BEES: Bayesian Ensemble Estimation from SAS.
暂无分享,去创建一个
Jeff Wereszczynski | Samuel Bowerman | Joseph E Curtis | Joseph Clayton | Emre H Brookes | S. Bowerman | J. Wereszczynski | J. E. Curtis | E. Brookes | Joseph Clayton
[1] Bartosz Różycki,et al. Large, dynamic, multi-protein complexes: a challenge for structural biology , 2014, Journal of physics. Condensed matter : an Institute of Physics journal.
[2] Hirotugu Akaike,et al. Akaike's Information Criterion , 2011, International Encyclopedia of Statistical Science.
[3] Jesper Ferkinghoff-Borg,et al. Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models , 2010, BMC Bioinformatics.
[4] Guangfeng Zhou,et al. Bayesian inference of conformational state populations from computational models and sparse experimental observables , 2014, J. Comput. Chem..
[5] Marlon E. Pierce,et al. The GenApp framework integrated with Airavata for managed compute resource submissions , 2015, Concurr. Comput. Pract. Exp..
[6] D. Kern,et al. Dynamic personalities of proteins , 2007, Nature.
[7] Max C. Watson,et al. Rapid and accurate calculation of small‐angle scattering profiles using the golden ratio , 2013 .
[8] P. V. Konarev,et al. ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions , 2017, Journal of applied crystallography.
[9] Nicholas J. Terrill,et al. Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS) , 2016, Journal of applied crystallography.
[10] Jeff Wereszczynski,et al. Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations. , 2017, Journal of chemical theory and computation.
[11] Dmitri I. Svergun,et al. A posteriori determination of the useful data range for small-angle scattering experiments on dilute monodisperse systems , 2015, IUCrJ.
[12] G. Schwarz. Estimating the Dimension of a Model , 1978 .
[13] Lauren Boldon,et al. Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application , 2015, Nano reviews.
[14] Andrej Sali,et al. FoXS: a web server for rapid computation and fitting of SAXS profiles , 2010, Nucleic Acids Res..
[15] C. Luchinat,et al. A critical assessment of methods to recover information from averaged data. , 2016, Physical chemistry chemical physics : PCCP.
[16] Joseph E. Curtis,et al. Monte Carlo simulation algorithm for B‐DNA , 2016, J. Comput. Chem..
[17] Wei Huang,et al. Fast-SAXS-pro: a unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes. , 2013, The Journal of chemical physics.
[18] Vincent A Voelz,et al. Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and Parameterization. , 2018, The journal of physical chemistry. B.
[19] A. Menzel,et al. Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation , 2015, PloS one.
[20] Jill Trewhella,et al. Bayesian inference of protein conformational ensembles from limited structural data , 2018, PLoS Comput. Biol..
[21] J. Hub,et al. Interpretation of solution x-ray scattering by explicit-solvent molecular dynamics. , 2015, Biophysical journal.
[22] Kresten Lindorff-Larsen,et al. On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations. , 2018, Journal of molecular biology.
[23] Collin M. Stultz,et al. Modeling Intrinsically Disordered Proteins with Bayesian Statistics , 2010, Journal of the American Chemical Society.
[24] Renwick C J Dobson,et al. Tyrosine Latching of a Regulatory Gate Affords Allosteric Control of Aromatic Amino Acid Biosynthesis* , 2011, The Journal of Biological Chemistry.
[25] Patrice Vachette,et al. Direct observation in solution of a preexisting structural equilibrium for a mutant of the allosteric aspartate transcarbamoylase , 2007, Proceedings of the National Academy of Sciences.
[26] Greg L. Hura,et al. Structure and flexibility within proteins as identified through small angle X-ray scattering. , 2009, General physiology and biophysics.
[27] D. Svergun,et al. CRYSOL : a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates , 1995 .
[28] Lee Makowski,et al. Modeling the hydration layer around proteins: applications to small- and wide-angle x-ray scattering. , 2011, Biophysical journal.
[29] Andrej Sali,et al. Recovering a representative conformational ensemble from underdetermined macromolecular structural data. , 2013, Journal of the American Chemical Society.
[30] Andrej Sali,et al. FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles , 2016, Nucleic Acids Res..
[31] John A. Tainer,et al. Accurate assessment of mass, models and resolution by small-angle scattering , 2013, Nature.
[32] Xiaodong Cheng,et al. The Ubiquitin Binding Domain ZnF UBP Recognizes the C-Terminal Diglycine Motif of Unanchored Ubiquitin , 2006, Cell.
[33] Lee Makowski,et al. Multidomain assembled states of Hck tyrosine kinase in solution , 2010, Proceedings of the National Academy of Sciences.
[34] Joseph E Curtis,et al. Conformation of the HIV-1 Gag protein in solution. , 2007, Journal of molecular biology.
[35] Keegan E. Hines,et al. A primer on Bayesian inference for biophysical systems. , 2015, Biophysical journal.
[36] J. Hub,et al. Interpreting solution X-ray scattering data using molecular simulations. , 2018, Current opinion in structural biology.
[37] Dmitri I. Svergun,et al. Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering , 2015, IUCrJ.
[38] David B. Dunson,et al. Bayesian Data Analysis , 2010 .
[39] Bradley P. Carlin,et al. Bayesian measures of model complexity and fit , 2002 .
[40] Thibault Mayor,et al. The diversity of ubiquitin recognition: hot spots and varied specificity. , 2010, Molecular cell.
[41] Osman Bilsel,et al. Sub-millisecond time-resolved SAXS using a continuous-flow mixer and X-ray microbeam , 2013, Journal of synchrotron radiation.
[42] Ron Elber,et al. Revealing the distinct folding phases of an RNA three-helix junction , 2018, Nucleic acids research.
[43] Jill Trewhella,et al. Small-angle scattering and 3D structure interpretation. , 2016, Current opinion in structural biology.
[44] J. Hub,et al. Validating solution ensembles from molecular dynamics simulation by wide-angle X-ray scattering data. , 2014, Biophysical journal.
[45] Dmitri I. Svergun,et al. 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update , 2017, Acta crystallographica. Section D, Structural biology.
[46] Nancy Wilkins-Diehr,et al. XSEDE: Accelerating Scientific Discovery , 2014, Computing in Science & Engineering.