Genome informatics. International Conference on Genome Informatics最新文献_第3页

Strategies of non-sequential protein structure alignments. 非序列蛋白质结构比对策略。

Genome informatics. International Conference on Genome Informatics Pub Date : 2010-01-01

Aysam Guerler, Ernst-Walter Knapp

{"title":"Strategies of non-sequential protein structure alignments.","authors":"Aysam Guerler, Ernst-Walter Knapp","doi":"","DOIUrl":"","url":null,"abstract":"Due to the large number of available protein structure alignment algorithms, a lot of effort has been made to define robust measures to evaluate their performances and the quality of generated alignments. Most quality measures involve the number of aligned residues and the RMSD. In this work, we analyze how these two properties are influenced by different residue assignment strategies as employed in common non-sequential structure alignment algorithms. Therefore, we implemented different residue assignment strategies into our non-sequential structure alignment algorithm GANGSTA+. We compared the resulting numbers of aligned residues and RMSDs for each residue assignment strategy and different alignment algorithms on a benchmark set of circular-permuted protein pairs. Unfortunately, differences in the residue assignment strategies are often ignored when comparing the performances of different algorithms. However, our results clearly show that this may strongly bias the observations. Bringing residue assignment strategies in line can explain observed performance differences between entirely different alignment algorithms. Our results suggest that performance comparison of non-sequential protein structure alignment algorithms should be based on the same residue assignment strategy.","PeriodicalId":73143,"journal":{"name":"Genome informatics. International Conference on Genome Informatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28783006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization and classification of adverse drug interactions. 药物不良反应的特征和分类。

Genome informatics. International Conference on Genome Informatics Pub Date : 2010-01-01

Masataka Takarabe, Daichi Shigemizu, Masaaki Kotera, Susumu Goto, Minoru Kanehisa

引用次数: 0

Genome-wide analysis of plant UGT family based on sequence and substrate information. 基于序列和底物信息的植物UGT家族全基因组分析。

Genome informatics. International Conference on Genome Informatics Pub Date : 2010-01-01

Yosuke Nishimura, Toshiaki Tokimatsu, Masaaki Kotera, Susumu Goto, Minoru Kanehisa

{"title":"Genome-wide analysis of plant UGT family based on sequence and substrate information.","authors":"Yosuke Nishimura, Toshiaki Tokimatsu, Masaaki Kotera, Susumu Goto, Minoru Kanehisa","doi":"","DOIUrl":"","url":null,"abstract":"UGTs (UDP glycosyltransferase) are the largest glycosyltransferase gene family in higher plants, modifying secondary metabolites, hormones, and xenobiotics. This gene family plays an important role in the vast diversity of plant secondary metabolites specific to species. Experimental data of biochemical activities and physiological roles of plant UGTs are increasing but most UGTs are not still functionally characterized. To understand their catalytic specificity and function from sequence data, phylogenetic analyses have been achieved mainly in Arabidopsis, but massive and comprehensive approach covering various species has not been applied yet. In this study, we collected 733 UGT sequences derived from 96 plant species and 252 substrate specificity data. We constructed a phylogenetic tree and divided most part of these genes into nine sequence groups, which are characterized by biochemical specificity. Furthermore, we performed genome-wide analysis of seven plant species UGTs by mapping them into these groups. We propose this is the first step to understand whole glycosylated secondary metabolites of each plant species from its genome information.","PeriodicalId":73143,"journal":{"name":"Genome informatics. International Conference on Genome Informatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30252342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

On the performance of methods for finding a switching mechanism in gene expression. 关于寻找基因表达转换机制的方法的性能。

Genome informatics. International Conference on Genome Informatics Pub Date : 2010-01-01 DOI: 10.1142/9781848166585_0006

Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, K. Tsuda, Hiroshi Mamitsuka

{"title":"On the performance of methods for finding a switching mechanism in gene expression.","authors":"Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, K. Tsuda, Hiroshi Mamitsuka","doi":"10.1142/9781848166585_0006","DOIUrl":"https://doi.org/10.1142/9781848166585_0006","url":null,"abstract":"We address an issue of detecting a switching mechanism in gene expression, where two genes are positively correlated for one experimental condition while they are negatively correlated for another. We compare the performance of existing methods for this issue, roughly divided into two types: interaction test (IT) and the difference of correlation coefficients. Interaction test, currently a standard approach for detecting epistasis in genetics, is the log-likelihood ratio test between two logistic regressions with/without an interaction term, resulting in checking the strength of interaction between two genes. On the other hand, two correlation coefficients can be computed for two experimental conditions and the difference of them shows the alteration of expression trends in a more straightforward manner. In our experiments, we tested three different types of correlation coefficients: Pearson, Spearman and a midcorrelation (biweight midcorrelation). The experiment was performed by using ~ 2.3 × 10(9) combinations selected out of the GEO (Gene Expression Omnibus) database. We sorted all combinations according to the p-values of IT or by the absolute values of the difference of correlation coefficients and then visually evaluated the top ranked combinations in terms of the switching mechanism. The result showed that 1) combinations detected by IT included non-switching combinations and 2) Pearson was affected by outliers easily while Spearman and the midcorrelation seemed likely to avoid them.","PeriodicalId":73143,"journal":{"name":"Genome informatics. International Conference on Genome Informatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76784928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Annotating gene functions with integrative spectral clustering on microarray expressions and sequences. 利用微阵列表达和序列的整合谱聚类来注释基因功能。

Genome informatics. International Conference on Genome Informatics Pub Date : 2010-01-01 DOI: 10.1142/9781848165786_0009

Limin Li, Motoki Shiga, W. Ching, Hiroshi Mamitsuka

引用次数: 13

Predicting protein complex geometries with linear scoring functions. 用线性评分函数预测蛋白质复杂几何形状。

Genome informatics. International Conference on Genome Informatics Pub Date : 2010-01-01 DOI: 10.1142/9781848166585_0002

Ozgur Demir-Kavuk, Florian Krull, Myong-Ho Chae, E. Knapp

{"title":"Predicting protein complex geometries with linear scoring functions.","authors":"Ozgur Demir-Kavuk, Florian Krull, Myong-Ho Chae, E. Knapp","doi":"10.1142/9781848166585_0002","DOIUrl":"https://doi.org/10.1142/9781848166585_0002","url":null,"abstract":"Protein-Protein interactions play an important role in many cellular processes. However experimental determination of the protein complex structure is quite difficult and time consuming. Hence, there is need for fast and accurate in silico protein docking methods. These methods generally consist of two stages: (i) a sampling algorithm that generates a large number of candidate complex geometries (decoys), and (ii) a scoring function that ranks these decoys such that nearnative decoys are higher ranked than other decoys. We have recently developed a neural network based scoring function that performed better than other state-of-the-art scoring functions on a benchmark of 65 protein complexes. Here, we use similar ideas to develop a method that is based on linear scoring functions. We compare the linear scoring function of the present study with other knowledge-based scoring functions such as ZDOCK 3.0, ZRANK and the previously developed neural network. Despite its simplicity the linear scoring function performs as good as the compared state-of-the-art methods and predictions are simple and rapid to compute.","PeriodicalId":73143,"journal":{"name":"Genome informatics. International Conference on Genome Informatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84629995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

CaMPDB: a resource for calpain and modulatory proteolysis. CaMPDB:钙蛋白酶和调节性蛋白水解的资源。

Genome informatics. International Conference on Genome Informatics Pub Date : 2010-01-01 DOI: 10.1142/9781848165786_0017

David duVerle, Ichigaku Takigawa, Y. Ono, H. Sorimachi, Hiroshi Mamitsuka

引用次数: 51

Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer. 基于整数规划的信号通路完成方法及其在结直肠癌分析中的应用。

Genome informatics. International Conference on Genome Informatics Pub Date : 2010-01-01 DOI: 10.1142/9781848166585_0016

Takeyuki Tamura, Yoshihiro Yamanishi, M. Tanabe, S. Goto, M. Kanehisa, K. Horimoto, T. Akutsu

引用次数: 3

Structural features and evolution of protein-protein interactions. 蛋白质-蛋白质相互作用的结构特征和演化。

Genome informatics. International Conference on Genome Informatics Pub Date : 2010-01-01

Joachim Von Eichborn, Stefan Günther, Robert Preissner

{"title":"Structural features and evolution of protein-protein interactions.","authors":"Joachim Von Eichborn, Stefan Günther, Robert Preissner","doi":"","DOIUrl":"","url":null,"abstract":"Solved structures of protein-protein complexes give fundamental insights into protein function and molecular recognition. Although the determination of protein-protein complexes is generally more difficult than solving individual proteins, the number of experimentally determined complexes increased conspicuously during the last decade. Here, the interfaces of 750 transient protein-protein interactions as well as 2,000 interactions between domains of the same protein chain (obligate interactions) were analyzed to obtain a better understanding of molecular recognition and to identify features applicable for protein binding site prediction. Calculation of knowledge-based potentials showed a preference of contacts between amino acids having complementary physicochemical properties. The analysis of amino acid conservation of the entire interface area showed a weak but significant tendency to a higher evolutionary conservation of protein binding sites compared to surface areas that are permanently exposed to solvent. Remarkably, contact frequencies between outstandingly conserved residues are much higher than expected confirming the so-called \"hot spot\" theory. The comparisons between obligate and transient domain contacts reveal differences and point out that structural diversification and molecular recognition of protein-protein interactions are subjected to other evolutionary aspects than obligate domain-domain interactions.","PeriodicalId":73143,"journal":{"name":"Genome informatics. International Conference on Genome Informatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28783004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Predicting protein complex geometries with linear scoring functions. 用线性评分函数预测蛋白质复杂几何形状。

Genome informatics. International Conference on Genome Informatics Pub Date : 2010-01-01

Ozgur Demir-Kavuk, Florian Krull, Myong-Ho Chae, Ernst-Walter Knapp

引用次数: 0