ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.

[1]  Adrien Treuille,et al.  Predicting protein structures with a multiplayer online game , 2010, Nature.

[2]  Samuel L. DeLuca,et al.  Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You , 2010, Biochemistry.

[3]  Sergey Lyskov,et al.  PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta , 2010, Bioinform..

[4]  J. Karanicolas,et al.  Atomic accuracy in predicting and designing non-canonical RNA structure , 2010, Nature Methods.

[5]  E. Coutsias,et al.  Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling , 2009, Nature Methods.

[6]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[7]  Ian W. Davis,et al.  RosettaLigand docking with full ligand and receptor flexibility. , 2009, Journal of molecular biology.

[8]  Rhiju Das,et al.  Macromolecular modeling with rosetta. , 2008, Annual review of biochemistry.

[9]  Eric A. Althoff,et al.  Kemp elimination catalysts by computational enzyme design , 2008, Nature.

[10]  Jack Snoeyink,et al.  On-the-Fly Rotamer Pair Energy Evaluation in Protein Design , 2008, ISBRA.

[11]  Eric A. Althoff,et al.  De Novo Computational Design of Retro-Aldol Enzymes , 2008, Science.

[12]  Kimberly A. Reynolds,et al.  An object‐oriented library for computational protein design , 2007, J. Comput. Chem..

[13]  Chu Wang,et al.  Protein-protein docking with backbone flexibility. , 2007, Journal of molecular biology.

[14]  D. Baker,et al.  Automated de novo prediction of native-like RNA tertiary structures , 2007, Proceedings of the National Academy of Sciences.

[15]  Jens Meiler,et al.  New algorithms and an in silico benchmark for computational enzyme design , 2006, Protein science : a publication of the Protein Society.

[16]  J. Meiler,et al.  ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility , 2006, Proteins.

[17]  Jack Snoeyink,et al.  Rotamer-Pair Energy Calculations Using a Trie Data Structure , 2005, WABI.

[18]  O. Schueler‐Furman,et al.  Improved side‐chain modeling for protein–protein docking , 2005, Protein science : a publication of the Protein Society.

[19]  Jack Snoeyink,et al.  An Adaptive Dynamic Programming Algorithm for the Side Chain Placement Problem , 2004, Pacific Symposium on Biocomputing.

[20]  David P. Anderson,et al.  BOINC: a system for public-resource computing and storage , 2004, Fifth IEEE/ACM International Workshop on Grid Computing.

[21]  D. Case,et al.  Exploring protein native states and large‐scale conformational changes with a modified generalized born model , 2004, Proteins.

[22]  D. Baker,et al.  Computational redesign of protein-protein interaction specificity , 2004, Nature Structural &Molecular Biology.

[23]  Chaok Seok,et al.  A kinematic view of loop closure , 2004, J. Comput. Chem..

[24]  D. Baker,et al.  A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. , 2003, Journal of molecular biology.

[25]  Jeffrey J. Gray,et al.  Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. , 2003, Journal of molecular biology.

[26]  Adrian A Canutescu,et al.  Cyclic coordinate descent: A robotics algorithm for protein loop closure , 2003, Protein science : a publication of the Protein Society.

[27]  Niles A Pierce,et al.  Protein design is NP-hard. , 2002, Protein engineering.

[28]  Richard Bonneau,et al.  De novo prediction of three-dimensional structures for major protein families. , 2002, Journal of molecular biology.

[29]  David Baker,et al.  Progress in AB Initio Protein Structure Prediction , 2002, TheScientificWorldJournal.

[30]  Alexander A. Stepanov,et al.  C++ Standard Template Library , 2000 .

[31]  D. Baker,et al.  Native protein sequences are close to optimal for their structures. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[32]  C Kooperberg,et al.  Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. , 1997, Journal of molecular biology.

[33]  S. L. Mayo,et al.  Protein design automation , 1996, Protein science : a publication of the Protein Society.

[34]  Michael J. Vilot,et al.  Standard template library , 1996 .

[35]  Ruben Abagyan,et al.  ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation , 1994, J. Comput. Chem..

[36]  Johan Desmet,et al.  The dead-end elimination theorem and its use in protein side-chain positioning , 1992, Nature.

[37]  F. Richards,et al.  Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry. , 1991, Journal of molecular biology.

[38]  F M Richards,et al.  Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin. , 1991, Journal of molecular biology.

[39]  J. Ponder,et al.  Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.

[40]  R. Brent.  Table errata: Algorithms for minimization without derivatives (Prentice-Hall, Englewood Cliffs, N. J., 1973) , 1975 .

[41]  D. Anderson,et al.  Algorithms for minimization without derivatives , 1974 .

[42]  Hollis G. Potter,et al.  Author Manuscript , 2013 .

[43]  Oliver F. Lange,et al.  Structure prediction for CASP8 with all‐atom refinement using Rosetta , 2009, Proteins.

[44]  Jens Meiler,et al.  Small Molecule Rotamers Enable Simultaneous Optimization of Small Molecule and Protein Degrees of Freedom in ROSETTALIGAND Docking , 2008 .

[45]  Andrew M Wollacott,et al.  Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@home , 2007, Proteins.

[46]  David E. Kim,et al.  Free modeling with Rosetta in CASP6 , 2005, Proteins.

[47]  Lars Malmström,et al.  Automated prediction of CASP‐5 structures using the Robetta server , 2003, Proteins.

[48]  Richard Bonneau,et al.  Rosetta in CASP4: Progress in ab initio protein structure prediction , 2001, Proteins.

[49]  De Yonker,et al.  A New Approach to Protein Design: Grafting of a Buried Transition Metal Binding Site into Escherichia coli Thioredoxin , 1992 .

[50]  W. Braun,et al.  Rapid calculation of first and second derivatives of conformational energy with respect to dihedral angles for proteins general recurrent equations , 1984, Comput. Chem..

[51]  C. Rohl,et al.  Modeling structurally variable regions in homologous proteins with rosetta , 2004, Proteins.