CrowdPhase: crowdsourcing the phase problem

Jorda, Julien; Sawaya, Michael R.; Yeates, Todd O.

doi:10.1107/s1399004714006427

Title: CrowdPhase: crowdsourcing the phase problem

Journal Article · Fri May 23 00:00:00 EDT 2014 · Acta Crystallographica. Section D: Biological Crystallography (Online)

DOI:https://doi.org/10.1107/s1399004714006427· OSTI ID:1625716

Jorda, Julien ^[1]; Sawaya, Michael R. ^[1]; Yeates, Todd O. ^[2]

Univ. of California, Los Angeles, CA (United States). UCLA-DOE Institute for Genomics and Proteomics
Univ. of California, Los Angeles, CA (United States). UCLA-DOE Institute for Genomics and Proteomics; Univ. of California, Los Angeles, CA (United States). Molecular Biology Institute and Department of Chemistry and Biochemistry

The human mind innately excels at some complex tasks that are difficult to solve using computers alone. For complex problems amenable to parallelization, strategies can be developed to exploit human intelligence in a collective form: such approaches are sometimes referred to as 'crowdsourcing'. Here, a first attempt at a crowdsourced approach for low-resolution ab initio phasing in macromolecular crystallography is proposed. A collaborative online game named CrowdPhase was designed, which relies on a human-powered genetic algorithm, where players control the selection mechanism during the evolutionary process. The algorithm starts from a population of `individuals', each with a random genetic makeup, in this case a map prepared from a random set of phases, and tries to cause the population to evolve towards individuals with better phases based on Darwinian survival of the fittest. Players apply their pattern-recognition capabilities to evaluate the electron-density maps generated from these sets of phases and to select the fittest individuals. A user-friendly interface, a training stage and a competitive scoring system foster a network of well trained players who can guide the genetic algorithm towards better solutions from generation to generation via gameplay. CrowdPhase was applied to two synthetic low-resolution phasing puzzles and it was shown that players could successfully obtain phase sets in the 30° phase error range and corresponding molecular envelopes showing agreement with the low-resolution models. The successful preliminary studies suggest that with further development the crowdsourcing approach could fill a gap in current crystallographic methods by making it possible to extract meaningful information in cases where limited resolution might otherwise prevent initial phasing.

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Research Organization:: Univ. of California, Los Angeles, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI ID:: 1625716

Journal Information:: Acta Crystallographica. Section D: Biological Crystallography (Online), Vol. 70, Issue 6; ISSN 1399-0047

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 8 works

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References (44)

Finding crystal structures of peptides by random search and evolutionary algorithms Immirzi, Attilio; Erra, Loredana; Tedesco, Consiglia Journal of Applied Crystallography, Vol. 42, Issue 5 https://doi.org/10.1107/S0021889809025138	journal	August 2009
Use of the information on electron density distribution in macromolecules Lunin, V. Yu. Acta Crystallographica Section A Foundations of Crystallography, Vol. 44, Issue 2 https://doi.org/10.1107/S0108767387009784	journal	March 1988
Rfam: Wikipedia, clans and the "decimal" release Gardner, P. P.; Daub, J.; Tate, J. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1129	journal	November 2010
WikiPathways: building research communities on biological pathways Kelder, T.; van Iersel, M. P.; Hanspers, K. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1074	journal	November 2011
An evolutionary computational approach to the phase problem in macromolecular X-ray crystallography Webster, Gordon; Hilgenfeld, Rolf Acta Crystallographica Section A Foundations of Crystallography, Vol. 57, Issue 3 https://doi.org/10.1107/S0108767301000496	journal	April 2001
Molecular replacement then and now Scapin, Giovanna Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 11 https://doi.org/10.1107/S0907444913011426	journal	October 2013
The bacterial redox signaller pyocyanin as an antiplasmodial agent: comparisons with its thioanalog methylene blue Kasozi, D. M.; Gromer, S.; Adler, H. Redox Report, Vol. 16, Issue 4 https://doi.org/10.1179/174329211X13049558293678	journal	July 2011
A phased translation function Read, R. J.; Schierbeek, A. J. Journal of Applied Crystallography, Vol. 21, Issue 5 https://doi.org/10.1107/S002188988800562X	journal	October 1988
Improving experimental phases for strong reflections prior to density modification Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 10 https://doi.org/10.1107/S0907444913018167	journal	September 2013
Electron-denisty histograms and the phase problem Lunin, V. Yu. Acta Crystallographica Section D Biological Crystallography, Vol. 49, Issue 1 https://doi.org/10.1107/S0907444992009247	journal	January 1993
Crowdsourcing Malaria Parasite Quantification: An Online Game for Analyzing Images of Infected Thick Blood Smears Luengo-Oroz, Miguel Angel; Arranz, Asier; Frean, John Journal of Medical Internet Research, Vol. 14, Issue 6 https://doi.org/10.2196/jmir.2338	journal	January 2012
Determining protein structure from electron-density maps using pattern matching Holton, Thomas; Ioerger, Thomas R.; Christopher, Jon A. Acta Crystallographica Section D Biological Crystallography, Vol. 56, Issue 6 https://doi.org/10.1107/S0907444900003450	journal	June 2000
The Map Correlation Coefficient for Optimally Superposed Maps Lunin, V. Yu.; Lunina, N. L. Acta Crystallographica Section A Foundations of Crystallography, Vol. 52, Issue 3 https://doi.org/10.1107/S0108767395015868	journal	May 1996
Seminvariant density decomposition and connectivity analysis and their application to very low resolution macromolecular phasing Lunin, V. Y.; Lunina, N. L.; Urzhumtsev, A. G. Acta Crystallographica Section A Foundations of Crystallography, Vol. 55, Issue 5 https://doi.org/10.1107/S0108767399005000	journal	September 1999
Histogram specification as a method of density modification Harrison, R. W. Journal of Applied Crystallography, Vol. 21, Issue 6 https://doi.org/10.1107/S0021889888008222	journal	December 1988
Mean phase error and the map-correlation coefficient Lunin, V. Yu.; Woolfson, M. M. Acta Crystallographica Section D Biological Crystallography, Vol. 49, Issue 6 https://doi.org/10.1107/S0907444993005852	journal	November 1993
SnB: crystal structure determination via shake-and-bake Miller, R.; Gallo, S. M.; Khalak, H. G. Journal of Applied Crystallography, Vol. 27, Issue 4 https://doi.org/10.1107/S0021889894000191	journal	August 1994
Evaluation of phase accuracy via topological and geometrical analysis of electron-density maps Colovos, Christos; Toth, Eric A.; Yeates, Todd O. Acta Crystallographica Section D Biological Crystallography, Vol. 56, Issue 11 https://doi.org/10.1107/S0907444900011227	journal	November 2000
Ab initio phasing of high-symmetry macromolecular complexes: successful phasing of authentic poliovirus data to 3.0 Å resolution11Edited by I. A. Wilson Miller, Stephen T.; Hogle, James M.; Filman, David J. Journal of Molecular Biology, Vol. 307, Issue 2 https://doi.org/10.1006/jmbi.2001.4485	journal	March 2001
The molecular replacement method Rossmann, M. G. Acta Crystallographica Section A Foundations of Crystallography, Vol. 46, Issue 2 https://doi.org/10.1107/S0108767389009815	journal	February 1990
Solving the Sayre equations for centrosymmetric structures with a genetic algorithm Zhou, Yi; Su, Wu-Pei Acta Crystallographica Section A Foundations of Crystallography, Vol. 60, Issue 4 https://doi.org/10.1107/S0108767304010001	journal	June 2004
Genetic Algorithm Application in Solving Crystallographic Phase Problem Abdurahman, I.; Purwanto, A.; Ikram, Abarrul NEUTRON AND X-RAY SCATTERING 2007: The International Conference, AIP Conference Proceedings https://doi.org/10.1063/1.2906069	conference	January 2008
Atomic View of a Toxic Amyloid Small Oligomer Laganowsky, Arthur; Liu, Cong; Sawaya, Michael R. Science, Vol. 335, Issue 6073 https://doi.org/10.1126/science.1213151	journal	March 2012
Connectivity properties of high-density regions and ab initio phasing at low resolution Lunin, Vladimir Y.; Lunina, Natalia L.; Urzhumtsev, Alexandre G. Acta Crystallographica Section A Foundations of Crystallography, Vol. 56, Issue 4 https://doi.org/10.1107/S0108767300004633	journal	July 2000
Determination of macromolecular structures from anomalous diffraction of synchrotron radiation Hendrickson, W. Science, Vol. 254, Issue 5028 https://doi.org/10.1126/science.1925561	journal	October 1991
Crowdsourcing for bioinformatics Good, B. M.; Su, A. I. Bioinformatics, Vol. 29, Issue 16 https://doi.org/10.1093/bioinformatics/btt333	journal	June 2013
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard Terwilliger, Thomas C.; Adams, Paul D.; Read, Randy J. Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 6 https://doi.org/10.1107/S0907444909012098	journal	May 2009
On the Ab Initio Solution of the Phase Problem for Macromolecules at Very Low Resolution. II. Generalized Likelihood Based Approach to Cluster Discrimination Lunin, V. Y.; Lunina, N. L.; Petrova, T. E. Acta Crystallographica Section D Biological Crystallography, Vol. 54, Issue 5 https://doi.org/10.1107/S0907444997012456	journal	September 1998
Prize-based contests can provide solutions to computational biology problems Lakhani, Karim R.; Boudreau, Kevin J.; Loh, Po-Ru Nature Biotechnology, Vol. 31, Issue 2 https://doi.org/10.1038/nbt.2495	journal	February 2013
Connectivity-based ab initio phasing: from low resolution to a secondary structure Lunina, Natalia; Lunin, Vladimir Y.; Urzhumtsev, Alexandre Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 10 https://doi.org/10.1107/S0907444903015154	journal	September 2003
A Cross-Correlation Method for Merging Electron Crystallographic Image Data Thomas, Irene M.; Schmid, Michael F. Microscopy and Microanalysis, Vol. 1, Issue 4 https://doi.org/10.1017/S1431927695111678	journal	August 1995
Marching cubes: A high resolution 3D surface construction algorithm Lorensen, William E.; Cline, Harvey E. ACM SIGGRAPH Computer Graphics, Vol. 21, Issue 4 https://doi.org/10.1145/37402.37422	journal	August 1987
Algorithm discovery by protein folding game players Khatib, F.; Cooper, S.; Tyka, M. D. Proceedings of the National Academy of Sciences, Vol. 108, Issue 47 https://doi.org/10.1073/pnas.1115898108	journal	November 2011
Map-likelihood phasing Terwilliger, Thomas C. Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 12 https://doi.org/10.1107/S0907444901013749	journal	November 2001
Crystal structure of a monomeric retroviral protease solved by protein folding game players Khatib, Firas; DiMaio, Frank; Cooper, Seth Nature Structural & Molecular Biology, Vol. 18, Issue 10 https://doi.org/10.1038/nsmb.2119	journal	September 2011
Optimization by Simulated Annealing Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P. Science, Vol. 220, Issue 4598 https://doi.org/10.1126/science.220.4598.671	journal	May 1983
The Protein Data Bank Berman, Helen M.; Battistuz, Tammy; Bhat, T. N. Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 6 https://doi.org/10.1107/S0907444902003451	journal	May 2002
The protein data bank: A computer-based archival file for macromolecular structures Bernstein, Frances C.; Koetzle, Thomas F.; Williams, Graheme J. B. Journal of Molecular Biology, Vol. 112, Issue 3 https://doi.org/10.1016/S0022-2836(77)80200-3	journal	May 1977
Direct low-resolution phasing from electron-density histograms in protein crystallography Lunin, V. Yu.; Urzhumtsev, A. G.; Skovoroda, T. P. Acta Crystallographica Section A Foundations of Crystallography, Vol. 46, Issue 7 https://doi.org/10.1107/S0108767390003464	journal	July 1990
A likelihood-based search for the macromolecular position in the crystalline unit cell Petrova, T. E.; Lunin, V. Y.; Podjarny, A. D. Acta Crystallographica Section A Foundations of Crystallography, Vol. 55, Issue 4 https://doi.org/10.1107/S0108767399001890	journal	July 1999
Crystallographic fast Fourier transforms Ten Eyck, L. F. Acta Crystallographica Section A, Vol. 29, Issue 2 https://doi.org/10.1107/S0567739473000458	journal	March 1973
Predicting protein structures with a multiplayer online game Cooper, Seth; Khatib, Firas; Treuille, Adrien Nature, Vol. 466, Issue 7307 https://doi.org/10.1038/nature09304	journal	August 2010
Uniqueness and the ab initio phase problem in macromolecular crystallography Baker, D.; Krukowski, A. E.; Agard, D. A. Acta Crystallographica Section D Biological Crystallography, Vol. 49, Issue 1 https://doi.org/10.1107/S0907444992008801	journal	January 1993
Some improvements on adaptive genetic algorithms for reliability-related applications Ye, Zhisheng; Li, Zhizhong; Xie, Min Reliability Engineering & System Safety, Vol. 95, Issue 2 https://doi.org/10.1016/j.ress.2009.09.001	journal	February 2010

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Mask-based approach to phasing of single-particle diffraction data Lunin, Vladimir Y.; Lunina, Natalia L.; Petrova, Tatiana E. Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 1 https://doi.org/10.1107/s2059798315022652	journal	January 2016

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