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177 results on '"Pan, Xian-Ming"'

18. A novel method for high accuracy sumoylation site prediction from protein sequences

Author

Yuan Jiangang, Qiang Boqin, He Yun, Xu Jialin, Peng Xiaozhong, and Pan Xian-Ming

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Protein sumoylation is an essential dynamic, reversible post translational modification that plays a role in dozens of cellular activities, especially the regulation of gene expression and the maintenance of genomic stability. Currently, the complexities of sumoylation mechanism can not be perfectly solved by experimental approaches. In this regard, computational approaches might represent a promising method to direct experimental identification of sumoylation sites and shed light on the understanding of the reaction mechanism. Results Here we presented a statistical method for sumoylation site prediction. A 5-fold cross validation test over the experimentally identified sumoylation sites yielded excellent prediction performance with correlation coefficient, specificity, sensitivity and accuracy equal to 0.6364, 97.67%, 73.96% and 96.71% respectively. Additionally, the predictor performance is maintained when high level homologs are removed. Conclusion By using a statistical method, we have developed a new SUMO site prediction method – SUMOpre, which has shown its great accuracy with correlation coefficient, specificity, sensitivity and accuracy.

Published
2008
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28. Surface hydrophobicity and thermal aggregation of adenylate kinase

Author

Zhou Jun‐Mei, Zhang Yan-Ling, and Pan Xian‐Ming

Subjects
Conformational change, Ammonium sulfate, Clinical Biochemistry, Adenylate kinase, Cell Biology, Biochemistry, Solvent, chemistry.chemical_compound, Sulfonate, chemistry, Genetics, Biophysics, Organic chemistry, Solubility, Binding site, Molecular Biology, Ethylene glycol
Abstract

The fluorescence probe, 8-anilinonaphthalene-1 sulfonate (ANS), is used to study the thermal denaturation of adenylate kinase (AK). Native AK has one ANS binding site. With increasing temperature, the ANS binding fluorescence intensity increases, showing that the enzyme undergoes a thermally induced conformational change that causes the exposure of the hydrophobic surfaces. With the exposure of the hydrophobic surfaces, the partially denatured enzyme proceeds to aggregate. This result suggests that the formation of the aggregates may be correlated with increases in the surface hydrophobicity of the intermediates. The thermally unfolded AK become resistant to aggregation in the presence of ammonium sulfate or ethylene glycol. These observations are discussed in terms of a model where the ethylene glycol enhances the hydrophobicity of the solvent and increases the solubility of the intermediates.

Published
1998

37. Reactive oxygen species induce cell death via Akt signaling in rat osteoblast-like cell line ROS 17/2.8.

Author

Zhang, Bo, Xie, Qing-yun, Quan, Yi, Pan, Xian-ming, and Liao, Dong-fa

Subjects
REACTIVE oxygen species, CELL death, CELLULAR signal transduction, OSTEOBLASTS, CELL lines, LABORATORY rats
Abstract

In bones, osteoblasts are responsible for bone formation. The cell death of osteoblasts may cause a series of bone diseases and lead to bone loss, such as osteoarthrosis, hyperparathyroidism, and Paget’s disease. Reactive oxygen species (ROS) are reported as a main factor for osteoblast cell death and further several bone diseases. However, the detailed mechanism is still largely unknown. Here, we found that ROS could induce cell death of rat osteoblast-like cell line ROS 17/2.8 via Akt (protein kinase B). Also, the mammalian target of rapamycin signaling was involved in this process. Our findings could help to reveal the cellular mechanism of osteoblast cell death, which is served for the pursuit of clinical treatment targets of relative bone diseases. [ABSTRACT FROM AUTHOR]

Published
2015
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48. An Improved Method for Predicting Linear B-cell Epitope Using Deep Maxout Networks.

Author

LIAN, Yao, HUANG, Ze Chi, GE, Meng, and PAN, Xian Ming

Subjects
AMINO acid sequence, B cells, EPITOPES, IMMUNOGLOBULINS, GRAPHICS processing units, PREDICTION theory
Abstract

To establish a relation between an protein amino acid sequence and its tendencies to generate antibody response, and to investigate an improved in silico method for linear B-cell epitope (LBE) prediction. We present a sequence-based LBE predictor developed using deep maxout network (DMN) with dropout training techniques. A graphics processing unit (GPU) was used to reduce the training time of the model. A 10-fold cross-validation test on a large, non-redundant and experimentally verified dataset (Lbtope_Fixed_ non_redundant) was performed to evaluate the performance. DMN-LBE achieved an accuracy of 68.33% and an area under the receiver operating characteristic curve (AUC) of 0.743, outperforming other prediction methods in the field. A web server, DMN-LBE, of the improved prediction model has been provided for public free use. We anticipate that DMN-LBE will be beneficial to vaccine development, antibody production, disease diagnosis, and therapy. [ABSTRACT FROM AUTHOR]

Published
2015
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