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ABSTRACT: In this paper, we propose a novel force field parameter optimization method based on LSSVR and optimize the torsion energy parameters of ECEPP force field. In this method force field parameter optimization problem is turned into a support vector regression problem. Protein samples for regression model training are chosen from Protein Data Bank. The experiments show that the optimized force-field parameters make both α-helix and β-hairpin structures more consistent with the experimental implications than the original parameters.
FEBS letters 02/2011; 585(6):888-92. · 3.54 Impact Factor
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Jianjun Lu,
Hong Pan,
Yucai Chen,
Yuehua Zhang,
Xiaoyan Liu,
Yuwu Jiang,
Xinhua Bao,
Xiru Wu,
Yan Shen,
Husheng Wu,
Keming Xu
American Journal of Medical Genetics Part A 01/2004; 123A(2):197-200. · 2.39 Impact Factor
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Yucai Chen, Jianjun Lu,
Hong Pan,
Yuehua Zhang,
Husheng Wu,
Keming Xu,
Xiaoyan Liu,
Yuwu Jiang,
Xinhua Bao,
Zhijian Yao,
Keyue Ding,
Wilson H Y Lo,
Boqin Qiang,
Piu Chan,
Yan Shen,
Xiru Wu
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ABSTRACT: Direct sequencing of exons 3 to 35 and the exon-intron boundaries of the CACNA1H gene was conducted in 118 childhood absence epilepsy patients of Han ethnicity recruited from North China. Sixty-eight variations have been detected in the CACNA1H gene, and, among the variations identified, 12 were missense mutations and only found in 14 of the 118 patients in a heterozygous state, but not in any of 230 unrelated controls. The identified missense mutations occurred in the highly conserved residues of the T-type calcium channel gene. Our results suggest that CACNA1H might be an important susceptibility gene involved in the pathogenesis of childhood absence epilepsy.
Annals of Neurology 09/2003; 54(2):239-43. · 11.09 Impact Factor
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Jianjun Lu,
Yucai Chen,
Hong Pan,
Yuehua Zhang,
Husheng Wu,
Keming Xu,
Xiaoyan Liu,
Yuwu Jiang,
Xinhua Bao,
Yan Shen,
Xiru Wu
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ABSTRACT: Childhood absence epilepsy (CAE) is considered to be a genetic disease, but the genes responsible for it have not yet been identified. To investigate whether or not the GABBR1 gene is a susceptibility gene for CAE in the Chinese Han population, we systematically screened all the 22 exons and nearby intron regions of the gene and found 12 single nucleotide polymorphisms (SNPs). Using four SNPs as markers, we conducted a case-control study in 96 CAE patients and 96 normal controls. There were no significant discrepancies between the cases and controls in allele and phenotype frequencies of the four SNPs. There were still no significant differences in haplotype distributions between the cases and controls. We postulate that the GABBR1 gene might not be a susceptibility gene for CAE at least in the Chinese population.
Neuroscience Letters 07/2003; 343(3):151-4. · 2.11 Impact Factor
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Yucai Chen, Jianjun Lu,
Yuehua Zhang,
Hong Pan,
Husheng Wu,
Keming Xu,
Xiaoyan Liu,
Yuwu Jiang,
Xinhua Bao,
Jing Zhou,
Wei Liu,
Guibin Shi,
Yan Shen,
Xiru Wu
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ABSTRACT: We investigated whether the T-type calcium channel gene alpha (1G) is associated with childhood absence epilepsy (CAE), a form of idiopathic generalized epilepsy. We carried out direct sequencing of exons 1-37 and the exon-intron boundaries of the alpha (1G) gene in 48 Han Chinese patients with CAE and 48 normal controls. We found no mutation in the exons of alpha (1G). However, we did identify six single nucleotide polymorphisms (SNPs). Using two of these as markers, we carried out a case-control study in 192 patients with CAE and 192 normal controls. The allele and genotype distributions of all the SNPs studied were not significantly different between cases and control groups, thus the alpha (1G) gene is not an important susceptibility gene for CAE, at least in the Chinese population.
Neuroscience Letters 05/2003; 341(1):29-32. · 2.11 Impact Factor
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Jianjun Lu,
Yucai Chen,
Yuehua Zhang,
Hong Pan,
Husheng Wu,
Keming Xu,
Xiaoyan Liu,
Yuwu Jiang,
Xinhua Bao,
Keyue Ding,
Yan Shen,
Xiru Wu
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ABSTRACT: Childhood absence epilepsy (CAE) is considered to be a genetic disease, the genes responsible for which have not yet been identified. To investigate whether or not GABA(A) receptor gamma 2 subunit gene (GABRG2) is the susceptibility gene for CAE in the Chinese population, we screened 68 CAE patients of Han ethnicity from North China for mutations in the nine exons of GABRG2. Although we found no mutation in the exons of GABRG2, we did identify two single nucleotide polymorphisms (SNPs) in exon 3 and exon 5. Using the two SNPs as markers, we carried out a transmission/disequilibrium test (TDT) in 68 trios with CAE. TDT results showed that there were no significant discrepancies between the CAE patients and 'internal controls' in allele frequencies of the two SNPs. We postulate that the GABRG2 gene might be neither a susceptibility gene for CAE nor in linkage disequilibrium with disease-predisposing sites in the Chinese population.
Neuroscience Letters 11/2002; 332(2):75-8. · 2.11 Impact Factor
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ABSTRACT: To investigate whether or not the gamma-aminobutyric acid GABA receptor subtype Alpha genes GABRA5 and GABRB3 are associated with childhood absence epilepsy CAE .
Five microsatellite DNA 69CA 85CA 155CA1 155CA2 and A55CA1 adjacent to chromosome 15q11-15q13 were used as genetic markers. Fluorescence-based semi-automated genotyping technique was used in 90 CAE patients and 100 normal controls to conduct genotyping. Case-control study was used to do association analysis.
In Chinese normal population the allele frequencies of the five microsatellite DNAs were in good agreement with Hardy- Weinberg equilibrium. The polymorphism information content PIC of the five microsatellite DNA were 0.47 0.82 0.66 0.86, and 0.86 respectively. The frequencies of some alleles of the 5 microsatellite DNAs in CAE patients were significantly higher than those in normal controls.
Four of the five microsatellite DNAs are good genetic markers. GABA subtype Alpha genes GABRA5 and GABRB3 may be associated with the pathogenic mechanism of CAE.
Zhonghua yi xue za zhi 09/2002; 82(15):1029-32.
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Jianjun Lu,
Yucai Chen,
Yuehua Zhang,
Hong Pan,
Xiaoyan Liu,
Yuwu Jiang,
Weinan Du,
Yan Shen,
Keming Xu,
Husheng Wu,
Xiru Wu
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ABSTRACT: To investigate whether or not the gamma-aminobutyric acid (GABA) receptor subtype A genes GABRA5 and GABRB3 are associated with childhood absence epilepsy (CAE).
Two microsatellite DNA, GABRA5 and GABRB3, adjoining to chromosome 15q11.2-q12 were used as genetic markers. Both case-control study and transmission/disequilibrium test (TDT) as well as fluorescence-based semi-automated genotyping technique were used in 90 trios with CAE and 100 controls to conduct association analysis.
The allele frequencies of the 2 microsatellite DNA in Chinese normal population are in good agreement with Hardy-Weinberg equilibrium. The polymorphism information content of microsatellite DNA GABRA5 and GABRB3, are 0.80 and 0.66 respectively. The allele 2 frequency of microsatellite DNA GABRA5 and the allele 5 frequency of microsatellite DNA GABRB3 are significantly higher in CAE patients than those in normal controls(P<0.001).
Both microsatellite DNA GABRA5 and GABRB3 are good genetic markers. The gamma-aminobutyric acid receptor subtype A genes GABRA5 and GABRB3 may be directly involved either in the etiology of CAE or in linkage disequilibrium with disease-predisposing sites.
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics 06/2002; 19(3):183-6.
