李炜疆
研究领域:1.生物信息学;2.计算分子生物学。
个性化签名
- 姓名:李炜疆
- 目前身份:
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- 学位:
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学术头衔:
博士生导师
- 职称:-
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学科领域:
生物化学
- 研究兴趣:研究领域:1.生物信息学;2.计算分子生物学。
李炜疆,男,1964年3月出生。1981-85年于兰州大学物理系攻读本科,获理论物理专业学士学位;1988-91年于内蒙古大学物理系攻读硕士,获理论生物物理专业硕士学位;1991-94年于内蒙古大学物理系攻读博士,获理论生物物理专业博士学位。1985-88年于内蒙古工业大学基础部任助教;1994-99年于内蒙古大学物理系历任讲师、副教授、教授;2000年起于江南大学生物工程学院任教授;2002-06年于日本国立九州工业大学生命科学与生物信息学系,访问教授。研究领域:1.生物信息学;2.计算分子生物学。主持国家自然科学基金项目:蛋白质与抑制剂的结合动力学及其在药物设计中的应用(39760027),1998—2000。1999年获得国家自然科学三等奖:基因序列的信息学研究。
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主页访问
1346
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关注数
0
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成果阅读
432
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成果数
10
【期刊论文】A grid layout algorithm for automatic drawing of biochemical networks
李炜疆, Weijiang Li and Hiroyuki Kurata*
Systems biology, 2036-2042,-0001,():
-1年11月30日
Motivation: Visualization is indispensable in the research of complex biochemical networks. Available graph layout algorithms are not adequate for satisfactorily drawing such networks. New methods are required to visualize automatically the topological architectures and facilitate the understanding of the functions of the networks. Results: We propose a novel layout algorithm to draw complex biochemical networks. A network is modeled as a system of interacting nodes on squared grids. A discrete cost function between each node pair is designed based on the topological relation and the geometric positions of the two nodes. The layouts are produced by minimizing the total cost. We design a fast algorithm to minimize the discrete cost function, by which candidate layouts can be produced efficiently. A simulated annealing procedure is used to choose better candidates. Our algorithm demonstrates its ability to exhibit cluster structures clearly in relatively compact layout areas without any prior knowledge. We developed Windows software to implement the algorithm for CADLIVE.
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【期刊论文】A novel model to determine the dipeptides responsible for optimum temperature in F/10 xylanase
李炜疆, Liangwei Liua, b, Minglei Wanga, Weilan Shaoa, Weijiang Lia, *
Process Biochemistry 40(2005)1389-1394,-0001,():
-1年11月30日
A bioinformatics method was used to analyze the characteristic dipeptides responsible for optimum temperature of xylanase in the F/10 family. It was found that the positive dipeptides are: TD, GH, and WY; and the negative dipeptides are: GA, IA, FH, LH, SR, and NH. The calculated temperature fitted the optimum temperature of the xylanase very well and the maximal and minimal optimum temperatures were calculated as, 150.46 and -29.06℃. The thermostable mechanism was discussed and the result is useful for xylanase engineering for high temperature activity, for it also provided position information for engineering.
Xylanase, Thermostability, Mechanism, dipeptides, Amino acid, Enzyme engineering
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42浏览
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67下载
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【期刊论文】A novel method of analyzing proline synonymous codons in E. coli☆
李炜疆, Ming-Lei Wanga, b, *, Jiang-Ning Songa, Wen-Bo Xuc, Wei-Jiang Lia
FEBS Letters 576(2004)336-338,-0001,():
-1年11月30日
Proline is a special imino acid in protein and the isomerization of the prolyl peptide bond has notable biological significance and influences the final structure of protein greatly, so the correlation between proline synonymous codon usage and local amino acid, the correlation between proline synonymous codon usage and the isomerization of the prolyl peptide bond were both investigated in the Escherichia coli genome by using a novel method based on information theory. The results show that in peptide chain, the residue at the first position C-terminal influences the usage of proline synonymous codon greatly and proline synonymous codons contain some factors influencing the isomerization of the prolyl peptide bond.
Proline synonymous codon, E., coli, Information theory
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32浏览
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51下载
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李炜疆, Jiang-Ning Song, a, b, *, Ming-Lei Wang, Wei-Jiang Li, b and Wen-Bo Xuc
Biochemical and Biophysical Research Communications 318(2004)142-147,-0001,():
-1年11月30日
In this paper, a novel approach has been introduced to predict the disulfide-bonding state of cysteines in proteins by means of a linear discriminator based on their dipeptide composition. The prediction is performed with a newly enlarged dataset with 8114 cysteine-containing segments extracted from 1856 non-homologous proteins of well-resolved three-dimensional structures. Theoxidation of cysteines exhibits obvious cooperativity: almost all cysteines in disulfide-bond-containing proteins are in the oxidized form. This cooperativity can be well described by protein's dipeptide composition, based on which the prediction accuracy of the oxidation form of cysteines scores as high as 89.1% and 85.2%, when measured on cysteine and protein basis using the rigorous jackknife procedure, respectively. The result demonstrates the applicability of this new relatively simple method and provides superior prediction performance compared with existing methods for the prediction of the oxidation states of cysteines in proteins.
Cysteine, Disulfide-bonding state, Protein folding, Dipeptide composition, Bioinformatics, Cooperativity
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【期刊论文】Related dipeptide and characteristic dipeptide of optimal pH in a-amylase☆
李炜疆, Ge-Xin Zhanga, * and Wei-Jiang Lib
Biochemical and Biophysical Research Communications 299(2002)647-651,-0001,():
-1年11月30日
α-Amylase is an enzyme of great significance to industry, but most a-amylases are unstable at lower pH. In this paper, we have studied the related dipeptide and characteristic dipeptide of optimal pH in a-amylase. On analysis, it gives the explicit results as follows: (1) Ten dipeptides are associated with a-amylase soptimal pH. AH, DV, EH, HR, and YV are of positive correlation, AM, IC, NG, NL, and PS are of negative correlation. (2) GE, RE, GS, and KS are higher pH a-amylase characteristic dipeptides; AS, GS, DY, and GI are high pH a-amylase characteristic dipeptides; TE, VR, DS, and ET are middle pH a-amylase characteristic dipeptides; DK, NT, PT, and RV are low pH a-amylase characteristic dipeptides; AT, DS, GR, and SR are lower pH a-amylase characteristic dipeptides.
α-Amylase, Protein sequence, Dipeptide, Optimal pH, Bioinformatics
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35浏览
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李炜疆, 李炜疆**
生物化学与生物物理进展,2001,28(3):413、513、613、713,-0001,():
-1年11月30日
全局极小化方法及其在结构生物学中的应用近年来取得了显著的进展。适当简化的分子对接问题是全局极小化方法的一个很好目标,并且是当前一个相当活跃的研究领域。对接可分为两类:主要用于从头配体设计的细致对接和用于已知化合物数据库筛选以发现药物的粗略对接,它们对全局极小化算法的要求是不同的。简要评述了新出现的适合于对接问题的随机和确定性全局极小化算法,其中势能平滑算法看来很有希望,值得密切关注。
分子对接,, 全局极小化,, 势能平滑
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83浏览
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【期刊论文】Statistical correlation of nucleotides in a DNA sequence
李炜疆, Liaofu Luo*, Weijiang Lee†, Lijun Jia, Fengmin Ji, and Lu Tsai
PHYSICAL REVIEW E VOLUME 58, NUMBER 1 JULY 1998,-0001,():
-1年11月30日
We review methods in the study of nucleotide correlation in DNA sequence, and demonstrate two basic properties of the correlation through statistical analysis, namely, the short-range dominance of nucleotide correlation in most DNA sequences and the coarse-grained evolutionary dependence of the short-range correlation in coding sequences. A corresponding evolutionary mechanism is suggested. By the use of spectral analysis a large inhomogeneity in long-range base correlations for different sequences is indicated. Some results on three-dimensional DNA walks are reported. The linguistic differences between coding and noncoding sequences are also indicated.
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39浏览
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李炜疆
生物物理学报,2001,17(3):529~534,-0001,():
-1年11月30日
研究了大肠杆菌编码区不同位置上的同义密码子用语,发现许多氨基酸的密码子用语在转译起始区有显著的变化,仅有少数氨基酸在转译终止区有较弱的变化。由于密码子用语与基因表达关系密切,这些结果与实验发现的编码区5'端密码子用语对表达的重要性是一致的。更进一步的结果还暗示了哪些密码子在特定位置的使用可能会影响基因表达。
同义密码子用语, 位点差异, 大肠杆菌
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54浏览
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李炜疆, 张有广, 李炜疆*
生物物理学报,2001,17(1):181~186,-0001,():
-1年11月30日
随机聚点搜索算法是一种普遍的全局极小化方法,在目标函数自变量数目不很大时,计算效率较高。将该算法应用于分子对接,首先要通过模型分子对接,反复调整算法各控制参数使效率最高。对于HIV-1蛋白酶与苯甲醚配体的刚性对接,算法成功的找到了相互作用能量全局极小,与晶体结构的均方根偏差(RMSD)仅0.2Å。这表明,该算法可高效率找到分子对接的能量最适构型。
随机聚点搜索算法, 刚性分子对接, 全局极小化
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27浏览
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【期刊论文】Periodicity of base correlation in nucleotide sequence
李炜疆, Weijiang Lee* and Liaofu Luo
PHYSICAL REVIEW E VOLUME 56, NUMBER 1 JULY 1997,-0001,():
-1年11月30日
The correlation spectrum of a symbolic sequence is defined. The harmonic heights in the spectrum of a nucleotide sequence are calculated rigorously. A model of coding sequences is proposed and the origin of 3-periodicity is explained. The possible occurrence of a hidden periodicity of base correlation with no peak in the spectrum is discussed.
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