Rosetta Papers

Structure Prediction papers

Protein Design

Protein Interface

Protein-protein Dock

Rosetta Ligand

Homology Modeling

Loop Modeling

NME data

Enzyme Design

Other Rosetta Papers

CASP papers

CAPRI Papers

Applications

Reviews

Large-Scale Prediction Efforts

Other references

Related Software

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(a) Scheme for using Rosetta to build design scaffolds that adopt a fibronectin fold. Residues built from β-strand fragments are shown as hexagons, and residues built from loop fragments are shown as circles. Hydrogen-bonding constraints (green dashes) define the topology of the structure. (b) An example of one of the fibronectin scaffolds built with Rosetta using the scheme from panel a. Butterfoss GL, Kuhlman B. Computer-based design of novel protein structures. Annu Rev Biophys Biomol Struct. 2006;35:49-65.Click here to read.

Ab initio structure prediction:

André I, Bradley P, Wang C, Baker D"Prediction of the structure of symmetrical protein assemblies." Proc. Natl. Acad. Sci. U.S.A. 104, 17656-61. 2007
Rohl, C.A., Strauss, C.E., Misura, K.M.S., & Baker, D."Protein structure prediction using Rosetta" Methods in Enzymology 383, 66-93, 2004.
Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. "High resolution protein structure prediction and the crystallographic phase problem." Nature. 2007 Nov 8;450(7167):176-7.
Das, R. and Baker, D. "Automated de novo prediction of native-like RNA tertiary structures" Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14664-9. Epub 2007 Aug 28.

Protein Design:
Renfrew PD, Butterfoss GL, Kuhlman B "Using quantum mechanics to improve estimates of amino acid side chain rotamer energies." Proteins.. 2008 Jun;71(4):1637-46.
Hu X, Wang H, Ke H, Kuhlman B"High-resolution design of a protein loop. " Proc Natl Acad Sci U S A.. Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17668-73. Epub 2007 Oct 30
Dantas G., Kuhlman B., Callender D., Wong M., & Baker D. "A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins" J. Mol. Biol., 332, 449-460, 2003
Dantas, G., Watters, A.L., Lunde, B.M., Eletr, Z.M., Isern, N.G., Roseman, T., Lipfert, J., Doniach, S., Tompa, M., Kuhlman, B., Stoddard, B.L., Varani, G., Baker, D. "Mis-translation of a Computationally Designed Protein Yields an Exceptionally Stable Homodimer: Implications for Protein Engineering and Evolution" J Mol Biol. 362(5): 1004-1024, 2006
Sammond DW, Eletr ZM, Purbeck C, Kimple RJ, Siderovski DP, Kuhlman B. "Structure-based protocol for identifying mutations that enhance protein-protein binding affinities." J Mol Biol. 2007 Aug 31;371(5):1392-404. Epub 2007
Leaver-Fay A, Butterfoss GL, Snoeyink J, Kuhlman B. "Maintaining solvent accessible surface area under rotamer substitution for protein design."J Comput Chem. 2007 Jun;28(8):1336-41.

Protein Interface:

Kortemme, T, & Baker, D. "A simple physical model for binding energy hot spots in protein-protein complexes." Proc Natl Acad Sci U S A. 2002 Oct 29
Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL. "Design, activity, and structure of a highly specific artificial endonuclease." Mol Cell. 2002 Oct
Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, Baker D. "Computational redesign of protein-protein interaction specificity." Nat Struct Mol Biol. 2004
Joachimiak LA, Kortemme T, Stoddard BL, Baker D."Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface."J Mol Biol. 2006 Aug 4
Humphris EL, Kortemme T."Design of multi-specificity in protein interfaces." PLoS Comput Biol. 2007 Aug 24

Docking:

Chaudhury, S. & Gray, J. J"Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles". accepted for publication in J. Mol. Biol. (2008)
M. Berrondo, M. Ostermeier & J. J. Gray"Structure prediction of domain insertion proteins from structures of the individual domains".Structure 16(4), 513-527 (2008).
Gray, J.J., S.E. Moughan, C. Wang, O. Schueler-Furman, B. Kuhlman, C.A. Rohl, D. Baker "Protein-Protein Docking with Simultaneous Optimization of Rigid-Body Displacement and Side-Chain Conformations".J. Mol. Biol.. vol.331. 1 (2003). pp. 281 - 299.
Wang, C., Schueler-Furman, O., Baker, D. "Improved side-chain modeling for protein-protein docking". Protein Sci 14, 1328-1339, 2005.
Sivasubramanian A, Maynard JA, Gray JJ. "Modeling the structure of mAb 14B7 bound to the anthrax protective antigen.". Proteins. 2007 Aug 1; [Epub ahead of print]
Wang C, Bradley P, Baker D. "Protein-protein docking with backbone flexibility.". J Mol Biol. 2007 Oct 19;373(2):503-19. Epub 2007 Aug 2.
M. Berrondo, M. Ostermeier & J. J. Gray"Protein-Protein Docking with Simultaneous Optimization of Rigid-Body Displacement and Side-Chain Conformations".J. Mol. Biol.. vol.331. 1 (2003). pp. 281 - 299.

Rosetta Ligand:

Meiler J., Baker D. "ROSETTALIGAND: Protein Small Molecule Docking ROSETTALIGAND: Protein Small Molecule Docking with Full Side-Chain Flexibility" Proteins, 65, (3), 538-548. ; 2006

Homology modeling:

Chivian, D., & Baker, D. "Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection" Nucleic Acids Res., 34(17), e112, 2006
Misura, K.M., Chivian, D., Rohl, C.A., Kim, D.E., & Baker, D. "Physically realistic homology models built with ROSETTA can be more accurate than their templates" Proc Natl Acad Sci U S A, 103(14), 5361-5366, 2006

Loop Modeling:

Rohl, C.A.,Strauss, C.E.,Chivian,D.,&Baker, D. "Modeling structurally variable regions in homologous proteins with Rosetta" Proteins 55, 656-677, 2004.
Sood VD, Baker D. "Recapitulation and design of protein binding peptide structures and sequences." J Mol Biol. 2006 Mar 31;357(3):917-27. Epub 2006 Jan 31

NMR data:

Rohl, C.A. "Protein structure estimation using RosettaNMR" Methods in Enzymology 394, 244-260, 2005.

Enzyme Design:

Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, Hilvert D, Houk KN, Stoddard BL, Baker D"De novo computational design of retro-aldol enzymes."Science 319, 1387-91.
Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, RNvthlisberger D, Baker D."New algorithms and an in silico benchmark for computational enzyme design."Protein Sci. 2006 Dec;15(12):2785-94.

Other Rosetta Papers:

Wollacot, A.M., Zanghellini, A. , Murphy, P. , Baker, D."Prediction of structures of multidomain proteins from structures of individual domains"Protein Science. 16: 165-175. 2007
Makrodimitris K, Masica DL, Kim ET, Gray JJ. "Structure Prediction of Protein-Solid Surface Interactions Reveals a Molecular Recognition Motif of Statherin for Hydroxyapatite." J Am Chem Soc. 2007 Oct 12; [Epub ahead of print]
Kortemme, T., Morozov, A.V., & Baker, D. "An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein complexes"J. Mol. Biol. 326, 1239-1259, 2003.
Morozov AV, Kortemme T, Tsemekhman K, Baker D."Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations." Proc Natl Acad Sci U S A. 2004 May 4
Kortemme, T., Joachimiak, L.A., Bullock, A.N., Schuler, A.D., Stoddard, B.L. & Baker, D. "Computational redesign of protein-protein interaction specificity:"Nat Struct Mol Biol 11, 371-379, 2004.
Kim, D.E., Chivian, D., Malmstrom, L., & Baker, D."Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM"Proteins, 61 Suppl 7, 193-200, 2005
Leaver-Fay, A., Kuhlman, B., Snoeyink, J. "Rotamer-Pair Energy Calculations Using a Trie Data Structure"5th Workshop on Algorithms in Bioinformatics (WABI) 389-400, 2005.

CASP papers:

CASP7:
Rhiju Das, Bin Qian, Srivatsan Raman, Robert Vernon, James Thompson, Philip Bradley, Sagar Khare, Michael D. Tyka, Divya Bhat, Dylan Chivian, David E. Kim, William H. Sheffler, Lars MalmstrNvm, Andrew M. Wollacott, Chu Wang, Ingemar Andre, David Bakerr "Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home" Proteins. 2007 Sep 25; [Epub ahead of print]
CASP6:
Bradley, P., Malmstrom, L., Qian, B., Schonbrun, J., Chivian, D., Kim, D.E., Meiler, J., Misura, K.M., & Baker, D. "Free modeling with Rosetta in CASP6" Proteins, 61 Suppl 7, 128-34, 2005
Chivian, D., Kim, D.E., Malmstrom, L., Schonbrun, J., Rohl, C.A., & Baker, D. "Prediction of CASP6 structures using automated Robetta protocols" Proteins, 61 Suppl 7, 157-166, 2005
Kim, D.E., Chivian, D., Malmstrom, L., & Baker, D."Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM"Proteins, 61 Suppl 7, 193-200, 2005
CASP5:
Bradley, P., Chivian, D., Meiler, J., Misura, K.M., Rohl, C.A., Schief, W.R., Wedemeyer, W.J., Schueler-Furman, O., Murphy, P., Schonbrun, J., Strauss, C.E., & Baker D. "Rosetta predictions in CASP5: successes, failures, and prospects for complete automation" Proteins, 53 Suppl 6, 457-68, 2003
Chivian, D., Kim, D.E., Malmstrom, L., Bradley, P., Robertson, T., Murphy, P., Strauss, C.E., Bonneau, R., Rohl, C.A., & Baker, D. "Automated prediction of CASP-5 structures using the Robetta server" Proteins, 53 Suppl 6, 524-533, 2003
CASP4:
Bonneau, R., Tsai, J., Ruczinski, I., Chivian, D., Rohl, C., Strauss, C.E., & Baker, D."Rosetta in CASP4: progress in ab initio protein structure prediction"Proteins, Suppl 5, 119-126, 2001

CAPRI Papers :
Chaudhury S, Sircar A, Sivasubramanian A, Berrondo M, Gray JJ. "Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12."Proteins. 2007 Sep 25; [Epub ahead of print]
M.D. Daily, D. Masica, A. Sivasubramanian, S. Somarouthu, and J.J. Gray. "CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock." Proteins, vol. 60. 2(2005). pp. 181-186.
Schueler-Furman, O., Wang, C., Baker, D. "Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility "Proteins 60, 187-194.2005
Gray, J.J, Moughon, S.E., Kortemme, T., Schueler-Furman, O., Misura, K.M.S., Morozov, A.V. & Baker D. "Protein-protein docking predictions for the CAPRI experiment"Proteins: Structure, Function and Genetics 52, 118-122, 2003

Applications :
Design of a protein with a novel topology:
Kuhlman, B., Dantas, G., Ireton, G.C., Varani, G., Stoddard, B.L., & Baker, D. "Design of a novel globular protein fold with atomic-level accuracy"Science, 302, 1364-1368, 2003

Engineering specific DNA recognition:

Ashworth, J., Havranek, J.J., Duarte, C.M., Sussman, D., Monnat, R.J., Jr., J., Stoddard, B.L., & Baker, D. "Computational redesign of endonuclease DNA binding and cleavage specificity"Nature, 441, 656-659, 2006

Significant progress in high-resolution prediction:

Bradley, P., Misura, K.M., & Baker, D. "Toward high-resolution de novo structure prediction for small proteins"Science, 309, 1868-1871, 2005

Antibody docking:

A. Sivasubramanian, G. Chao, H.M. Pressler, K.D. Witrup, and J.J. Gray. "Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis."Structure, vol. 14. 3(2006). pp.401-414.
Design of a Protein Conformational Switch
Ambroggio, X.I., Kuhlman, B. "Computational design of a single amino acid sequence that can switch between two distinct protein folds."JACS, 128, 1154-61, 2006

Reviews:

O. Schueler-Furman, C. Wang, P. Bradley, K. Misura, and D. Baker "Progress in Modeling of Protein Structures and Interactions."Science 310, 638-642 2005
Gray, J.J."High-resolution protein-protein docking".
Curr. Op. Struct. Biol., vol. 16. 2(2006). pp. 183-193.
Kortemme, T, & Baker, D. "Computational design of protein-protein interactions.".Curr Opin Chem Biol 8, 91-97, 2004.
Morozov, AV. & Kortemme, T. "Potential functions for hydrogen bonds in protein structure prediction and design." Advances in Protein Chemistry 72, 1-38.

Large-Scale Prediction Efforts :

Predicting Pfam:

Bonneau, R., Strauss, C.E., Rohl, C.A., Chivian, D., Bradley, P., Malmstrom, L., Robertson, T., & Baker D. "De novo prediction of three-dimensional structures for major protein families"J Mol Biol, 322, 65-78, 2002

Other references :

Davis IW, Arendall WB 3rd, Richardson DC, Richardson JS."The backrub motion: how protein backbone shrugs when a sidechain dances." Structure. 2006 Feb;14(2):265-74. http://dx.doi.org/10.1016/j.str. 2005.10.007
Betancourt MR."Efficient Monte Carlo trial moves for polypeptide simulations."J Chem Phys. 2005 Nov 1;123(17):174905. http://dx.doi.org/10.1063/1.2102896

Related Software:

Chivian, D., Kim, D.E., Malmstrom, L., Bradley, P., Robertson, T., Murphy, P., Strauss, C.E., Bonneau, R., Rohl, C.A., & Baker, D."Automated prediction of CASP-5 structures using the Robetta server" Proteins, 53 Suppl 6, 524-533, 2003
Chivian, D., & Baker, D."Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection" Nucleic Acids Res., 34(17), e112, 2006
Kortemme, T, Kim, DE. & Baker, D."Computational alanine scanning of protein-protein interfaces" Sci STKE 2004, pl2
Liu, Y., & Kuhlman B." RosettaDesign server for protein design." Nucleic Acids Res., 34, W235-8, 2006
S. Lyskov & J. J. Gray "The RosettaDock server for local protein-protein docking" Nucleic Acids Res. 2008 Jul 1;36