Abstract
The practice of scoring of protein crystallization screening results is more honored in the breach than in the observance. However, as we hope to show in the balance of this treatise, it can lead to a means for extracting more information than immediately apparent from a crystallization experiment. Scoring has advantages beyond simple good scientific note-keeping practice; the act of objectively examining one’s results, with some thought added, can lead to a deeper appreciation of what led to those results, be it at the protein, screening solution, or mechanics of setting up the plate level. The first goal is to have a system which reflects an increase in the desirability of the results obtained with the numerical score. The scoring scale does not have to be complex or extensive; a 10-point scale is elaborated on herein. However, the scale should clearly distinguish between classes of desirable outcomes.
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Bern, M., Goldberg, D., Stevens, R. C., & Kuhn, P. (2004). Automatic classification of protein crystallization images using a curve-tracking algorithm. Journal of Applied Crystallography, 37(2), 279–287.
Berry, I. M., Dym, O., Esnouf, R., Harlos, K., Meged, R., Perrakis, A., et al. (2006). Spine high-throughput crystallization, crystal imaging and recognition techniques: current state, performance analysis, new technologies and future aspects. Acta Crystallographica Section D: Biological Crystallography, 62(10), 1137–1149.
Brodersen, D. E., Andersen, G. R., & Andersen, C. B. F. (2013). Mimer: an automated spreadsheet-based crystallization screening system. Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 69(7), 815–820.
Cumbaa, C., & Jurisica, I. (2005). Automatic classification and pattern discovery in high-throughput protein crystallization trials. Journal of Structural and Functional Genomics, 6(2–3), 195–202.
Cumbaa, C. A., & Jurisica, I. (2010). Protein crystallization analysis on the world computing grid. Journal of Structural and Functional Genomics, 11(1), 61–69.
Cumbaa, C. A., Lauricella, A., Fehrman, N., Veatch, C., Collins, R., Luft, J., et al. (2003). Automatic classification of sub-microlitre protein-crystallization trials in 1536-well plates. Acta Crystallographica Section D: Biological Crystallography, 59(9), 1619–1627.
D’Arcy, A., Bergfors, T., Cowan-Jacob, S. W., & Marsh, M. (2014). Microseed matrix screening for optimization in protein crystallization: what have we learned? Acta Crystallographica Section F: Structural Biology Communications, 70(9), 1117–1126.
Forsythe, E., Achari, A., & Pusey, M. L. (2006). Trace fluorescent labeling for high-throughput crystallography. Acta Crystallographica Section D: Biological Crystallography, 62(3), 339–346.
Pan, S., Shavit, G., Penas-Centeno, M., Xu, D. -H., Shapiro, L., Ladner, R., et al. (2006). Automated classification of protein crystallization images using support vector machines with scale-invariant texture and gabor features. Acta Crystallographica Section D: Biological Crystallography, 62(3), 271–279.
Po, M. J., & Laine, A. F. (2008) Leveraging genetic algorithm and neural network in automated protein crystal recognition. In 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2008. (pp. 1926–1929). IEEE.
Pusey, M., Barcena, J., Morris, M., Singhal, A., Yuan, Q., & Ng, J. (2015). Trace fluorescent labeling for protein crystallization. Acta Crystallographica Section F: Structural Biology Communications, 71(7), 806–814.
Saitoh, K., Kawabata, K., & Asama, H. (2006). Design of classifier to automate the evaluation of protein crystallization states. In Proceedings 2006 IEEE International Conference on Robotics and Automation, ICRA 2006 (pp. 1800–1805). IEEE.
Sigdel, M., Dinc, I., Sigdel, M. S., Dinc, S., Pusey, M. L., & Aygun, R. S. (2017). Feature analysis for classification of trace fluorescent labeled protein crystallization images. BioData Mining, 10, 14.
Spraggon, G., Lesley, S. A., Kreusch, A., & Priestle, J. P. (2002). Computational analysis of crystallization trials. Acta Crystallographica Section D: Biological Crystallography, 58(11), 1915–1923.
Yang, X., Chen, W., Zheng, Y. F., & Jiang, T. (2006). Image-based classification for automating protein crystal identification. Intelligent computing in signal processing and pattern recognition (pp. 932–937). Berlin: Springer.
Yann, M. L. -J., & Tang, Y. (2016). Learning deep convolutional neural networks for x-ray protein crystallization image analysis. In Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence (AAAI-16).
Zhu, X., Sun, S., & Bern, M. (2004). Classification of protein crystallization imagery. In 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, IEMBS’04. (Vol. 1, pp. 1628–1631). IEEE.
Zuk, W. M., & Ward, K. B. (1991). Methods of analysis of protein crystal images. Journal of Crystal Growth, 110(1), 148–155.
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Pusey, M.L., Aygün, R.S. (2017). Scoring and Phases of Crystallization. In: Data Analytics for Protein Crystallization. Computational Biology, vol 25. Springer, Cham. https://doi.org/10.1007/978-3-319-58937-4_2
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DOI: https://doi.org/10.1007/978-3-319-58937-4_2
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