Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold.
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David Baker | Lindsey Doyle | Nephi Stella | Alberto Schena | Kai Johnsson | Per Greisen | D. Baker | B. Stoddard | L. Doyle | Per Greisen | K. Johnsson | N. Stella | Barry Stoddard | Austin L Day | Alberto Schena | A. Day | D. Baker
[1] Mark J. Uline,et al. Molecular Dynamics at Constant Pressure: Allowing the System to Control Volume Fluctuations via a "Shell" Particle , 2013, Entropy.
[2] Barry L. Stoddard,et al. Computational Design of Ligand Binding Proteins , 2016, Methods in Molecular Biology.
[3] David Baker,et al. Computational design of ligand-binding proteins with high affinity and selectivity , 2013, Nature.
[4] K Dane Wittrup,et al. Yeast surface display for protein engineering and characterization , 2007, Current Opinion in Structural Biology.
[5] Garrett M. Morris,et al. One Size Does Not Fit All: The Limits of Structure-Based Models in Drug Discovery , 2013, Journal of chemical theory and computation.
[6] Sergey Lyskov,et al. The RosettaDock server for local protein–protein docking , 2008, Nucleic Acids Res..
[7] Ross C. Walker,et al. An overview of the Amber biomolecular simulation package , 2013 .
[8] Jens Meiler,et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. , 2011, Methods in enzymology.
[9] Paul S. Freemont,et al. Computational protein design with backbone plasticity , 2016, Biochemical Society transactions.
[10] N. Kunishima,et al. Packing Space Expansion of Protein Crystallization Screening with Synthetic Zeolite as a Heteroepitaxic Nucleant , 2011 .
[11] D. Baker,et al. Computational design of a protein-based enzyme inhibitor. , 2013, Journal of molecular biology.
[12] Tom L. Blundell,et al. Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity? , 2014, J. Chem. Inf. Model..
[13] David Baker,et al. Computational design of environmental sensors for the potent opioid fentanyl , 2017, eLife.
[14] Randy J. Read,et al. Phaser crystallographic software , 2007, Journal of applied crystallography.
[15] Modesto Orozco,et al. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations , 2012, Bioinform..
[16] D. Moras,et al. The crystal structure of the nuclear receptor for vitamin D bound to its natural ligand. , 2000, Molecular cell.
[17] Luhua Lai,et al. Computational design of ligand-binding proteins. , 2017, Current opinion in structural biology.
[18] K D Wittrup,et al. Yeast surface display for directed evolution of protein expression, affinity, and stability. , 2000, Methods in enzymology.
[19] Eric T. Boder,et al. Yeast surface display for screening combinatorial polypeptide libraries , 1997, Nature Biotechnology.
[20] Michael Schroeder,et al. PLIP: fully automated protein–ligand interaction profiler , 2015, Nucleic Acids Res..
[21] Peter M. Kasson,et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..
[22] William Sheffler,et al. De novo design of a fluorescence-activating β-barrel , 2018, Nature.
[23] Benjamin T. Porebski,et al. The role of protein dynamics in the evolution of new enzyme function. , 2016, Nature chemical biology.
[24] Nihar R. Mahapatra,et al. A Comparative Assessment of Ranking Accuracies of Conventional and Machine-Learning-Based Scoring Functions for Protein-Ligand Binding Affinity Prediction , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[25] L. Abriata,et al. Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory. , 2016, Molecular biology and evolution.
[26] David Baker,et al. Sampling and energy evaluation challenges in ligand binding protein design , 2017, Protein science : a publication of the Protein Society.
[27] Ruth Nussinov,et al. PatchDock and SymmDock: servers for rigid and symmetric docking , 2005, Nucleic Acids Res..
[28] K Dane Wittrup,et al. Isolating and engineering human antibodies using yeast surface display , 2006, Nature Protocols.
[29] J. Klinman,et al. Evolutionary Aspects of Enzyme Dynamics* , 2014, The Journal of Biological Chemistry.
[30] Alex Bateman,et al. Filling out the structural map of the NTF2-like superfamily , 2013, BMC Bioinformatics.
[31] L. Benatuil,et al. An improved yeast transformation method for the generation of very large human antibody libraries. , 2010, Protein engineering, design & selection : PEDS.