Automatic classification and pattern discovery in high-throughput protein crystallization trials.
Conceptually, protein crystallization can be divided into two phases search and optimization. Robotic protein crystallization screening can speed up the search phase, and has a potential to increase process quality. Automated image classification helps to increase throughput and consistently generate objective results. Although the classification accuracy can always be improved, our image analysis system can classify images from 1,536-well plates with high classification accuracy (85%) and ROC score (0.87), as evaluated on 127 human-classified protein screens containing 5,600 crystal images and 189,472 non-crystal images. Data mining can integrate results from high-throughput screens with information about crystallizing conditions, intrinsic protein properties, and results from crystallization optimization. We apply association mining, a data mining approach that identifies frequently occurring patterns among variables and their values. This approach segregates proteins into groups based on how they react in a broad range of conditions, and clusters cocktails to reflect their potential to achieve crystallization. These results may lead to crystallization screen optimization, and reveal associations between protein properties and crystallization conditions. We also postulate that past experience may lead us to the identification of initial conditions favorable to crystallization for novel proteins.
Cumbaa
Christian
C
Ontario Cancer Institute, Northeast Structural Genomics Consortium, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada.
Jurisica
Igor
I
D000465:Algorithms; D019295:Computational Biology; D003460:Crystallization / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods; D011506:Proteins / Q000737:chemistry / Q000145:classification* / Q000302:isolation & purification*; D040901:Proteomics / Q000379:methods*
D011506:Proteins