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Pubblicazioni

 

 

Biologia e Medicina

(Biology and Medicine)

 

DrugDiscovery ° Denis ° FightMalaria ° GpuGrid ° MalariaControl ° Rna Word ° Rosetta

 


 

drugdiscovery

DrugDiscovery

 

Voronkov A., Shultz J. - "Drugdiscovery@home - distributed volunteer computing project in the fields of cancer, aging and stem cells". SENS Research Conference 4, 2009. Link

 


Denis

 

Carro J., Rodriguez-Matas J.F., Pueyo E. - "A Methodology to improve human ventricular models for the investigation of cardiac arrhythmias". Biophys J 112(3). Link

Castro J., Monasterio V., Carro J. - "Volunteer Computing Approach for the Collaborative Simulation of Electrophysiological Models". 25th IEEE Collaborative Modeling & Simulation Track. Link

 


 

Fight Malaria/Find@Home

 

--2014--

Jaafar H., Chubb A. et al. - "Visualization of a number of large datasets of compounds that have been tested for effectiveness against the Plasmodium Falciparum strain 3D7". Irish J. of Medical Science 183(12). Link

--2007--

Lavin P., Whelan N. - "Distributed biological screening through Volunteer Computing to find useful protein/drug matches for the purpose of malarial drug research". Degree of Master in Comput Science Univ of Dublin. Link

 


 gpugrid

GpuGrid

 

2018 -2017 -2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2007 - 2006 - 2005 - 2004

 

--2018--

Martinez-Rossel G., De Fabritiis G. et al. - "Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors". J Chem Inf Model 58(3), 2018. Link

Ferruz N., Doerr S., De Fabritiis G. et al. - "Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs". Nature Scient Reports 8 (897), 2018. Link

--2017--

Doerr S., Harvey M.J., De Fabritiis G. et al. - "Dimensionality reduction methods for molecular simulations". Arxive 2017. Link

Kapoor R., Provasi D., De Fabritiis G. et al. - "Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity". Nature Scient Reports 7(11255), 2017. Link

Martinez-Rosell G., Giorgino T., De Fabritiis G. et al. - "Drug Discovery and Molecular Dynamics: Methods, Applications and Perspective Beyond the Second Timescale". Current Topics in Med Chem 17(32), 2017. Link

Doerr S., Giorgino T., De Fabritiis G. et al. - "High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD". J Chem Theory Comput, 2017. Link

Plattner N., Doerr S, De Fabritiis G. - "Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling". Nature Chemistry 2785, 2017. Link

--2016--

Ferruz N., Tresadern G., De Fabritiis G. - "Multibody cofactor and substrate molecular recognition in the myo-inositol monophosphatase enzyme". Scientific Reports 6(30275). Link

Ferruz N., De Fabritiis G. - "Binding Kinetics in Drug Discovery". Molecular Informatics 35(6-7). Link

Doerr S., Harvey M.J, De Fabritiis G. et al. - "HTMD: High throughput molecular dynamics for molecular discovery". J. Chem. Theory Comput. 12(4). Link

--2015--

Stanley N., Esteban-Martin S., De Fabritiis G. - "Progress in studying intrinsically disordered proteins with atomistic simulations". Progress in Biophys and Molec Biol 119(1). Link

Ferruz N., Harvey M.J, De Fabritiis G. et al. - "Insights from Fragment Hit Binding Assays by Molecular Simulations". J Chem Inf Model 55(10). Link

--2014--

Doerr S., De Fabritiis G. - "On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations". J. Chem. Theory Comput. 10(5). Link

Stanley N., Esteban-Martin S, De Fabritiis G. - "Kinetic modulation of a disordered protein domain by phosphorylation". Nature Communications 5(5272). Link

Lauro G., Ferruz N., Fulle S et al. - "Reranking Docking Poses Using Molecular Simulations and Approximate Free Energy Methods". J. Chem. Inf. Model 54(8). Link

Bisignano P., Doerr S., Harvey M.J., Favia A., Cavalli A., De Fabritiis G. - "Kinetic characterization of fragment binding in AmpC Beta-lactamase by high-throughput molecular simulations". J. Chem. Inf. Model. Link

Huang X., De Fabritiis G. - "Understanding Molecular Recognition by Kinetic Network Models Constructed from Molecular Dynamics Simulations". Adv. Exp. Med. Biol. 797. Link

Dainese E., De Fabritiis G., Sabatucci A., Oddi S. et al. - "Membrane lipids are key-modulators of the endocannabinoid-hydrolase FAAH". Biochem J. 457(3). Link

--2013--

Buch I., Ferruz N., De Fabritiis G. - "Computational modeling of an EGFR single-mutation resistance to cetuximab in colorectal cancer treatment". J. Chem. Inf. Model. 53(12). Link 

Doerr S., De Fabritiis G. - "On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations". J. Chem. Theory Comput. Link

Pérez-Hernández G., Paul F., Giorgino T., De Fabritiis G., Noé F. - "Identification of slow molecular order parameters for Markov model construction". J. Chem. Phys. 139. Link

Venken T., Voet A., De Maeyer M., De Fabritiis G., Sadiq K. - "Rapid conformational fluctuations of disordered HIV-1 fusion peptide in solution". J. Chem. Theory Comput. 9. Link

Sadiq K., Guixà-González R., Dainese E., Pastor M., De Fabritiis G., Selent J. - "Molecular modeling and simulation of membrane lipid-mediated effects on GPCRs". Current med. chem. 20(1).  Link

--2012--

D. W. Wright, S. K. Sadiq, De Fabritiis G. and P. V. Coveney - "Thumbs down for HIV: Domain level rearrangements do occur in the NNRTI bound HIV-1 Reverse Transcriptase". J. Am. Chem. Soc.  Link

Bruno A., Costantino G., De Fabritiis G., Pastor M., Selent J. - "Membrane-Sensitive Conformational States of Helix 8 in the Metabotropic Glu2 Receptor, a Class C GPCR". PLoS ONE 7(8). Link

Sadiq S.K., Noe F., De Fabritiis G. - "Kinetic characterization of the critical step in HIV-1 protease maturation". PNAS 109(50). Link

Harvey M.J., De Fabritiis G. - "A Survey of Computational Molecular Science using Graphics Processing Units". Wiley Comp. Mol. Sci. 2(9). Link

Harvey M.J., De Fabritiis G. - "High-throughput molecular dynamics: The powerful new tool for drug discovery". Drug Discovery Today 17(19-20). Link

Giorgino T., Buch I., De Fabritiis G. - "Visualizing the induced binding of SH2-phosphopeptide". J. Chem. Theory Comput. 8(4). Link

--2011--

Buch I., Sadiq S.K., De Fabritiis G. - "Optimized potential of mean force calculations of standard binding free energy". J. Chem. Theory Comput. 7. Link

Giorgino T, De Fabritiis G. - "A high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A". J. Chem. Theory Comput. 7(6). Link

I. Buch, Giorgino T. and De Fabritiis G. - "Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations". PNAS 108. Link

--2010--

Harvey M.J., De Fabritiis G., "Swan: A tool for porting CUDA programs to OpenCL". Comp. Phys. Commun. 182. Link

Selent J., Sanz F., Pastor M., De Fabritiis G. - "Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors". PLOS Computational Biology 6. Link

Sadiq S. K., De Fabritiis G. - "Explicit solvent dynamics and energetics of HIV-1 protease flap-opening and closing". Proteins 78.  Link

Cooper J., Cervenansky F., De Fabritiis G.,Fenner J., et al. - "The Virtual Physiological Human Toolkit". Phil. Trans. R. Soc. A 368. Link

Giorgino T., Harvey M. J., De Fabritiis G. - "Distributed computing as a virtual supercomputer: Tools to run and manage large-scale BOINC simulations". Comp. Phys. Commun. 181. Link

Buch I, Harvey M.J., Giorgino T., Anderson D., De Fabritiis G. - "High-throughput all-atom molecular dynamics simulations using distributed computing". J. Chem. Inf. and Mod. 50.  Link

Lopez Garcia de Lomana A., Beg Q.K., De Fabritiis G., Villa-Freixa J. - "Global Connectivity and Activity Distributions in Cellular Networks". J. Comp. Bio. 17(7). Link

--2009--

Harvey M. J., De Fabritiis G. - "An implementation of the smooth particle-mesh Ewald (PME) method on GPU hardware". J. Chem. Theory Comput. 5(9). Link

Harvey M. J., Giupponi G., De Fabritiis G. - "ACEMD: Accelerated molecular dynamics simulations in the microseconds timescale". J. Chem. Theory and Comput. 5. Link

Giorgino T., Buch I., De Fabritiis G. et al. - "Submitting and managing distributed computations". 5th Boinc Workshop. Link

Guix F.X., Ill-Raga G., Bravo R., Nakaya T., De Fabritiis G., Muñoz F.J. - "Amyloid-dependent triosephosphate isomerase nitrotyrosination induces glycation and tau fibrillation". Brain 132. Link

--2008--

Giupponi G., Harvey M. J. and De Fabritiis G., - "The impact of accelerator processors for high-throughput molecular modeling and simulation". Drug Discovery Today 13. Link

Harvey M. J., De Fabritiis G., Giupponi G. - "Accuracy of the Lattice Boltzmann method on the Cell processor". Phys. Rev. E 78. Link

De Fabritiis G., Geroult S. , Coveney P. V., Waksman G. - "Insights from the energetics of water binding at the domain-ligand interface of the Src SH2 domain". Proteins 72(4). Link

Delgado-Buscalioni R., Coveney P.V., De Fabritiis G. - "Towards multiscale modelling of complex liquids", Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science 222. Link

De Fabritiis G., Coveney P. V., Villa-Freixa J. - "Energetics of K+ permeability through Gramicidin A by forward-reverse steered molecular dynamics", Proteins 73(184). Link

--2007--

STEP Consortium - "Seeding the Euro Physiome: A Roadmap to the Virtual Physiological Human". Link

Delgado-Buscalioni R, De Fabritiis G. - "Embedding molecular dynamics within fluctuating hydrodynamics in multiscale simulations of liquids". Phys. Rev. E 76. Link

Harvey M. J., Giupponi G., Villa-Freixa J., De Fabritiis G. - "PS3GRID.NET: Building a distributed supercomputer using the Playstation 3". Distributed & Grid Computing - Science Made Transparent for Everyone. Link

Giupponi G., De Fabritiis G., Coveney P.V., "Hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules". J. Chem. Phys. 126.  Link

De Fabritiis G. - "Performance of the Cell processor for biomolecular simulations". Comp. Phys. Commun. 176. Link

De Fabritiis G., Villa-Freixa J., Coveney P.V. - "Multiscale modelling of permeation through membrane channels using pregenerated molecular dynamics trajectories". Int. J. Mod. Phys. C, 18. Link

Giupponi G., De Fabritiis G., Coveney P.V. - "A coupled molecular-continuum hybrid model for the simulation of macromolecular dynamics". Int. J. Mod. Phys. C 18. Link

De Fabritiis G., Serrano M., Delgado-Buscalioni R., Coveney P.V. - "Fluctuating hydrodynamic modelling of fluids at the nanoscale". Phys. Rev. E 75. Link

Lloyd S., Gavaghan D., Simpson A., Mascord M., De Fabritiis G. et al. - "Integrative Biology: The Challenges of Developing a Collaborative Research Environment for Heart and Cancer Modelling". Future Generation Computer Systems 23. Link

--2006--

De Fabritiis G., Delgado-Buscalioni R., Coveney P.V. - "Multiscale Modeling of Liquids with Molecular Specificity". Phys. Rev. Lett. 97. Link

Coveney P.V., De Fabritiis G., Harvey M. J., Pickles S., Porter A. - "Coupling applications on distributed resources". Comp. Phys. Commun. 175. Link

Serrano M., De Fabritiis G., Espanol P., Coveney P.V. - "A stochastic Trotter integration scheme for dissipative particle dynamics". Math. Comput. Simul. 72. Link

De Fabritiis G., Serrano M., Espanol P., Coveney P.V. - "Efficient numerical integrators for stochastic models". Physica A 361. Link

--2005--

Coveney P.V., De Fabritiis G., Harvey M. J., Pickles S., Porter A. - "On steering coupled models". UK E-Science AHM2005. Link

Delgado-Buscalioni R., De Fabritiis G., Coveney P.V. - "Determination of the chemical potential using energy biased sampling". J. Chem. Phys. 123. Link

--2004--

De Fabritiis G., Delgado-Buscalioni R., Coveney P.V. - "Energy controlled insertion of polar molecules in dense fluids". J. Chem. Phys. 121. Link

 

 


 malaria

MalariaControl

 

2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008

 

--2016--

Penny M.A., Verity R., Bever C.A. et al. - "The public health impact and cost-effectiveness of malaria vaccine RTS,S/AS01: a systematic comparison of predictions and four mathematical models". Lancet 387. Link

--2015--

Penny M.A., Maire N., Bever C.A. et al. - "Distribution of malaria exposure in endemic countries in Africa considering country levels of effective treatment". Malar J 14. Link

Pemberton-Ross P., Smith T.A. et al. - "Age-shifting in malaria incidence as a result of induced immunological deficit: a simulation study". Malaria J. 14(287). Link

Penny M.A., Galactionova K. et al. - "The public health impact of malaria vaccine RTS,S in malaria endemic Africa: country-specific predictions using 18 month follow-up Phase III data and simulation models". BCM Medicine 13(170). Link

--2014--

Stuckey E.M., Stevenson J., Galactionova K. et al. - "Modeling the Cost Effectiveness of Malaria Control Interventions in the Highlands of Western Kenya". Plos One 9(10). Link

--2013--

Briet O.J.T., Penny M.A., Hardy D. et al. - "Effects of pyrethroid resistance on the cost effectiveness of a mass distribution of long-lasting insecticidal nets: a modelling study".  Malaria Journal 12:77. Link

--2012--

Crowell V., Hardy D., Briet O., Chitnis N., Maire N., Smith T. - "Can we depend on case management to prevent re-establishment of P. falciparum malaria, after local interruption of transmission?". Epidemics 4. Link

Briet O.J.T., Hardy D., Smith T.A. - "Importance of factors determining the effective lifetime of a mass, long-lasting, insecticidal net distribution: a sensitivity analysis". Malaria Journal 11:20. Link

Smith T., Ross A., Maire M., Chitnis N., Studer A., et al. - "Ensemble Modeling of the Likely Public Health Impact of a Pre-Erythrocytic Malaria Vaccine". PLoS Med 9(1). Link

Maire N., Shilcutt S.D., WalkerM D.G., Tediosi F., Smith T.A. - "Cost-Effectiveness of the Introduction of a Pre-Erythrocytic Malaria Vaccine into the Expanded Program on Immunization in Sub-Saharan Africa: Analysis of Uncertainties Using a Stochastic Individual-Based Simulation Model of Plasmodium falciparum Malaria". Value in Health 14. Link

Brooks A., Briet O.J.T., Hardy D., Steketee R., Smith T.A. - "Simulated Impact of RTS,S/AS01 Vaccination Programs in the Context of Changing Malaria Transmission". PLoS ONE 7(3). Link 

--2011--

Ross A., Maire N., Sicuri E., Smith T.A., Conteh L. - "Determinants of the Cost-Effectiveness of Intermittent Preventive Treatment for Malaria in Infants and Children". PLoS ONE 6(4). Link

Smith T.A., Chitnis N.,Briet O.J.T., Tanner M. - "Uses of mosquito-stage transmission-blocking vaccines against Plasmodium falciparum". Trends Parasitol. 27(5). Link

Bretscher M.T., Maire N., Chitnis N., Felger I., Owusu-Agyei S., Smith T.A. - "The distribution of Plasmodium falciparum infection durations". Epidemics 3. Link

--2010--

N. Chitnis,A. Schapira,Smith T.A.,R. Steketee, "Comparing the effectiveness of malaria vector-control interventions through a mathematical model". J. Am. Trop. Med. Hyg. 83(2). Link

Carneiro I., Smith L., Ross A., Roca-Feltrer A., Greenwood B et al. - "Intermittent preventive treatment for malaria in infants: a decision-support tool for sub-Saharan Africa". Bulletin of the World Health Organization. Link

Ross A., Smith T.A. - "Interpreting malaria age-prevalence and incidence curves: a simulation study of the effects of different types of heterogeneity". Malaria Journal 9(132). Link

--2009--

Tediosi F., Maire N., Penny M.A., Studer A., Smith T.A. - "Simulation of the cost-effectiveness of malaria vaccines". Malaria Journal 8(127). Link

Gosoniu L., Vounatsou P., Sogoba P., Maire N., Smith T. - "Mapping malaria risk in West Africa using a Bayesian nonparametric non-stationary model". Computational Statistics and Data Analysis 53. Link

Maire N. - "Estimating parameters for mathematical models of malaria epidemiology". 5th Boinc Workshop. Link

--2008--

Penny M.A., Maire N., Studer A., Schapira A., Smithm T.A. - "What Should Vaccine Developers Ask? Simulation of the Effectiveness of Malaria Vaccines". PLoS ONE 3(9). Link

Ross A., Penny M., Maire N., Studer A., Carneiro I., et al. - "Modelling the Epidemiological Impact of Intermittent Preventive Treatment against Malaria in Infants". PLoS ONE 3(7). Link

Smith T.A., Maire N., Ross A., Penny M., Chitnis N., et al. - "Towards a comprehensive simulation model of malaria epidemiology and control". Parasitology 13. Link

 


 

 rna

RNA World

 

2015 - 2014 - 2013 - 2009

 

--2015--

Hoch P.G., Burenina O.Y., Weber M.H.W. et al. - "Phenotypic characterization and complementation analysis of Bacillus subtilis 6S RNA single and double deletion mutants". Biochimie 117. Link

--2014--

Sinha A., Kohrer C., Weber M.H.W. et al. - "Biochemical characterization of pathogenic mutations in human mitochondrial methionyl-tRNA formyltransferase". J of Biol Chem 289(47). Link

--2013--

Arora S., Bhamidimarri SP., Weber M.H.W., Varshney U. - "Role of the ribosomal P-site elements of m²G966, m(5)C967, and the S9 C-terminal tail in maintenance of the reading frame during translational elongation in Escherichia coli". J. Bacteriol. 195(16). Link

Arora S., Bhamidimarri SP., Bhattacharyya M., Govindan A., et al. - "Distinctive contributions of the ribosomal P-site elements m2G966, m5C967 and the C-terminal tail of the S9 protein in the fidelity of initiation of translation in Escherichia coli". Nucleic Acids Res. 41(9). Link

--2009--

Seshadri A., Dubey B., Weber M.H.W., Varshney U. - "Impact of rRNA methylations on ribosome recycling and fidelity of initiation in Escherichia coli". Mol. Microbiol. 72(3). Link

Weber M.H.W. - "RNA World – A BOINC-based Distributed Supercomputer for High-Throughput Bioinformatic Studies to Advance RNA Research". 5th Boinc Workshop. Link

 


 rosetta

Rosetta@Home

 

2018 - 2017 - 2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2007 - 2006 - 2005 - 2004 - 2003

 

--2018--

Park H., Kim D.E., Baker D. et al. - "Automatic structure prediction of oligomeric assemblies using Robetta in CASP12". Proteins 86(S1), 2018. Link

Ovchinnikov S., Park H. et al. - "Protein structure prediction using Rosetta in CASP12". Proteins 86(S1), 2018. Link

--2017--

Hosseinzadeh P., Bhardwaj G, Baker D. et al. - "Comprehensive computational design of ordered peptide macrocycles". Science 358(6369), 2017. Link

Chevalier A., Colvim T, Baker D. et al. - "Massively parallel de novo protein design for targeted therapeutics". Nature 2017. Link

Ovchinnikov S., Park H, Baker D. et al. - "Topology modeling using Rosetta - coevolution restraints". CASP 12, 2017. Link

Rocklin G., Goreshnik I, Baker D. et al. - "Global  analysis  of  protein  folding  using  massively  parallel  design,  synthesis and testing". Science 357(6347), 2017. Link

Ovchinnikov S., Park H, Baker D. et al. - "Protein structure determination using metagenome sequence data". Science 335(6322). Link

--2016--

Bhardwaj G., Mulligan V.K., Baker D. et al. - "Accurate de novo design of hyperstable constrained peptides". Nature 538(7625). Link

Bale J.B., Gonen S., Baker D. et al. - "Accurate design of megadalton-scale two-component icosahedral protein complexes". Science 353(6297). Link

Service R.F. - "Rules of the game". Science 353(6297). Link

Hsia Y., Bale J.B., Baker D. et al. - "Design of a hyperstable 60-subunit protein icosahedron". Nature 535(7610). Link

Boyken S.E., Chen Z., Baker D. et al. - "De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity". Science 352(6286). Link

Huang P.S., Feldmeier K., Baker D. et al. - "De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy". Nat Chem Biol 12(1).Link

Ovchinnikov S., Kim D.E., Baker D. et al. - "Improved de novo structure prediction in CASP11 by incorporating Co-evolution information into Rosetta". Proteins. Link

--2015--

Ovchinnikov S., Kinch L., Baker D. et al. - "Large-scale determination of previously unsolved protein structures using evolutionary information". Elife 4. Link

Brunette T.J., Parmeggiani F, Baker D. et al. - "Exploring the repeat protein universe through computational protein design". Nature 528. Link

Doyle L., Hallinan J, Baker D. et al. - "Rational design of alpha-helical tandem repeat proteins with closed architectures". Nature 528. Link

Antala S., Ovchinnikov S., Baker D. et al. - "Computational modeling and functional studies provide a structural scaffold for the zinc transporter hZIP4". J of Biological Chem 114. Link

Siegel J.B., Smith A.L., Baker D. et al. - "Computational protein design enables a novel one-carbon assimilation pathway." Proc National Academ Science USA 112(2). Link

Pearson A.D., Mills J.H., Baker D. et al. - "Transition states. Trapping a transition state in a computationally designed protein bottle." Science 347(6224). Link

Park K., Shen B.W., Huang P.S., Baker D. et al. - "Control of repeat-protein curvature by computational protein design". Nat. Struct. Mol. Biol. 22(2). Link

--2014--

Huang P.S., Oberdorfer G., Xu C., Baker D. et al. - "High thermodynamic stability of parametrically designed helical bundles". Science 346(6208). Link

Parmeggiani F., Huang P.S., Vorobiev S., Baker D. et al. - "A General Computational Approach for Repeat Protein Design". J. Mol. Biol. 427(2). Link

Griss R., Schena A., Reymond L., Baker D. et al. - "Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring". Nature Chem. Biol. 10. Link

Rajagopalan S., Wang C., Yu K, Baker D. et al. - "Design of activated serine–containing catalytic triads with atomic-level accuracy". Nature Chem. Biol. 10. Link

King C., Garza E.N., Baker D. et al. - "Removing T-cell epitopes with computational protein design". National Academy of Sciences of the USA. Link

Procko E., Berguig G.Y., Baker D. et al. - "A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells". Cell 157(7). Link

Ovchinnikov S., Kamisetty H, Baker D. - "Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information". Elife Journal 3 (02030). Link

King N.P., Bale J.B, Sheffler W., Baker D. et al. - "Accurate design of co-assembling multi-component protein nanomaterials". Nature 510 (103-108). Link

Baker D. - "Protein folding, structure prediction and design". Biochem Soc. Trans. 42(2). Link

Conway P., Tyka MD, DiMaio F., Konerding DE, Baker D. - "Relaxation of backbone bond geometry improves protein energy landscape modeling". Protein Science 23. Link

Correira B.E., Bates J.T., Loomis R.J., Baker D. et al. - "Proof of principle for epitope-focused vaccine design". Nature 507(7491). Link

Kim DE, Dimaio F., Yu-Ruei Wang R., Song Y., Baker D. - "One contact for every twelve residues allows robust and accurate topology-level protein structure modeling". Proteins 82. Link

--2013--

DiMaio F., Echols N., Baker D., et al. - "Improved low-resolution crystallographic refinement with Phenix and Rosetta". Nature Methods 10. Link

Cherny I., Greisen P.J, Baker D. et al. - "Engineering V-Type Nerve Agents Detoxifying Enzymes Using Computationally Focused Libraries". ACS Chemical Biology 8(11). Link

Strauch E-M., Fleishman S., Baker D. - "Computational design of a pH-sensitive IgG binding protein". National Academy of Sciences of the USA. Link

Adams DF, DiMaio F, Baker D, , et al. - "Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems". Annual Review of Biophysics 42. Link

Song Y, DiMaio F Kim D., Baker D., et al. - "High-resolution comparative modeling with RosettaCM". Cell 21(10). Link

DiMaio F., Terwilliger T., Read R., Wlodawar A. - "Increasing the Radius of Convergence of Molecular Replacement by Density and Energy Guided Protein Structure Optimization". Nature 473. Link

--2012--

Tyka M.D., Jung K., Baker D. - "Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers". J Comp. Chem. 33(31). Link

Stoddard B.L., Tawfik D.S., Baker D. , et al. - "Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis". Nature Chemical Biology 8. Link

Whitehead T., Chevalier A., Song Y., Dreyfus C., Fleishman S.J., De Mattos C., et al. - "Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing". Nat. Biotechnol. 30(6). Link

Azoitei M.L., Ban Y.E., Julien J.P., Bryson S., Schroeter A., Kalyuzhniy O., et al. - "Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope". J. Mol. Biol. 415(1). Link

Terwilliger T.C., Dimaio F., Read R.J., Baker D., et al. - "Mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta". J. Struct. Funct. Genomics 13(2). Link

Lange O.F., Rossi P., Montelione G.T., Baker D., et al. - "Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples". National Academy of Sciences of the USA 109(27). Link

King N., Sheffler W., Baker D., et al. - "Computational design of self-assembling protein nanomaterials with atomic level accuracy". Science 336. Link

--2011--

Karanicolas J., Corn J. E., Chen I., Joachimiak L. A., Dym O., Peck S. H., et al. - "A De Novo Protein Binding Pair By Computational Design and Directed Evolution". Molecular cell 42(2). Link

Kellogg, E. H., Leaver-Fay A., Baker D. - "Role of conformational sampling in computing mutation-induced changes in protein structure and stability". Proteins 79(3). Link

Fleishman S. J., Whitehead T. A., Ekiert D. C. , et al. - "Computational design of proteins targeting the conserved stem region of influenza hemagglutinin". Science 13(332). Link

Chen, D. - H., Baker M. L., Hryc C. F., DiMaio F., Jakana J., Wu W., , et al. - "Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus". National Academy of Sciences of the USA 108(4). Link

Ulge U. Y., Baker D., Monnat R. J. - "Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering". Nucleic acids research 39(10). Link

Li M., DiMaio F., Zhou D., Gustchina A., Lubkowski J., Dauter Z. , et al. - "Crystal structure of XMRV protease differs from the structures of other retropepsins". Nature structural & molecular biology 18(2). Link

Sgourakis N. G., Lange O. F., DiMaio F., Andre I., Fitzkee N. C., Rossi P. , et al., "Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings". J. of the American Chemical Society 113(16). Link

Khersonsky O., Röthlisberger D., Wollacott A. M., Murphy P., Dym O., Albeck S. , et al. - "Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution". J. of molecular biology 407(3). Link

Fleishman S. J., Khare S. D., Koga N., & Baker D. - "Restricted sidechain plasticity in the structures of native proteins and complexes". Protein science 20(4). Link

Guenaga J., Dosenovic P., Ofek G., Baker D., Schief W. R., Kwong P. D. , et al. - "Heterologous epitope-scaffold prime:boosting immuno-focuses B cell responses to the HIV-1 gp41 2F5 neutralization determinant". PloS one. 6(1). Link

Leaver-Fay A., Tyka M., Lewis S. M., Lange O. F., Thompson J., Jacak R. , et al. - "ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules". Methods in Enzymology 487. Link

--2010--

Correia B. E., Ban Y. - E. A., Holmes M. A., Xu H., Ellingson K., Kraft Z. , et al. - "Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope". Structure 18(9). Link

Ashworth J., Taylor G. K., Havranek J. J., Quadri A. S., Stoddard B. L., Baker D. - "Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs". Nucleic acids research 38(16). Link

Kiss G., Röthlisberger D., Baker D., & Houk K. N. - "Evaluation and ranking of enzyme designs". Protein science 19(9). Link

Fowler D. M., Araya C. L., Fleishman S. J., Kellogg E. H., Stephany J. J., Baker D., , et al. - "High-resolution mapping of protein sequence-function relationships". Nature methods 7(9). Link

Ofek G., Guenaga J. F., Schief W. R., Skinner J., Baker D., Wyatt R. , et al. - "Elicitation of structure-specific antibodies by epitope scaffolds". National Academy of Sciences of the USA 107(42). Link

Sheffler W., & Baker D. - "RosettaHoles2: a volumetric packing measure for protein structure refinement and validation". Protein science 19(10). Link

Tyka M. D., Keedy D. A., André I., DiMaio F., Song Y., Richardson D. C. , et al. - "Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping". J. molecular biology 405(2). Link

Sampathkumar P., Lu F., Zhao X., Li Z., Gilmore J., Bain K. , et al. - "Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution". Proteins 78(14). Link

Blum B., Jordan M. I., & Baker D. - "Feature space resampling for protein conformational search". Proteins 78(6). Link

Wang C., Vernon R., Lange O., Tyka M., & Baker D. - "Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry". Protein science 19(3). Link

Siegel J.B., Zanghellini A., Lovick H. M., Kiss G., Lambert A.R., St Clair J. L. , et al. - "Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction". Science 329(5989).  Link

Raman S., Huang Y. J., Mao B., Rossi P., Aramini J. M., Liu G., , et al. - "Accurate automated protein NMR structure determination using unassigned NOESY data". Journal of the American Chemical Society 132(1). Link

Raman S., Lange O. F., Rossi P., Tyka M., Wang X., Aramini J., , et al. - "NMR structure determination for larger proteins using backbone-only data". Science 327(5968). Link

Weerapana E., Wang C., Simon G.M., Richter F., Khare S., Dillon M.B.D., , et al. - "Quantitative reactivity profiling predicts functional cysteines in proteomes". Nature 468(7325). Link

Liu L., Murphy P., Baker D., & Lutz S., "Computational design of orthogonal nucleoside kinases". Chemical communications 46(46). Link

Tang Y., Schneider W. M., Shen Y., Raman S., Inouye M., Baker D. , et al. - "Fully automated high-quality NMR structure determination of small (2)H-enriched proteins". Journal of structural and functional genomics 11(4). Link

Baker D. - "An exciting but challenging road ahead for computational enzyme design". Protein science 19(10).  Link

Das R., Karanicolas J., Baker D., "Atomic accuracy in predicting and designing noncanonical RNA structure". Nature methods 7(4). Link

Fleishman S.J., Corn J.E., Strauch E.M., Whitehead T.A., Andre I., Thompson J. , et al. - "Rosetta in CAPRI rounds 13-19". Proteins 78(15). Link

Cooper S., Treuille A., Barbero J., Leaver-Fay A., Tuite K., Khatib F. , et al. - "The Challenge of Designing Scientific Discovery Games". 5th intern Conf on the Foundations of Digital Games. Link

Sanowar S., Singh P., Pfuetzner R. A., André I., Zheng H., Spreter T. , et al. - "Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System". mBio. 1(3). Link

--2009--

DiMaio F., Tyka M. D., Baker M. L., Chiu W., & Baker D. - "Refinement of protein structures into low-resolution density maps using rosetta". J. of molecular biology 392(1). Link

Davis I. W., Raha K., Head M. S., & Baker D. - "Blind docking of pharmaceutically relevant compounds using RosettaLigand". Protein science 18(9). Link

Rosato A., Bagaria A., Baker D., Bardiaux B., Cavalli A., Doreleijers J. F., , et al. "CASD-NMR: critical assessment of automated structure determination by NMR". Nature methods 6(9). Link

Thyme S. B., Jarjour J., Takeuchi R., Havranek J. J., Ashworth J., Scharenberg A. M., , et al. - "Exploitation of binding energy for catalysis and design". Nature 461(7268. Link

Kim D. E., Blum B., Bradley P., & Baker D. - "Sampling bottlenecks in de novo protein structure prediction". J. of molecular biology 393(1). Link

Das R., André I., Shen Y., Wu Y., Lemak A., Bansal S., , et al. - "Simultaneous prediction of protein folding and docking at high resolution". National Academy of Sciences of USA 106(45). Link

Sadreyev R. I., Shi S. Y., Baker D., & Grishin N. V. - "Structure similarity measure with penalty for close non-equivalent residues". Bioinformatics 25(10). Link

Spreter T., Yip C. K., Sanowar S., André I., Kimbrough T. G., Vuckovic M., , et al. - "A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system". Nature structural & molecular biology 16(5). Link

Murphy P. M., Bolduc J. M., Gallaher J. L., Stoddard B. L., & Baker D. - "Alteration of enzyme specificity by computational loop remodeling and design". National Academy of Sciences of the USA 106(23). Link

Ashworth J., & Baker D. - "Assessment of the optimization of affinity and specificity at protein-DNA interfaces". Nucleic acids research 37(10). Link

Havranek J. J., & Baker D. - "Motif-directed flexible backbone design of functional interactions". Protein science 18(6). Link

Davis I. W., & Baker D. - "RosettaLigand docking with full ligand and receptor flexibility". J. of molecular biology 385(2). Link

Sheffler W., & Baker D. - "RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation". Protein science 18(1). Link

Luo B. H., Karanicolas J., Harmacek L. D., Baker D., Springer T. A. - "Rationally designed integrin beta3 mutants stabilized in the high affinity conformation". J. of biological chemistry 284(6). Link

Barth P., Wallner B., & Baker D. - "Prediction of membrane protein structures with complex topologies using limited constraints". National Academy of Sciences of the USA 106(5). Link

Shen Y., Vernon R., Baker D., Bax A. - "De novo protein structure generation from incomplete chemical shift assignments". Journal of biomolecular NMR 43(2). Link

Das R., & Baker D. - "Prospects for de novo phasing with de novo protein models". Acta crystallographica 65(2). Link

Kidd B. A., Baker D., & Thomas W. E. - "Computation of conformational coupling in allosteric proteins". PLoS computational biology 5(8). Link

Zhu J., Luo B. H., Barth P., Schonbrun J., Baker D., Springer T. A. - "The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3". Molecular cell 34(2). Link

Muratore K. E., Seeliger M. A., Wang Z., Fomina D., Neiswinger J., Havranek J. J., et al. - "Comparative analysis of mutant tyrosine kinase chemical rescue". Biochemistry 48(15). Link

Dietrich J. A., Yoshikuni Y., Fisher K. J., Woolard F. X., Ockey D., McPhee D. J., et al. - "A novel semi-biosynthetic route for artemisinin production using engineered substrate-promiscuous P450(BM3)". ACS chemical biology. 4(4). Link

Ramelot T. A., Raman S., Kuzin A. P., Xiao R., Ma L. - C., Acton T. B., et al. - "Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study". Proteins 75(1). Link

Krieger E., Joo K., Lee J., Lee J., Raman S., Thompson J. , et al. - "Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8". Proteins 77 Suppl 9. Link

Raman S., Vernon R., Thompson J., Tyka M., Sadreyev R., Pei J., , et al. - "Structure prediction for CASP8 with all-atom refinement using Rosetta". Proteins 77 Suppl 9. Link

Ban Y. A., Correia B. E., Holmes M., Boni E., Sather N., Bretz C., , et al. - "4e10 epitope-scaffolds mimic the antibody-bound epitope conformation and block neutralization by sera from rare HIV+ individuals". Retrovirology 6. Link

--2008--

Sawaya M. R., Wojtowicz W. M., Andre I., Qian B., Wu W., Baker D., , et al. - "A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms". Cell 134(6). Link

André I., Strauss C. E. M., Kaplan D. B., Bradley P., & Baker D. - "Emergence of symmetry in homooligomeric biological assemblies". National Academy of Sciences of the USA 105(42). Link

Alexandrova A. N., Röthlisberger D., Baker D., & Jorgensen W. L. - "Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination". J. of the American Chemical Society 130(47). Link

Röthlisberger D., Khersonsky O., Wollacott A. M., Jiang L., DeChancie J., Betker J., et al., "Kemp elimination catalysts by computational enzyme design". Nature 453(7192). Link

Qiu J., Sheffler W., Baker D., & Noble W. S. - "Ranking predicted protein structures with support vector regression". Proteins 71(3). Link

Jiang L., Althoff E. A., Clemente F. R., Doyle L., Röthlisberger D., Zanghellini A., et al. - "De novo computational design of retro-aldol enzymes". Science 319(5868). Link

Shen Y., Lange O., Delaglio F., Rossi P., Aramini J. M., Liu G. , et al. - "Consistent blind protein structure generation from NMR chemical shift data". National Academy of Sciences of the USA 105(12). Link

Das R., Kudaravalli M., Jonikas M., Laederach A., Fong R., Schwans J. P., et al. - "Structural inference of native and partially folded RNA by high-throughput contact mapping". National Academy of Sciences of USA, 105(11). Link

Keeble A. H., Joachimiak L. A., Maté M. J., Meenan N., Kirkpatrick N., Baker D., et al. - "Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases". J. of molecular biology 379(4). Link

Cho H. D., Sood V. D., Baker D., & Weiner A. M. - "On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymes". RNA 14(7). Link

Goobes G., Goobes R., Shaw W. J., Gibson J. M., Long J. R., Raghunathan V., et al. - "The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite". Magnetic resonance in chemistry 45(S1). Link

McBeth C., Seamons A., Pizarro J. C., Fleishman S. J., Baker D., Kortemme T., et al. - "A new twist in TCR diversity revealed by a forbidden alphabeta TCR". J. of molecular biology. 375(5). Link

Das R., & Baker D., "Macromolecular modeling with rosetta". Annual review of biochemistry 77. Link

Fan E., Baker D., Fields S., Gelb M. H., Buckner F. S., Van Voorhis W. C., et al. - "Structural genomics of pathogenic protozoa: an overview". Methods in molecular biology 426. Link

Raman S., Qiuan B., Baker D. - "Advances in Rosetta Protein Structure Prediction on Massively Parallel Systems". J. of Research and Development 52(1-2). Link

--2007--

Wojtowicz W. M., Wu W., Andre I., Qian B., Baker D., & Zipursky L. S. - "A vast repertoire of Dscam binding specificities arises from modular interactions of variable Ig domains". Cell. 130(6). Link

Das, R., & Baker D. - "Automated de novo prediction of native-like RNA tertiary structures". National Academy of Sciences of USA. 104(37). Link

Barth P., Schonbrun J., & Baker D. - "Toward high-resolution prediction and design of transmembrane helical protein structures". National Academy of Sciences of the USA 104(40). Link

Lengyel C. S. E., Willis L. J., Mann P., Baker D., Kortemme T., Strong R. K., et al. - "Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity". J. of biological chemistry 282(42). Link

Wang C., Bradley P., & Baker D. - "Protein-protein docking with backbone flexibility". Journal of molecular biology 373(2). Link

Qian B., Raman S., Das R., Bradley P., McCoy A. J., Read R. J., et al. - "High-resolution structure prediction and the crystallographic phase problem". Nature 450(7167). Link

André I., Bradley P., Wang C., & Baker D. - "Prediction of the structure of symmetrical protein assemblies". National Academy of Sciences of USA 104(45). Link

Dantas G., Corrent C., Reichow S. L., Havranek J. J., Eletr Z. M., Isern N. G., et al. - "High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design". J. of molecular biology 366(4). Link

Stankunas K., Bayle H. J., Havranek J. J., Wandless T. J., Baker D., Crabtree G. R., et al. - "Rescue of degradation-prone mutants of the FK506-rapamycin binding (FRB) protein with chemical ligands". Chembiochem : a European journal of chemical biology 8(10). Link

Shcherbata H. R., Yatsenko A. S., Patterson L., Sood V. D., Nudel U., Yaffe D., et al. - "Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy". The EMBO journal 26(2). Link

Watters A. L., Deka P., Corrent C., Callender D., Varani G., Sosnick T., et al. - "The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection". Cell 128(3). Link

Wollacott A. M., Zanghellini A., Murphy P., & Baker D. - "Prediction of structures of multidomain proteins from structures of the individual domains". Protein science. 16(2). Link

Wang C., Schueler-Furman O., Andre I., London N., Fleishman S. J., Bradley P., et al. - "RosettaDock in CAPRI rounds 6-12". Proteins 69(4).  Link

Tsemekhman K., Goldschmidt L., Eisenberg D., & Baker D. - "Cooperative hydrogen bonding in amyloid formation". Protein science 16(4). Link

Malmström L., Riffle M., Strauss C. E. M., Chivian D., Davis T. N., Bonneau R., et al. - "Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology". PLoS biology 5(4). Link

Tress M., Cheng J., Baldi P., Joo K., Lee J., Seo J. - H., et al. - "Assessment of predictions submitted for the CASP7 domain prediction category". Proteins 69 (Sup. 8). Link

Knight J. D. R., Qian B., Baker D., & Kothary R. - "Conservation, variability and the modeling of active protein kinases". PloS one 2(10). Link

Das R., Qian B., Raman S., Vernon R., Thompson J., Bradley P., et al. - "Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home". Proteins. 69 (Sup 8). Link

--2006--

Dantas G., Watters A. L., Lunde B. M., Eletr Z. M., Isern N. G., Roseman T., et al. - "Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution". J. of molecular biology 362(5). Link

Goobes G., Goobes R., Schueler-Furman O., Baker D., Stayton P. S.,  Drobny G. P. - "Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals". National Academy of Sciences of USA 103(44). Link

Baker M. L., Jiang W., Wedemeyer W. J., Rixon F. J., Baker D., Chiu W. - "Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density". PLoS computational biology 2(10). Link

Meiler J., Baker D., "ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility". Proteins 65(3). Link

Yarov-Yarovoy V., Baker D., & Catterall W. A. - "Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels". National Academy of Sciences of the USA 103(19). Link

Palmer A. E., Giacomello M., Kortemme T., Hires A. S., Lev-Ram V., Baker D., et al. - "Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs". Chemistry & biology 13(5). Link

Dobson N., Dantas G., Baker D., & Varani G. - "High-resolution structural validation of the computational redesign of human U1A protein". Structure 14(5). Link

Sood V. D., Baker D. - "Recapitulation and design of protein binding peptide structures and sequences". J. of molecular biology 357(3). Link

Baker D. - "Prediction and design of macromolecular structures and interactions". Philosophical transactions of the Royal Society of London 361(1467). Link

Morozov A. V., Tsemekhman K., & Baker D. - "Electron density redistribution accounts for half the cooperativity of alpha helix formation". The journal of physical chemistry B. 110(10). Link

Thompson M. J., Sievers S. A., Karanicolas J., Ivanova M. I., Baker D., Eisenberg D. - "The 3D profile method for identifying fibril-forming segments of proteins". National Academy of Sciences of the USA 103(11).  Link

Yarov-Yarovoy V., Schonbrun J., & Baker D. - "Multipass membrane protein structure prediction using Rosetta". Proteins 62(4). Link

Ashworth J., Havranek J. J., Duarte C. M., Sussman D., Monnat R. J., Stoddard B. L., et al. - "Computational redesign of endonuclease DNA binding and cleavage specificity". Nature 441(7093). Link

Sprague E. R., Wang C., Baker D., & Bjorkman P. J. - "Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging". PLoS biology 4(6). Link

Song G., Lazar G. A., Kortemme T., Shimaoka M., Desjarlais J. R., Baker D., et al. - "Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion". J. of Biological Chemistry 281(8). Link

Bradley P., & Baker D. - "Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation". Proteins 65(4). Link

Zanghellini A., Jiang L., Wollacott A. M., Cheng G., Meiler J., Althoff E. A., et al. - "New algorithms and an in silico benchmark for computational enzyme design". Protein Science : a publication of the Protein Society 15(12). Link

Joachimiak L. A., Kortemme T., Stoddard B. L., & Baker D. - "Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface". J. of Molecular Biology 361(1). Link

Misura K. M. S., Chivian D., Rohl C. A., Kim D. E., & Baker D. - "Physically realistic homology models built with ROSETTA can be more accurate than their templates". National Academy of Sciences of the USA 103(14). Link

Chivian D., & Baker D. - "Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection". Nucleic acids research 34(17). Link

--2005--

Bradley P., Misura K. M. S., & Baker D. - "Toward high-resolution de novo structure prediction for small proteins". Science 309(5742). Link

Schueler-Furman O., Wang C., Bradley P., Misura K., & Baker D. - "Progress in modeling of protein structures and interactions". Science 310(5748). Link

Lacy B. D., Lin H. C., Melnyk R. A., Schueler-Furman O., Reither L., Cunningham K., et al. - "A model of anthrax toxin lethal factor bound to protective antigen". National Academy of Sciences of the USA 102(45). Link

Korkegian A., Black M. E., Baker D., & Stoddard B. L. - "Computational thermostabilization of an enzyme". Science 308(5723). Link

Wang C., Schueler-Furman O., & Baker D. - "Improved side-chain modeling for protein-protein docking". Protein science 14(5). Link

Jiang L., Kuhlman B., Kortemme T., & Baker D. - "A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces". Proteins 58(4). Link

Saunders C. T., Baker D. - "Recapitulation of protein family divergence using flexible backbone protein design". J. of Molecular Biology 346(2). Link

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(2). Link

Misura K. M. S., & Baker D. - "Progress and challenges in high-resolution refinement of protein structure models". Proteins 59(1). Link

Meiler J., & Baker D. - "The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy". J. of Magnetic Resonance 173(2). Link

Kim, D. E., Chivian D., Malmström L., Baker D. - "Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM". Proteins 61(Sup 7). Link

Graña O., Baker D., MacCallum R. M., Meiler J., Punta M., Rost B., et al. - "CASP6 assessment of contact prediction". Proteins 61(Sup 7). Link

Bradley P., Malmström L., Qian B., Schonbrun J., Chivian D., Kim D. E., et al. - "Free modeling with Rosetta in CASP6". Proteins 61(Sup 7). Link

Cheng G., Qian B., Samudrala R., Baker D. - "Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design". Nucleic acids research 33(18). Link

Chivian D., Kim D. E., Malmström L., Schonbrun J., Rohl C. A., Baker D. - "Prediction of CASP6 structures using automated Robetta protocols". Proteins 61 Suppl 7. Link

Morozov A. V., Havranek J. J., Baker D., Siggia E. D. - "Protein-DNA binding specificity predictions with structural models". Nucleic acids research 33(18). Link

--2004--

Misura K. M. S., Morozov A. V., Baker D. - "Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction". J. of molecular biology 342(2). Link

Qian B., Ortiz A. R., & Baker D. - "Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation". National Academy of Sciences of the USA 101(43). Link

Havranek J. J., Duarte C. M., Baker D. - "A simple physical model for the prediction and design of protein-DNA interactions". J. of molecular biology 344(1). Link

Morozov A. V., Kortemme T., Tsemekhman K., Baker D. - "Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations". National Academy of Sciences of the USA 101(18). Link

Rohl C. A., Strauss C. E. M., Chivian D., Baker D. - "Modeling structurally variable regions in homologous proteins with rosetta". Proteins 55(3). Link

Watters A. L., Baker D. - "Searching for folded proteins in vitro and in silico". European Journal of Biochemistry 271(9). Link

Svensson H. G., Wedemeyer W. J., Ekstrom J. L., Callender D. R., Kortemme T., Kim D. E., et al. - "Contributions of amino acid side chains to the kinetics and thermodynamics of the bivalent binding of protein L to Ig kappa light chain". Biochemistry 43(9). Link

Schlosshauer M., Baker D. - "Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness". Protein science 13(6). Link

Kim D. E., Chivian D., Baker D. - "Protein structure prediction and analysis using the Robetta server". Nucleic acids research 32(Web Server issue). Link

Kortemme T., Kim D. E., Baker D. - "Computational alanine scanning of protein-protein interfaces". Science's STKE 209. Link

Kuhn M., Meiler J., & Baker D. - "Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins". Proteins 54(2). Link

Kortemme T., Baker D. - "Computational design of protein-protein interactions". Current Opinion in Chemical Biology 8(1). Link

Scalley-Kim M., Baker D. - "Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection". J. of Molecular Biology 338(3). Link

Kortemme T., Joachimiak L. A., Bullock A. N., Schuler A. D., Stoddard B. L., Baker D. - "Computational redesign of protein-protein interaction specificity". Nature Structural & Molecular Biology 11(4). Link

Chen, Y., Kortemme T., Robertson T., Baker D., Varani G. - "A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys". Nucleic Acids Research 32(17). Link

Rohl, C. A., Strauss C. E. M., Misura K. M. S., Baker D. - "Protein structure prediction using Rosetta". Methods in Enzymology 383. Link

Baker D. - "Dimerization Energy Landscapes for Pairs of Ring-Containing Amino Acids in Proteins". J. of Physical Chemistry B. Link

--2003--

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. of Molecular Biology 332(2). Link

Ivankov D. N., Garbuzynskiy S. O., Alm E., Plaxco K. W., Baker D., Finkelstein A. V. - "Contact order revisited: influence of protein size on the folding rate". Protein Science 12(9). Link

Boulanger M. J., Bankovich A. J., Kortemme T., Baker D., Garcia C. K. - "Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130". Molecular Cell. 12(3). Link

Meiler J., Baker D. - "Coupled prediction of protein secondary and tertiary structure". National Academy of Sciences of USA 100(21). Link

Tsai J., Bonneau R., Morozov A. V., Kuhlman B., Rohl C. A., Baker D. - "An improved protein decoy set for testing energy functions for protein structure prediction". Proteins 53(1). Link

Sadreyev R. I., Baker D.,  Grishin N. V. - "Profile-profile comparisons by COMPASS predict intricate homologies between protein families". Protein science 12(10). Link

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(5649). Link

Wedemeyer W. J., Baker D. - "Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates". Proteins 53(2). Link

Millet O., Mittermaier A., Baker D., Kay L. E. - "The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings". J. of molecular biology 329(3). Link

Gray J. J., Moughon S. E., Kortemme T., Schueler-Furman O., Misura K. M. S., Morozov A. V., et al. - "Protein-protein docking predictions for the CAPRI experiment". Proteins 52(1). Link

Kortemme T., Morozov A. V., Baker D. "An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes". J. of Molecular Biology 326(4). Link

Scalley-Kim M., Minard P., Baker D. - "Low free energy cost of very long loop insertions in proteins". Protein Science 12(2). Link

Meiler J., Baker D. - "Rapid protein fold determination using unassigned NMR data". National Academy of Sciences of the USA 100(26). Link

Hazbun T. R., Malmström L., Anderson S., Graczyk B. J., Fox B., Riffle M., et al. - "Assigning function to yeast proteins by integration of technologies". Molecular Cell 12(6). Link

Schueler-Furman O., & Baker D. - "Conserved residue clustering and protein structure prediction". Proteins 52(2).  Link

Gray J. J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C. A., et al. - "Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations". J. of Molecular Biology 331(1). Link

Yi Q., Rajagopal P., Klevit R. E., Baker D. - "Structural and kinetic characterization of the simplified SH3 domain FP1". Protein Science 12(4). Link

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