Correlation between Protein Sequence Similarity and Crystallization Reagents in the Biological Macromolecule Crystallization Database
Abstract
:1. Introduction
2. Results and Discussion
2.1. Datasets
2.2. Establishing the Large Sequence Similarity Clusters (LSSC) Dataset and Random Datasets
2.3. Statistical Analysis of Reagent Consistency within Each LSSC and Random Group
2.4. Statistical Analysis of Reagent Variety between Each LSSC and Random Group
3. Methods and Experimental Section
3.1. Datasets
3.2. Calculating the Frequency of each Kind of Crystallization Reagent
3.3. Clustering by Sequence Similarity to Establish the LSSC Datasets
3.4. Establishing the Random Datasets from the LSSC Datasets for Robust Analysis
3.5. Statistical Analysis of Reagent Consistency within Each Group
3.6. Statistical Analysis of Reagent Variety between Groups
4. Conclusions
Acknowledgments
References and Notes
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LSSC datasets | Number of clusters | Amount of entries | Average size of each cluster |
---|---|---|---|
LSSC30 | 173 | 3,921 | 22.7 |
LSSC40 | 144 | 3,006 | 20.9 |
LSSC50 | 122 | 2,433 | 19.9 |
LSSC60 | 105 | 2,068 | 19.7 |
LSSC70 | 87 | 1,757 | 20.2 |
LSSC80 | 81 | 1,586 | 19.6 |
LSSC90 | 70 | 1,340 | 19.1 |
Datasets | VARtotal | Group number under VARtotal | Group size | Proportion of lower VARj than VARtotal |
---|---|---|---|---|
LSSC30 | 0.109 | 132 | 173 | 76.3% |
LSSC60 | 0.111 | 81 | 105 | 77.1% |
LSSC90 | 0.097 | 53 | 70 | 75.7% |
RAN30 | 0.099 | 93 | 173 | 53.8% |
RAN60 | 0.101 | 58 | 105 | 55.2% |
RAN90 | 0.098 | 38 | 70 | 54.3% |
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Lu, H.-M.; Yin, D.-C.; Liu, Y.-M.; Guo, W.-H.; Zhou, R.-B. Correlation between Protein Sequence Similarity and Crystallization Reagents in the Biological Macromolecule Crystallization Database. Int. J. Mol. Sci. 2012, 13, 9514-9526. https://doi.org/10.3390/ijms13089514
Lu H-M, Yin D-C, Liu Y-M, Guo W-H, Zhou R-B. Correlation between Protein Sequence Similarity and Crystallization Reagents in the Biological Macromolecule Crystallization Database. International Journal of Molecular Sciences. 2012; 13(8):9514-9526. https://doi.org/10.3390/ijms13089514
Chicago/Turabian StyleLu, Hui-Meng, Da-Chuan Yin, Yong-Ming Liu, Wei-Hong Guo, and Ren-Bin Zhou. 2012. "Correlation between Protein Sequence Similarity and Crystallization Reagents in the Biological Macromolecule Crystallization Database" International Journal of Molecular Sciences 13, no. 8: 9514-9526. https://doi.org/10.3390/ijms13089514