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Network Modeling Analysis in Health Informatics and Bioinformatics
Erschienen in: Network Modeling Analysis in Health Informatics and Bioinformatics 1/2020

01.12.2020 | Original Article

Visual-X2: interactive visualization and analysis tool for protein crystallization

verfasst von: Suraj Subedi, Imren Dinc, Truong X. Tran, Diwas Sharma, Buddha R. Shrestha, Marc L. Pusey, Ramazan S. Aygun

Erschienen in: Network Modeling Analysis in Health Informatics and Bioinformatics | Ausgabe 1/2020

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Abstract

In high-throughput systems, the crystallization experiments require the inspection and analysis of a large number of trial images. The visualization and analysis tools are needed to view and analyze the experimental results, and recommend novel crystalline conditions by analyzing prior results. It is essential to integrate all these components into a single system. Therefore, we developed Visual-X2, an interactive visualization software developed to aid the user for quick and efficient visualization and analysis of the results of the experiments. Visual-X2 has a number of useful features for visualization and analysis: dual plate view (thumbnail and symbolic), detailed well view with scoring option, multiple-scan and time-course views, support for screening analysis based on multiple screens, three novel screen analysis methods (associative experimental design, GenScreen, and novelty methods), and generating pipetting file with a family of conditions varying concentrations based on stock concentration.
Vorheriger Artikel Targeting galectin-3 by natural glycosides: a computational approach
Nächster Artikel A study on MANOVA as an effective feature reduction technique in classification of childhood medulloblastoma and its subtypes

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Fußnoten
1
Contact Dr. Ramazan Aygun (aygunr@uah.edu) to evaluate Visual-X2 tool.
 
Literatur
Acharya S (2017) GenScreen : A genetic algorithm for protein crystallization screening, Master’s thesis, The University of Alabama in Huntsville, Huntsville, Alabama, USA
Bhattarai B, Shrestha M, Aygun RS, Pusey ML (2017) Optimizing genetic algorithm for protein crystallization screening using an exploratory fitness function. In: 2017 IEEE international conference on bioinformatics and biomedicine (BIBM), Kansas City, MO, 2017, pp 2083–2090. https://​doi.​org/​10.​1109/​BIBM.​2017.​8217981
Daniel E, Lin B, Diprose JM, Griffiths SL, Morris C, Berry IM, Owens RJ, Blake R, Wilson KS, Stuart DI et al (2011) xtalpims: a pims-based web application for the management and monitoring of crystallization trials. J Struct Biol 175(2):230–235CrossRef
Dinç I, Pusey ML, Aygün RS (2015) Protein crystallization screening using associative experimental design. In: Harrison R, Li Y, Măndoiu I. (eds) Bioinformatics Research and Applications. ISBRA 2015. Lecture Notes in Computer Science, vol 9096. Springer, Cham
Dinc I, Pusey M, Aygun RS (2016b) Visual-x2: scoring and symbolic visualization tool for analysis of protein crystallization trial images. In: Frontiers in structural biology of membrane protein & Pittsburgh Diffraction Conference, Huntsville, AL
Esser L, Xia D (2011) Cryspage: a program for displaying images of crystallization trials, rapid comparisons and analysis. J Appl Crystallogr 44(5):1130–1131CrossRef
Hiraki M, Kato R, Nagai M, Satoh T, Hirano S, Ihara K, Kudo N, Nagae M, Kobayashi M, Inoue M et al (2006) Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses. Acta Crystallogr Sect D Biol Crystallogr 62(9):1058–1065CrossRef
Juttu MK, Pusey ML, Aygun RS (2019) Protein crystallization screening using enhanced associative experimental design. Netw Model Anal Health Inform Bioinform 8(1):17CrossRef
Luft JR, Collins RJ, Fehrman NA, Lauricella AM, Veatch CK, DeTitta GT (2003) A deliberate approach to screening for initial crystallization conditions of biological macromolecules. J Struct Biol 142(1):170–179CrossRef
Nagel RM, Luft JR, Snell EH (2008) Autosherlock: a program for effective crystallization data analysis. J Appl Crystallogr 41(6):1173–1176CrossRef
Newman J, Pham TM, Peat TS (2008) Phoenito experiments: combining the strengths of commercial crystallization automation. Acta Crystallogr Sect F Struct Biol Crysta Commun 64(11):991–996CrossRef
Pusey ML, Aygun RS (2017) Data analytics for protein crystallization. Springer, ChamCrossRef
Shrestha M, Bhattarai B, Aygun RS, Pusey ML (2017) Schema matching and data integration on protein crystallization screens. In: IEEE international conference on bioinformatics and biomedicine (BIBM), Kansas City, MO, 2017, USA, pp 2306–2308. https://​doi.​org/​10.​1109/​BIBM.​2017.​8218037
Sigdel M, Pusey ML, Aygun RS (2013) Real-time protein crystallization image acquisition and classification system. Cryst Growth Des 13(7):2728–2736CrossRef
Sigdel M, Pusey ML, Aygun RS (2015) Crystpro: spatiotemporal analysis of protein crystallization images. Cryst Growth Des 15(11):5254–5262CrossRef
Sigdel MS, Sigdel M, Dinç S, Dinc I, Pusey ML, Aygün RS (2016) Focusall: focal stacking of microscopic images using modified harris corner response measure. IEEE/ACM Trans Comput Biol Bioinform 13(2):326–340CrossRef
Sigdel M, Dinc I, Sigdel MS, Dinc S, Pusey ML, Aygun RS (2017) Feature analysis for classification of trace fluorescent labeled protein crystallization images. Biodata Min 10(1):14CrossRef
Snell EH, Nagel RM, Wojtaszcyk A, O’Neill H, Wolfley JL, Luft JR (2008) The application and use of chemical space mapping to interpret crystallization screening results. Acta Crystallogr Sect D Biol Crystallogr 64(12):1240–1249CrossRef
Subedi S, Pusey ML, Aygun RS (2017) Visual-x2: scoring and visualization tool for analysis of protein crystallization trial images. In: 2017 IEEE international conference on bioinformatics and biomedicine (BIBM), Kansas City, MO, 2017, USA, pp 2316–2318. https://​doi.​org/​10.​1109/​BIBM.​2017.​8218041
Walter TS, Diprose JM, Mayo CJ, Siebold C, Pickford M G, Carter L, Sutton G C, Berrow N S, Brown J, Berry I M et al (2005) A procedure for setting up high-throughput nanolitre crystallization experiments. Crystallization workflow for initial screening, automated storage, imaging and optimization. Acta Crystallogr Sect D Biol Crystallogr 61(6):651–657CrossRef
Ware C (2012) Information visualization: perception for design. Elsevier, New York
Metadaten
Titel
Visual-X2: interactive visualization and analysis tool for protein crystallization
verfasst von
Suraj Subedi
Imren Dinc
Truong X. Tran
Diwas Sharma
Buddha R. Shrestha
Marc L. Pusey
Ramazan S. Aygun
Publikationsdatum
01.12.2020
Verlag
Springer Vienna
Erschienen in
Network Modeling Analysis in Health Informatics and Bioinformatics / Ausgabe 1/2020
Print ISSN: 2192-6662
Elektronische ISSN: 2192-6670
DOI
https://doi.org/10.1007/s13721-020-0220-6

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