Table of contents

Rosetta papers

Ab initio structure prediction:

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. manuscript accepted."

Nature. 2007 Oct 14; [Epub ahead of print]

RNA folding

Das, R. and Baker, D.

"Automated de novo prediction of native-like RNA tertiary structures"

Proceedings of the National Academy of Sciences U.S.A. 104, 14644-14669.

Design:

Kuhlman, B., & Baker D.

"Native protein sequences are close to optimal for their structures"

Proc Natl Acad Sci USA, 97, 10383-10388, 2000

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 Jun 8

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.

Rosetta Interface / Protein Interface Design:

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:

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.

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 (with alignment ensembles):

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

Homology modeling (without a fixed template):

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

Interface alanine scanning:

Kortemme, T., & Baker, D.

"A simple physical model for binding energy hotspots in protein protein complexes"

Proc Natl Acad Sci U S A, 99, 14116-14121, 2002.

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:

C. E. M. Strauss, P. M. Bowers, D. Baker

"De novo protein structure determiniation using sparse NMR data"

Biomolecular NMR, 18 (4):311-318 (2000)

Enzyme Design:

Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Röthlisberger D, Baker D.

"New algorithms and an in silico benchmark for computational enzyme design."

Protein Sci. 2006 Dec;15(12):2785-94.

Domain Assembly:

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

Solid Surface

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]

Orientation-dependent hydrogen bonding potential:

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

Original Rosetta papers:

Simons, K.T., Ruczinski, I., Kooperberg, C., Fox, B., Bystroff, C., & Baker, D.

"Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins"

Proteins, 34, 82-95, 1999

Simons, K.T., Kooperberg, C., Huang, E., & Baker, D.

"Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions"

J Mol Biol, 268, 209-225, 1997

Redesign of protein-protein interactions:

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.

RosettaDOM:

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

Rotamer-Pair Energy Computation:

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:

"Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home"

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 Malmström, Andrew M. Wollacott, Chu Wang, Ingemar Andre, David Baker

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

CASP3:

Simons, K.T., Bonneau, R., Ruczinski, I., & Baker, D.

"Ab initio protein structure prediction of CASP III targets using ROSETTA"

Proteins., Suppl 3, 171-176, 1999

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. (2005). 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.

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

Progress in Modeling of Protein Structures and Interactions.

O. Schueler-Furman, C. Wang, P. Bradley, K. Misura, and D. Baker (2005)

Science 310, 638-642

Rohl CA, Strauss CEM, Misura K, Baker D. Protein Structure Prediction Using Rosetta. (2004) Methods in Enzymology. 383: 66-93.

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

Backrub Monte Carlo:

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

Ginzu:

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

K*Sync:

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

Robetta:

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

Robetta Alanine scanning:

Kortemme, T, Kim, DE. & Baker, D.

"Computational alanine scanning of protein-protein interfaces. "

Sci STKE 2004, pl2

RosettaDesign Server:

Liu, Y., & Kuhlman B.

RosettaDesign server for protein design.

Nucleic Acids Res., 34, W235-8, 2006

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