Pubblicazioni Bio e Med
Valutazione attuale: 5 / 5
Biologia e Medicina
(Biology and Medicine)
Denis ° GpuGrid ° Rna Word ° Rosetta ° Sidock
Monasterio V., Carro J. et al. - "Cardiac cells stimulated with an axial current-like waveform reproduce electrophysiological properties of tissue fibers". Comput Methods and Programs in Biomedicine 226, 2022. Link
Gomez M., Carro J. et al. - "An in Silico Investigation Into The Role of SK Channels in Failing Ventricular Myocytes". CinC (Comput in Cardiology) Conference 2022. Link
Carro J. - "New Methodologies for the Development and Validation of Electrophysiological Models". Phd Thesis, 2019. Link
Monasterio V., Castro-Mur J. et al. - "DENIS: Solving cardiac electrophysiological simulations with volunteer computing". Plos One 13(10), 2018. Link
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), 2017. Link
Castro J., Monasterio V., Carro J. - "Volunteer Computing Approach for the Collaborative Simulation of Electrophysiological Models". 25th IEEE Collaborative Modeling & Simulation Track, 2016. Link
2024 - 2023 - 2022 - 2021 - 2020 - 2019 - 2018 - 2017 - 2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2007 - 2006 - 2005 - 2004
--2024--
Zariquiey F.S., Galvelis R. et al. - "Enhancing Protein–Ligand Binding Affinity Predictions Using Neural Network Potentials". J. Chem. Inf. Model. 64(5), 2024. Link
--2023--
Herrena-Nieto P., DeFabritiis G. et al. - "Binding-and-Folding Recognition of an Intrinsically Disordered Protein Using Online Learning Molecular Dynamics". J. Chem. Theory Comput 19(13), 2023. Link
Majewski M., Perez A. et al. - "Machine Learning Coarse-Grained Potentials of Protein Thermodynamics". Nature Commun 14(5739), 2023. Link
Galvelis R., Easteman P. et al. - "NNP/MM: Fast molecular dynamics simulations with machine learning potentials and molecular mechanics". J. Chem. Inf. Model. 63(18), 2023. Link
--2022--
Perez Culubret A. - "Learning how to simulate : Applying machine learning methods to improve molecular dynamics simulations". Phd Thesis, 2022. Link
Torrens Fontanals M. - "Making protein dynamics FAIR : Research platforms for the collection, dissemination, and analysis of molecular dynamics simulations". Phd Thesis, 2022. Link
--2021--
Doerr S., Majewski M. et al. - "TorchMD: A deep learning framework for molecular simulations". J Chem Theory Comp 17(4), 2021. Link
Bollati M., Diomede L. et al. - "A novel hotspot of gelsolin instability triggers an alternative mechanism of amyloid aggregation". Computat and Struct Biotech Jour 19, 2021. Link
--2020--
Herrera-Nieto P., Perez A. et al. - "Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations". Nature Scientific Reports 10(12402), 2020. Link
Cossu F., Sorrentino L., et al. - "Computational and experimental characterization of NF023, a candidate anticancer compound inhibiting cIAP2/TRAF2 assembly". J. Chem. Inf. Model. 60(10), 2020. Link
Herrera-Nieto P., Perez A. et al. - "Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations". J. Chem. Inf. Model. 60(10), 2020. Link
Rodriguez-Espigarez I., Selent J. et al. - "GPCRmd uncovers the dynamics of the 3D-GPCRome". Nature Methods 17, 2020. Link
Martinez-Rosell G., Lovera S. et al. - "PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations". J. Chem. Inf. Model. 60(4), 2020. Link
--2019--
Wang J., Olsson S. et al. - "Machine Learning of Coarse-Grained Molecular Dynamics ForceFields". ACS Cent Sci 5, 2019. Link
--2018--
Perez A., De Fabritiis G. et al. - "Simulations meet Machine Learning in Structural Biology". Current Option in Struct Biol 49(139), 2018. Link
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". Arxiv 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., De Fabritiis G. et al. - "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., 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
--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
2024 - 2023 - 2022 - 2021 - 2020 - 2019 - 2018 - 2017 - 2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2007 - 2006 - 2005 - 2004 - 2003
--2024--
Salveson P.J., Moyer A.P et al. - "Expansive discovery of chemically diverse structured macrocyclic oligoamides". Science 384(6694), 2024. Link
--2023--
Wu K., Bai H. et al. - "De novo design of modular peptide-binding proteins by superhelical matching". Nature 616, 2023. Link
Anndya R., Shi L. et al. - "De novo design of highly selective miniprotein inhibitors of integrins avß6 and avß8". Nat Commun 14 (5660), 2023. Link
Kim D.E., Jensen D.R. et al. - "De novo design of small beta barrel proteins". PNAS 120(11), 2023. Link
--2022--
Chidyausiku T.M., Mendes S.R. et al. - "De novo design of immunoglobulin-like domains". Nature Commun 13(5661), 2022. Link
Bhardway G., O'Connor J. et al. - "Accurate de novo design of membrane-traversing macrocycles". Cell 185(19), 2022. Link
--2021--
Koga N., Koga R. et al. - "Role of backbone strain in de novo design of complex a/ß protein structures". Nature Communic 12(3916), 2021. Link
Hsia Y., Mout R. et al. - "Design of multi-scale protein complexes by hierarchical building block fusion". Nature Communic 12(2294), 2021. Link
Norn C., Wicky B.I.M. et al. - "Protein sequence design by conformational landscape optimization". PNAS 118(11), 2021. Link
Qujano-Rubio A., Yeh H-W. et al. - "De novo design of modular and tunable protein biosensors". Nature, 2021. Link
--2020--
Cao L., Goreshnik I. et al. - "De novo design of picomolar SARS-CoV-2 miniprotein inhibitors". Science 370(6515), 2020. Link
Wey K.Y., Moschidi D. et al. - "De novo design of proteins with two isoenergetic but structurally divergent ground states". PNAS 117(13), 2020. Link
Mulligan V.K., Kang C.S. et al. - "Computational design of mixed chirality peptide macrocycles with internal symmetry". Protein Science 29, 2020. Link
Abbass J., Nebel J-C. - "Rosetta and the journey to predict proteins’ structures, 20 years on". Current Bioinform, 2020. Link
Leman J.K., Weitzner B.D. et al. - "Better together: Elements of successful scientific software development in a distributed collaborative community". PLOS Comp Biol 16(5), 2020. Link
Wey K.Y., Nerli S. et al. - "Computational design of a protein family that adopts two well-defined and structurally divergent de novo folds". PNAS 117 (13), 2020. Link
Yang J., Baker D. et al. - "Improved protein structure prediction using predicted interresidue orientations". PNAS 117(3), 2020. Link
Brunett T.J., Chow C.M. et al. - "Modular repeat protein sculpting using rigid helical junctions". PNAS 117(16), 2020. Link
--2019--
Wei K.Y., Moschidi D. et al. - "Controlling protein assembly on inorganic crystals through designed protein interfaces". Nature 571, 2019. Link
Dang L.T., Miao Y, Baker D. et al. - "Receptor subtype discrimination using extensive shape complementary designed interfaces". Nature Structural and molecular biology 26, 2019. Link
Silva D-A., Yu S., Baker D. et al. - "De novo design of potent and selective mimics of IL-2 and IL-15". Nature 565 (186-191), 2019. Link
Chen Z., Boyken S.E., Baker D. et al. - "Programmable design of orthogonal protein heterodimers". Nature 565(106-111), 2019. Link
--2018--
Marcos E., Carter L., Baker D. et al. - "De novo design of a non-local beta-sheet protein with high stability and accuracy". Nature Struct and Molec Biology 25(1028-1034), 2018.Link
Shen H, Fallas J.A., Baker D. et al. - "De novo design of self-assembling helical protein filaments". Science 362(6415), 2018. Link
Dou J., Vorobieva A. et al. - "De novo design of a fluorescence-activating beta-barrel". Nature 561, 2018. Link
Lu P., Min D., DiMaio F. et al. - "Accurate computational design of multipass transmembrane proteins". Science 359(6379), 2018. Link
Park H. - "Large-scale energy guided refinement using Rosettain CASP13". Casp13 Meeting, 2018. Link
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
McFarland B. J., Kortemme T., Yu S. F., Baker D., Strong R. K. - "Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands". Structure 11(4). Link
Chivian D., Robertson T., Bonneau R., Baker D. - "Ab initio methods". Methods of biochemical analysis 44. Link
Chivian D., Kim D. E., Malmström L., Bradley P., Robertson T., Murphy P., et al. - "Automated prediction of CASP-5 structures using the Robetta server". Proteins 53(Sup 6). Link
Bradley P., Chivian D., Meiler J., Misura K. M. S., Rohl C. A., Schief W. R., et al. - "Rosetta predictions in CASP5: successes, failures, and prospects for complete automation". Proteins 53(Sup 6). Link
Morozov A., Kortemme T., Baker D. - "Evaluation of Models of Electrostatic Interactions in Proteins". J. of Physical Chemistry B 107(9). Link
Nikitina N., Ivashko E. - "HiTViSc: High-Throughput Virtual Screening as a Service". Lecture Notes in Comp Science 14098, 2023. Link
Nikitina N., Ivashko E. - "Workflows of the High-Throughput Virtual Screening as a Service". Lecture Notes in Comp Science 14389, 2023. Link
Nikitina N., Ivashko E. - "Optimization of the Workflow in a BOINC-Based Desktop Grid for Virtual Drug Screening". RuSCDays 2022. Link
Nikitina N., Manzyuk M. et al. - "Performance estimation of a BOINC-based Desktop Grid for large-scale molecular docking". PacT 2021. Link
Nikitina N., Manzyuk M. et al. - "Volunteer computing project SiDock@home for virtual drug screening against SARS-CoV-2". Int Conf ANTYCOVID 2021 Workshop. Link
Nikitina N., Manzyuk M. et al. - "Toward crowdsourced drug discovery: start-up ofthe volunteer computing project SiDock@home". Russia Supercomp Days, 2021. Link
