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Search Results: 1 - 10 of 23054 matches for " Shide Liang "
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SVMTriP: A Method to Predict Antigenic Epitopes Using Support Vector Machine to Integrate Tri-Peptide Similarity and Propensity
Bo Yao, Lin Zhang, Shide Liang, Chi Zhang
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0045152
Abstract: Identifying protein surface regions preferentially recognizable by antibodies (antigenic epitopes) is at the heart of new immuno-diagnostic reagent discovery and vaccine design, and computational methods for antigenic epitope prediction provide crucial means to serve this purpose. Many linear B-cell epitope prediction methods were developed, such as BepiPred, ABCPred, AAP, BCPred, BayesB, BEOracle/BROracle, and BEST, towards this goal. However, effective immunological research demands more robust performance of the prediction method than what the current algorithms could provide. In this work, a new method to predict linear antigenic epitopes is developed; Support Vector Machine has been utilized by combining the Tri-peptide similarity and Propensity scores (SVMTriP). Applied to non-redundant B-cell linear epitopes extracted from IEDB, SVMTriP achieves a sensitivity of 80.1% and a precision of 55.2% with a five-fold cross-validation. The AUC value is 0.702. The combination of similarity and propensity of tri-peptide subsequences can improve the prediction performance for linear B-cell epitopes. Moreover, SVMTriP is capable of recognizing viral peptides from a human protein sequence background. A web server based on our method is constructed for public use. The server and all datasets used in the current study are available at http://sysbio.unl.edu/SVMTriP.
Prediction of antigenic epitopes on protein surfaces by consensus scoring
Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-302
Abstract: We present a new antigen Epitope Prediction method, which uses ConsEnsus Scoring (EPCES) from six different scoring functions - residue epitope propensity, conservation score, side-chain energy score, contact number, surface planarity score, and secondary structure composition. Applied to unbounded antigen structures from an independent test set, EPCES was able to predict antigenic eptitopes with 47.8% sensitivity, 69.5% specificity and an AUC value of 0.632. The performance of the method is statistically similar to other published methods. The AUC value of EPCES is slightly higher compared to the best results of existing algorithms by about 0.034.Our work shows consensus scoring of multiple features has a better performance than any single term. The successful prediction is also due to the new score of residue epitope propensity based on atomic solvent accessibility.Realistic prediction of protein surface regions that are preferentially recognized by antibodies (antigenic epitopes) can help in the design of vaccine components and immuno-diagnostic reagents. Antigenic epitopes are classified as continuous or discontinues epitopes. If the residues involved in an epitope are contiguous in the polypeptide chain, this epitope is called a continuous epitope or a linear epitope. On the other hand, a discontinuous or non-linear epitope is composed of residues that are not necessarily continuous in the polypeptide sequence but have spatial proximity on the surface of a protein structure. A significant fraction of epitopes are discontinuous in the sense that antibody binding is not fully determined by a linear peptide segment but also influenced by adjacent surface regions [1].However, the majority of available epitope prediction methods focus on continuous epitopes due to the convenience of the investigation in which the amino acid sequence of a protein is taken as the input. Such prediction methods are based upon the amino acid properties including hydrophilicity [2,3], so
Rational screenning in combinatorial peptide libraries of protein functional loop
Weizhong Li,Zhijie Liu,Shide Liang,Yuzhen Han,Luhua Lai
Chinese Science Bulletin , 1999, DOI: 10.1007/BF03182698
Abstract: Redesigning the sequences of protein loops is a frequent practice in protein design. Based on the new results of protein loop database analysis, a rational computer simulation strategy is proposed to obtain functional proteins, which exploits a fast and accurate program to calculate the protein loop conformation, and at the same time, combines molecular docking method with combinatorial chemistry strategy to screen the combinatorial peptide library of protein loops. A characteristic of this method is that it separates the conformation computation of backbone from that of side chain and incorporates side chain growth into the docking procedure and therefore greatly reduces the computation by converting the huge computation on explosive conformations to relatively small computation on limited canonical backbone structures and side chain growth. This method can be practically used in screening combinatorial peptide libraries of protein loops.
Conformational B-Cell Epitope Prediction on Antigen Protein Structures: A Review of Current Algorithms and Comparison with Common Binding Site Prediction Methods
Bo Yao, Dandan Zheng, Shide Liang, Chi Zhang
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0062249
Abstract: Accurate prediction of B-cell antigenic epitopes is important for immunologic research and medical applications, but compared with other bioinformatic problems, antigenic epitope prediction is more challenging because of the extreme variability of antigenic epitopes, where the paratope on the antibody binds specifically to a given epitope with high precision. In spite of the continuing efforts in the past decade, the problem remains unsolved and therefore still attracts a lot of attention from bioinformaticists. Recently, several discontinuous epitope prediction servers became available, and it is intriguing to review all existing methods and evaluate their performances on the same benchmark. In addition, these methods are also compared against common binding site prediction algorithms, since they have been frequently used as substitutes in the absence of good epitope prediction methods.
EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results
Shide Liang, Dandan Zheng, Daron M Standley, Bo Yao, Martin Zacharias, Chi Zhang
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-381
Abstract: In this work, we present two novel server applications for discontinuous epitope prediction: EPSVR and EPMeta, where EPMeta is a meta server. EPSVR, EPMeta, and datasets are available at http://sysbio.unl.edu/services webcite.The server application for discontinuous epitope prediction, EPSVR, uses a Support Vector Regression (SVR) method to integrate six scoring terms. Furthermore, we combined EPSVR with five existing epitope prediction servers to construct EPMeta. All methods were benchmarked by our curated independent test set, in which all antigens had no complex structures with the antibody, and their epitopes were identified by various biochemical experiments. The area under the receiver operating characteristic curve (AUC) of EPSVR was 0.597, higher than that of any other existing single server, and EPMeta had a better performance than any single server - with an AUC of 0.638, significantly higher than PEPITO and Disctope (p-value < 0.05).Antigenic epitopes are regions of protein surface that are preferentially recognized by antibodies. Prediction of antigenic epitopes can help during the design of vaccine components and immuno-diagnostic reagents, but predicting effective epitopes is still an open problem in bioinformatics. Usually, B-cell antigenic epitopes are classified as either continuous or discontinuous. The majority of available epitope prediction methods focus on continuous epitopes [1-12].Although discontinuous epitopes dominate most antigenic epitope families [13], due to their computational complexity, only a very limited number of prediction methods exist for discontinuous epitope prediction: CEP [14], DiscoTope [15], PEPITO [16], ElliPro [17], SEPPA [18], EPITOPIA[19,20] and our previous work, EPCES [21]. All discontinuous epitope prediction methods require the three-dimensional structure of the antigenic protein. The small number of available antigen-antibody complex structures limits the development of reliable discontinuous epitope prediction
Grafting of protein-protein binding sites
Shide Liang,Lan Xiao,Fenglou Mao,Lin Jiang,Yuzhen Han,Luhua Lai
Chinese Science Bulletin , 2000, DOI: 10.1007/BF02898992
Abstract: A strategy for grafting protein-protein binding sites is described. Firstly, key interaction residues at the interface of ligand protein to be grafted are identified and suitable positions in scaffold protein for grafting these key residues are sought. Secondly, the scaffold proteins are superposed onto the ligand protein based on the corresponding Cα and Cβ atoms. The complementarity between the scaffold protein and the receptor protein is evaluated and only matches with high score are accepted. The relative position between scaffold and receptor proteins is adjusted so that the interface has a reasonable packing density. Then the scaffold protein is mutated to corresponding residues in ligand protein at each candidate position. And the residues having bad steric contacts with the receptor proteins, or buried charged residues not involved in the formation of any salt bridge are mutated. Finally, the mutated scaffold protein in complex with receptor protein is co-minimized by Charmm. In addition, we deduce a scoring function to evaluate the affinity between mutated scaffold protein and receptor protein by statistical analysis of rigid binding data sets.
A Trust-Region-Based BFGS Method with Line Search Technique for Symmetric Nonlinear Equations
Gonglin Yuan,Shide Meng,Zengxin Wei
Advances in Operations Research , 2009, DOI: 10.1155/2009/909753
Abstract: A trust-region-based BFGS method is proposed for solving symmetric nonlinear equations. In this given algorithm, if the trial step is unsuccessful, the linesearch technique will be used instead of repeatedly solving the subproblem of the normal trust-region method. We establish the global and superlinear convergence of the method under suitable conditions. Numerical results show that the given method is competitive to the normal trust region method.
Studies on the degraduation of wood sawdust by Lentinus squarrosulus (Mont.) Singer
EG Shide, PA Wuyep, AJ Nok
African Journal of Biotechnology , 2004,
Abstract: Lentinus squarrosulus (Mont.) Singer, a basidiomycete also known as a white rot fungi, was immobilized on sodium alginate and tested for the effectiveness to degrade wood sawdust (WSD). Untreated and 0.1 M HCl-pretreated WSD samples were separately reacted in a micro-carrier bioreactor (mCBR) and the extent of degradation to form protein, glucose and ethanol was investigated. Pretreatment enhanced the production of both proteins and ethanol by average value of 72.0% over untreated WSD samples, after hydraulic retention time of 72 h. The maximum production of protein observed was 0.94 mg/ml-reaction volume and that of ethanol was 6.6 mg/ml-reaction volume, whereas glucose concentration fluctuated due to interconversion to ethanol. This report shows that L. squarrosulus (Mont.) Singer have the potentials of degrading WSD samples to important chemical compounds that are not hazardous to the environment.
Wind-Driven Ocean Circulation in Shallow Water Lattice Boltzmann Model
ZHONG Linhao,FENG Shide,GAO Shouting,
ZHONG Linhao
,FENG Shide,GAO Shouting

大气科学进展 , 2005,
Abstract: A lattice Boltzmann (LB) model with overall second-order accuracy is applied to the 1.5-layer shallow water equation for a wind-driven double-gyre ocean circulation. By introducing the second-order integral approximation for the collision operator, the model becomes fully explicit. In this case, any iterative technique is not needed. The Coriolis force and other external forces are included in the model with second-order accuracy, which is consistent with the discretized accuracy of the LB equation. The numerical results show correct physics of the ocean circulation driven by the double-gyre wind stress with different Reynolds numbers and different spatial resolutions. An intrinsic low-frequency variability of the shallow water model is also found. The wind-driven ocean circulation exhibits subannual and interannual oscillations, which are comparable to those of models in which the conventional numerical methods are used.
Research on adsorption of hexavalent chromium in water onto grapefruit husk powder

Shen Shide,Xu Juan,

环境工程学报 , 2010,
Abstract: 采用柚皮粉吸附去除水中Cr(Ⅵ)。考察了pH、吸附时间、柚皮粉用量和Cr(Ⅵ)初始浓度等因素对吸附效果的影响,测定了吸附等温线,对等温吸附规律及吸附机理进行了探讨。结果表明,pH、吸附时间、柚皮粉用量、Cr(Ⅵ)初始浓度、温度等因素对柚皮粉吸附水中Cr(Ⅵ)有显著影响。适宜的吸附条件为:pH 1.5,吸附时间6 h,柚皮粉用量0.5 g/100 mL,Cr(Ⅵ)初始浓度不大于10 mg/L,温度25℃。在该条件下,Cr(Ⅵ)的去除率可达98%以上。柚皮粉对水中Cr(Ⅵ)的等温吸附规律可用Freundlich、Langmuir和Temkin模式较好地描述,吸附呈单分层形式,吸附性能良好,吸附易于进行。柚皮细胞成分中的活性基团与Cr(Ⅵ)发生表面络合作用是吸附的主要机理。
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