Literature DB >> 20072819

Protein crystallization analysis on the World Community Grid.

Christian A Cumbaa1, Igor Jurisica.   

Abstract

We have developed an image-analysis and classification system for automatically scoring images from high-throughput protein crystallization trials. Image analysis for this system is performed by the Help Conquer Cancer (HCC) project on the World Community Grid. HCC calculates 12,375 distinct image features on microbatch-under-oil images from the Hauptman-Woodward Medical Research Institute's High-Throughput Screening Laboratory. Using HCC-computed image features and a massive training set of 165,351 hand-scored images, we have trained multiple Random Forest classifiers that accurately recognize multiple crystallization outcomes, including crystals, clear drops, precipitate, and others. The system successfully recognizes 80% of crystal-bearing images, 89% of precipitate images, and 98% of clear drops.

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Year:  2010        PMID: 20072819      PMCID: PMC2857471          DOI: 10.1007/s10969-009-9076-9

Source DB:  PubMed          Journal:  J Struct Funct Genomics        ISSN: 1345-711X


  13 in total

Review 1.  Towards the automated evaluation of crystallization trials.

Authors:  Julie Wilson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-10-21

2.  Computational analysis of crystallization trials.

Authors:  Glen Spraggon; Scott A Lesley; Andreas Kreusch; John P Priestle
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-10-21

3.  Automatic classification of sub-microlitre protein-crystallization trials in 1536-well plates.

Authors:  Christian A Cumbaa; Angela Lauricella; Nancy Fehrman; Christina Veatch; Robert Collins; Joe Luft; George DeTitta; Igor Jurisica
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2003-08-19

4.  Evaluation of protein crystallization states based on texture information derived from greyscale images.

Authors:  Kanako Saitoh; Kuniaki Kawabata; Hajime Asama; Taketoshi Mishima; Mitsuaki Sugahara; Masashi Miyano
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-06-24

5.  Evaluation of crystalline objects in crystallizing protein droplets based on line-segment information in greyscale images.

Authors:  Kuniaki Kawabata; Mutsunori Takahashi; Kanako Saitoh; Hajime Asama; Taketoshi Mishima; Mitsuaki Sugahara; Masashi Miyano
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2006-02-22

6.  Leveraging genetic algorithm and neural network in automated protein crystal recognition.

Authors:  Ming Jack Po; Andrew F Laine
Journal:  Conf Proc IEEE Eng Med Biol Soc       Date:  2008

7.  AutoSherlock: a program for effective crystallization data analysis.

Authors:  Raymond M Nagel; Joseph R Luft; Edward H Snell
Journal:  J Appl Crystallogr       Date:  2008-10-11       Impact factor: 3.304

8.  Image-based crystal detection: a machine-learning approach.

Authors:  Roy Liu; Yoav Freund; Glen Spraggon
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2008-11-18

9.  Establishing a training set through the visual analysis of crystallization trials. Part II: crystal examples.

Authors:  Edward H Snell; Angela M Lauricella; Stephen A Potter; Joseph R Luft; Stacey M Gulde; Robert J Collins; Geoff Franks; Michael G Malkowski; Christian Cumbaa; Igor Jurisica; George T DeTitta
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2008-10-18

10.  Establishing a training set through the visual analysis of crystallization trials. Part I: approximately 150,000 images.

Authors:  Edward H Snell; Joseph R Luft; Stephen A Potter; Angela M Lauricella; Stacey M Gulde; Michael G Malkowski; Mary Koszelak-Rosenblum; Meriem I Said; Jennifer L Smith; Christina K Veatch; Robert J Collins; Geoff Franks; Max Thayer; Christian Cumbaa; Igor Jurisica; George T Detitta
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2008-10-18
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  13 in total

1.  Lessons from high-throughput protein crystallization screening: 10 years of practical experience.

Authors:  Joseph R Luft; Edward H Snell; George T Detitta
Journal:  Expert Opin Drug Discov       Date:  2011-03-22       Impact factor: 6.098

2.  Super-Thresholding: Supervised Thresholding of Protein Crystal Images.

Authors:  Imren Dinc; Semih Dinc; Madhav Sigdel; Madhu S Sigdel; Marc L Pusey; Ramazan S Aygun
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2016-03-16       Impact factor: 3.710

3.  What's in a drop? Correlating observations and outcomes to guide macromolecular crystallization experiments.

Authors:  Joseph R Luft; Jennifer R Wolfley; Edward H Snell
Journal:  Cryst Growth Des       Date:  2011-03-02       Impact factor: 4.076

4.  Protein Crystallization Segmentation and Classification Using Subordinate Color Channel in Fluorescence Microscopy Images.

Authors:  Truong X Tran; Marc L Pusey; Ramazan S Aygun
Journal:  J Fluoresc       Date:  2020-04-20       Impact factor: 2.217

5.  Evaluation of Semi-supervised Learning for Classification of Protein Crystallization Imagery.

Authors:  Madhav Sigdel; İmren Dinç; Semih Dinç; Madhu S Sigdel; Marc L Pusey; Ramazan S Aygün
Journal:  Proc IEEE Southeastcon       Date:  2014-03

6.  Evaluation of Normalization and PCA on the Performance of Classifiers for Protein Crystallization Images.

Authors:  İmren Dinç; Madhav Sigdel; Semih Dinç; Madhu S Sigdel; Marc L Pusey; Ramazan S Aygün
Journal:  Proc IEEE Southeastcon       Date:  2014-03

7.  CrystPro: Spatiotemporal Analysis of Protein Crystallization Images.

Authors:  Madhav Sigdel; Marc L Pusey; Ramazan S Aygun
Journal:  Cryst Growth Des       Date:  2015-09-16       Impact factor: 4.076

8.  Characterization of Protein Nanocrystals Based on the Reversibility of Crystallization.

Authors:  Katerina Dörner; Jose M Martin-Garcia; Christopher Kupitz; Zhen Gong; T Conn Mallet; Liqing Chen; Rebekka M Wachter; Petra Fromme
Journal:  Cryst Growth Des       Date:  2016-05-10       Impact factor: 4.076

9.  Real-Time Protein Crystallization Image Acquisition and Classification System.

Authors:  Madhav Sigdel; Marc L Pusey; Ramazan S Aygun
Journal:  Cryst Growth Des       Date:  2013-07-03       Impact factor: 4.076

10.  Some practical guidelines for UV imaging in the protein crystallization laboratory.

Authors:  Sebastien Desbois; Shane A Seabrook; Janet Newman
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2013-01-26
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