Progress in low-resolution ab initio phasing with CrowdPhase

New developments in CrowdPhase, a collaborative online game for tackling the low-resolution phase problem, are presented. The new features address several crystallographic issues and extend the reach of CrowdPhase to a broader range of experimental data sets.

[1]  Benjamin M. Good,et al.  Dizeez: An Online Game for Human Gene-Disease Annotation , 2013, PloS one.

[2]  Genetic Algorithm Application in Solving Crystallographic Phase Problem , 2008 .

[3]  D. Blow,et al.  The detection of sub‐units within the crystallographic asymmetric unit , 1962 .

[4]  Z. Popovic,et al.  Crystal structure of a monomeric retroviral protease solved by protein folding game players , 2011, Nature Structural &Molecular Biology.

[5]  George M. Sheldrick,et al.  Experimental phasing with SHELXC/D/E: combining chain tracing with density modification , 2010, Acta crystallographica. Section D, Biological crystallography.

[6]  G. Vriend,et al.  The atomic structure of Mengo virus at 3.0 A resolution. , 1987, Science.

[7]  T. Smith,et al.  Atomic Structure of Cucumber Necrosis Virus and the Role of the Capsid in Vector Transmission , 2013, Journal of Virology.

[8]  V Y Lunin,et al.  Mean phase error and the map-correlation coefficient. , 1993, Acta crystallographica. Section D, Biological crystallography.

[9]  C. Dumas,et al.  Macromolecular structure solution by charge flipping. , 2008, Acta crystallographica. Section D, Biological crystallography.

[10]  Randy J. Read,et al.  Advancing Methods for Biomolecular Crystallography , 2013 .

[11]  D. Craik,et al.  Racemic and quasi-racemic X-ray structures of cyclic disulfide-rich peptide drug scaffolds. , 2014, Angewandte Chemie.

[12]  T Holton,et al.  Determining protein structure from electron-density maps using pattern matching. , 2000, Acta crystallographica. Section D, Biological crystallography.

[13]  Thomas C Terwilliger,et al.  SOLVE and RESOLVE: automated structure solution and density modification. , 2003, Methods in enzymology.

[14]  A likelihood-based search for the macromolecular position in the crystalline unit cell. , 1999, Acta crystallographica. Section A, Foundations of crystallography.

[15]  T. Yeates,et al.  CrowdPhase: crowdsourcing the phase problem , 2014, Acta crystallographica. Section D, Biological crystallography.

[16]  J. Berg,et al.  The structure of a centrosymmetric protein crystal , 1993, Proteins.

[17]  D. Filman,et al.  Ab initio phasing of high-symmetry macromolecular complexes: successful phasing of authentic poliovirus data to 3.0 A resolution. , 2001, Journal of molecular biology.

[18]  R. Read Improved Fourier Coefficients for Maps Using Phases from Partial Structures with Errors , 1986 .

[19]  D. Filman,et al.  A genetic algorithm for the ab initio phasing of icosahedral viruses. , 1996, Acta crystallographica. Section D, Biological crystallography.

[20]  R. Hilgenfeld,et al.  An evolutionary computational approach to the phase problem in macromolecular X-ray crystallography. , 2001, Acta crystallographica. Section A, Foundations of crystallography.

[21]  Todd O Yeates,et al.  Racemic protein crystallography. , 2012, Annual review of biophysics.

[22]  L. Christophorou Science , 2018, Emerging Dynamics: Science, Energy, Society and Values.

[23]  Connectivity properties of high-density regions and ab initio phasing at low resolution. , 2000, Acta crystallographica. Section A, Foundations of crystallography.

[24]  J. Berg,et al.  A racemic protein , 1992 .

[25]  Chris T. A. Evelo,et al.  WikiPathways: building research communities on biological pathways , 2011, Nucleic Acids Res..

[26]  M. Rossmann,et al.  Ab initio phase determination and phase extension using non-crystallographic symmetry. , 1995, Current opinion in structural biology.

[27]  V Y Lunin,et al.  Ab initio low-resolution phasing in crystallography of macromolecules by maximization of likelihood. , 2000, Acta crystallographica. Section D, Biological crystallography.

[28]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[29]  D A Agard,et al.  Uniqueness and the ab initio phase problem in macromolecular crystallography. , 1993, Acta crystallographica. Section D, Biological crystallography.

[30]  S. Harrison,et al.  Tomato bushy stunt virus at 5.5-Å resolution , 1977, Nature.

[31]  David Eisenberg,et al.  Atomic View of a Toxic Amyloid Small Oligomer , 2012, Science.

[32]  Electron-density histograms and the phase problem. , 1993 .

[33]  Direct phasing at low resolution of a protein copurified with human paraoxonase (PON1). , 2003, Acta crystallographica. Section D, Biological crystallography.

[34]  T. Terwilliger Electronic Reprint Biological Crystallography Map-likelihood Phasing Biological Crystallography Map-likelihood Phasing , 2022 .

[35]  B. C. Wang Resolution of phase ambiguity in macromolecular crystallography. , 1985, Methods in enzymology.

[36]  R. Read,et al.  Improving experimental phases for strong reflections prior to density modification , 2013, Acta crystallographica. Section D, Biological crystallography.

[37]  Alexandre Urzhumtsev,et al.  Connectivity-based ab initio phasing: from low resolution to a secondary structure. , 2003, Acta crystallographica. Section D, Biological crystallography.

[38]  Robert D. Finn,et al.  Rfam: Wikipedia, clans and the “decimal” release , 2010, Nucleic Acids Res..

[39]  Minjae Lee,et al.  RNA design rules from a massive open laboratory , 2014, Proceedings of the National Academy of Sciences.

[40]  Zachary F. Burton,et al.  α/β Proteins , 2018 .

[41]  G. Bricogne,et al.  Methods and programs for direct‐space exploitation of geometric redundancies , 1976 .

[42]  C Colovos,et al.  Evaluation of phase accuracy via topological and geometrical analysis of electron-density maps. , 2000, Acta crystallographica. Section D, Biological crystallography.

[43]  S. Kim,et al.  Structure of an enantiomeric protein, D-monellin at 1.8 A resolution. , 1998, Acta crystallographica. Section D, Biological crystallography.

[44]  David Baker,et al.  Algorithm discovery by protein folding game players , 2011, Proceedings of the National Academy of Sciences.

[45]  Ab Initio Low Resolution Phasing , 2013 .

[46]  Ab initio phase determination for viruses with high symmetry: a feasibility study. , 1992, Acta crystallographica. Section A, Foundations of crystallography.

[47]  N L Lunina,et al.  On the ab initio solution of the phase problem for macromolecules at very low resolution: the few atoms model method. , 1995, Acta crystallographica. Section D, Biological crystallography.

[48]  G. Langlet,et al.  International Tables for Crystallography , 2002 .