB)
(2012). Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.
Journal of molecular biology. 415(3), 615-25. Abstract
Download: wang12A.pdf (1.22 MB)
(2012). Protein Structure Determination from Pseudocontact Shifts Using ROSETTA.
Journal of molecular biology. Abstract
Download: schmitz12A.pdf (1.03 MB)
(2012). Structural basis for gating charge movement in the voltage sensor of a sodium channel.
Proceedings of the National Academy of Sciences of the United States of America. 109(2), E93-102. Abstract
Download: yarov-yarovoy12A.pdf (2.46 MB)
(2012). Blind testing of routine, fully automated determination of protein structures from NMR data.
Structure. 20(2), 227-36. Abstract
(2012). Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.
Nature chemical biology. Abstract
Download: khare12A.pdf (1.14 MB)
(2012). Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.
Nature biotechnology. 30(2), 190-2. Abstract
Download: eiben12A.pdf (552.17 KB)
(2012). Atomic model of the type III secretion system needle.
Nature. Abstract
Download: sgourakis12A.pdf (1015.62 KB)
(2011). Mining endonuclease cleavage determinants in genomic sequence data..
The Journal of biological chemistry. 286(37), 32617-27. Abstract
(2011). Solution structure of a minor and transiently formed state of a T4 lysozyme mutant.
Nature. 477(7362), 111-4. Abstract
Download: bouvignies11A.pdf (1023.45 KB)
(2011). Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.
Science. 334(6054), 373-6. Abstract
Download: azoitei11A.pdf (2.01 MB)
(2011). Crystal structure of a monomeric retroviral protease solved by protein folding game players.
Nature structural & molecular biology. 18(10), 1175-7. Abstract
Download: khatib11A.pdf (893.7 KB)
(2011). Algorithm discovery by protein folding game players..
Proceedings of the National Academy of Sciences of the United States of America. Abstract
Download: Khatib11B.pdf (2.4 MB)
(2011). Computational design of proteins targeting the conserved stem region of influenza hemagglutinin.
Science. 332(6031), 816-21. Abstract
Download: fleishman11B.pdf (643.74 KB)
(2011). A synthetic homing endonuclease-based gene drive system in the human malaria mosquito.
Nature. 473(7346), 212-5. Abstract
Download: windbichler11A.pdf (563.32 KB)
(2011). Improved molecular replacement by density- and energy-guided protein structure optimization.
Nature. Abstract
Download: dimaio11A.pdf (972.77 KB)
(2011). A De Novo Protein Binding Pair By Computational Design and Directed Evolution.
Molecular cell. Abstract
Download: karanicolas11A.pdf (1.2 MB)
(2011). Role of conformational sampling in computing mutation-induced changes in protein structure and stability.
Proteins. 79(3), 830-8. Abstract
Download: kellogg11A.pdf (430.48 KB)
(2011). Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation.
Nature. Abstract
Download: sievers11A.pdf (925.12 KB)
(2011). Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus.
Proceedings of the National Academy of Sciences of the United States of America. 108(4), 1355-60. Abstract
Download: chen11A.pdf (2.71 MB)
(2011). Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering.
Nucleic acids research. Abstract
Download: ulge11A.pdf (638.72 KB)
(2011). Crystal structure of XMRV protease differs from the structures of other retropepsins.
Nature structural & molecular biology. 18(2), 227-9. Abstract
Download: li11A.pdf (663.49 KB)
(2011). The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex.
Molecular cell. 44(6), 942-53. Abstract
Download: brzovic11A.pdf (1.14 MB)
(2011). Incorporation of evolutionary information into Rosetta comparative modeling..
Proteins. 79(8), 2380-8. Abstract
Download: thompson11A.pdf (624.44 KB)
(2011). Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings.
Journal of the American Chemical Society. Abstract
Download: sgourakis11A.pdf (655.81 KB)
(2011). Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution.
Journal of molecular biology. 407(3), 391-412. Abstract
Download: khersonsky11A.pdf (1.77 MB)
(2011). Restricted sidechain plasticity in the structures of native proteins and complexes.
Protein science. 20(4), 753-7. Abstract
Download: fleishman11A.pdf (295.85 KB)
(2011). Heterologous epitope-scaffold prime:boosting immuno-focuses B cell responses to the HIV-1 gp41 2F5 neutralization determinant.
PloS one. 6(1), e16074. Abstract
Download: guenaga11A.pdf (1.95 MB)
(2011). ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
Methods in enzymology. 487, 545-74. Abstract
Download: leaver-fay11A.pdf (1.53 MB)
(2010). Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope.
Structure. 18(9), 1116-26. Abstract
Download: correia10A.pdf (1.12 MB)
(2010). Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.
Nucleic acids research. 38(16), 5601-8. Abstract
Download: ashworth10.pdf (3.02 MB)
(2010). Evaluation and ranking of enzyme designs.
Protein science. 19(9), 1760-73. Abstract
Download: kiss10A.pdf (884.51 KB)
(2010). High-resolution mapping of protein sequence-function relationships.
Nature methods. 7(9), 741-6. Abstract
Download: fowler10A.pdf (1.09 MB)
(2010). Elicitation of structure-specific antibodies by epitope scaffolds.
Proceedings of the National Academy of Sciences of the United States of America. 107(42), 17880-7. Abstract
Download: ofek10A.pdf (2.68 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)
(2010). Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping.
Journal of molecular biology. Abstract
Download: tyka10A.pdf (2.13 MB)
(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). Feature space resampling for protein conformational search.
Proteins. 78(6), 1583-93. Abstract
Download: blum10A.pdf (621.02 KB)
(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). 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). 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). NMR structure determination for larger proteins using backbone-only data.
Science. 327(5968), 1014-8. Abstract
Download: raman10A.pdf (2.02 MB)
(2010). Quantitative reactivity profiling predicts functional cysteines in proteomes.
Nature. 468(7325), 790-5. Abstract
Download: weerapana10A.pdf (608.01 KB)
(2010). Computational design of orthogonal nucleoside kinases.
Chemical communications. 46(46), 8803-5. Abstract
Download: liu10A.pdf (1.22 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). Predicting protein structures with a multiplayer online game.
Nature. 466(7307), 756-60. Abstract
Download: cooper10A.pdf (1.33 MB)
(2010). An exciting but challenging road ahead for computational enzyme design.
Protein science. Download: baker10A.pdf (58.56 KB)
(2010). Atomic accuracy in predicting and designing noncanonical RNA structure.
Nature methods. 7(4), 291-4. Abstract
Download: das10A.pdf (1.13 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)
(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)
(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). Exploitation of binding energy for catalysis and design.
Nature. 461(7268), 1300-4. Abstract
Download: thyme09A.pdf (971.19 KB)
(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). 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). Structure similarity measure with penalty for close non-equivalent residues.
Bioinformatics. 25(10), 1259-63. Abstract
Download: sadreyev09A.pdf (259.16 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). 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). 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). RosettaLigand docking with full ligand and receptor flexibility.
Journal of molecular biology. 385(2), 381-92. Abstract
Download: davis09B.pdf (1.36 MB)
(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). 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). 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). 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). Computation of conformational coupling in allosteric proteins.
PLoS computational biology. 5(8), e1000484. Abstract
Download: kidd09A.pdf (484.92 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). Comparative analysis of mutant tyrosine kinase chemical rescue.
Biochemistry. 48(15), 3378-86. Abstract
Download: muratore09A.pdf (318.66 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). 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). 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). 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)
(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)
(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). 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)