IPSJ Transactions on Bioinformatics最新文献_第5页

Predicting Three-way Interactions of Proteins from Expression Profiles Based on Correlation Coefficient 基于相关系数的表达谱预测蛋白质的三方相互作用

IPSJ Transactions on Bioinformatics Pub Date : 2012-10-01 DOI: 10.2197/IPSJTBIO.5.34

E. Inoue, S. Murakami, T. Fujiki, Takuya Yoshihiro, Atsushi Takemoto, Haruka Ikegami, Kazuya Matsumoto, Masaru Nakagawa

引用次数: 5

DINE: A Novel Score Function for Modeling Multidomain Protein Structures with Domain Linker and Interface Restraints 基于结构域连接子和界面约束的多结构域蛋白质结构建模的一种新的评分函数

IPSJ Transactions on Bioinformatics Pub Date : 2012-04-19 DOI: 10.2197/IPSJTBIO.5.18

Satoru Hirako, M. Shionyu

{"title":"DINE: A Novel Score Function for Modeling Multidomain Protein Structures with Domain Linker and Interface Restraints","authors":"Satoru Hirako, M. Shionyu","doi":"10.2197/IPSJTBIO.5.18","DOIUrl":"https://doi.org/10.2197/IPSJTBIO.5.18","url":null,"abstract":"The functional sites of multidomain proteins are often found at the interfaces of two or more domains. Therefore, the spatial arrangement of the domains is essential in understanding the functional mechanisms of multidomain proteins. However, an experimental determination of the whole structure of a multidomain protein is often difficult due to flexibility in inter-domain arrangement. We have developed a score function, named DINE, to detect probable docking poses generated in a rigid-body docking simulation. This score function takes into account the binding energy, information about the domain interfaces of homologous proteins, and the end-to-end distance spanned by the domain linker. We have examined the performance of DINE on 55 non-redundant known structures of two-domain proteins. In the results, the near-native docking poses were scored within the top 10 in 65.5% of the test cases. DINE scored the near-native poses higher in comparison with an existing domain assembly method, which also used binding energy and linker distance restraints. The results demonstrate that the domain-interface restraints of DINE are quite efficient in selecting near-native domain assemblies.","PeriodicalId":38959,"journal":{"name":"IPSJ Transactions on Bioinformatics","volume":"5 1","pages":"18-26"},"PeriodicalIF":0.0,"publicationDate":"2012-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2197/IPSJTBIO.5.18","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68502155","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

Analysis of Correlation between Gene Expression and Aberrant Epigenetic Status in Alzheimer's Disease Brain 阿尔茨海默病脑基因表达与异常表观遗传状态的相关性分析

IPSJ Transactions on Bioinformatics Pub Date : 2012-02-24 DOI: 10.2197/IPSJTBIO.5.2

K. Yano

{"title":"Analysis of Correlation between Gene Expression and Aberrant Epigenetic Status in Alzheimer's Disease Brain","authors":"K. Yano","doi":"10.2197/IPSJTBIO.5.2","DOIUrl":"https://doi.org/10.2197/IPSJTBIO.5.2","url":null,"abstract":"Dysregulation of epigenetic mechanisms has been implicated in the pathogenesis of Alzheimer's disease (AD). It has been shown that epigenetic status in promoter regions can alter levels of gene expressions, but their influence on correlated expressions of genes and its dependency on the disease are unclear. Using publicly available microarray and DNA methylation data, this article infer how correlation in gene expression in non-demented (ND) and AD brain may be influenced by genomic promoter methylation. Pearson correlation coefficients of gene expression levels between each of 123 known hypomethylated genes and all other genes in the microarray dataset were calculated, and the mean absolute coefficients were obtained as an overall strength of gene expression correlation of the hypomethylated gene. The distribution of the mean absolute coefficients showed that the hypomethylated genes can be divided into two, by the mean coefficients above or below 0.15. The division of the hypomethylated genes by the mean coefficients was more evident in AD brain than in ND brain. On the other hand, hypermethylated genes had a single dominant group, and the majority of them had the mean coefficient below 0.15. These results suggest that the lower the DNA methylation, the higher the correlation of gene expression levels with the other genes in microarray data. The strength of gene expression correlation was also calculated between known AD risk genes and all other genes in microarray data. It was found that AD risk genes were more likely to have the mean absolute correlation coefficients above 0.15 in AD brain, when the evidence for their association with AD was strong, suggesting the link between DNA methylation and AD. In conclusion DNA methylation status is intimately associated with correlated gene expression, particularly in AD brain.","PeriodicalId":38959,"journal":{"name":"IPSJ Transactions on Bioinformatics","volume":"5 1","pages":"2-6"},"PeriodicalIF":0.0,"publicationDate":"2012-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2197/IPSJTBIO.5.2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68502704","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

A GPU Accelerated Fragment-based De Novo Ligand Design by a Bayesian Optimization Algorithm 基于贝叶斯优化算法的GPU加速碎片从头配体设计

IPSJ Transactions on Bioinformatics Pub Date : 2012-01-01 DOI: 10.2197/IPSJTBIO.5.7

M. Wahib, Asim Munawar, M. Munetomo, K. Akama

{"title":"A GPU Accelerated Fragment-based De Novo Ligand Design by a Bayesian Optimization Algorithm","authors":"M. Wahib, Asim Munawar, M. Munetomo, K. Akama","doi":"10.2197/IPSJTBIO.5.7","DOIUrl":"https://doi.org/10.2197/IPSJTBIO.5.7","url":null,"abstract":"De Novo ligand design is an automatic fragment-based design of molecules within a protein binding site of a known structure. A Bayesian Optimization Algorithm (BOA), a meta-heuristic algorithm, is introduced to join predocked fragments with a user-supplied list of fragments. A novel feature proposed is the simultaneous optimization of force field energy and a term enforcing 3D-overlap to known binding mode(s). The performance of the algorithm is tested on Liver X receptors (LXRs) using a library of about 14, 000 fragments and the binding mode of a known heterocyclic phenyl acetic acid to bias the design. We further introduce the use of GPU (Graphics Processing Unit) to overcome the excessive time required in evaluating each possible fragment combination. We show how the GPU utilization enables experimenting larger fragment sets and target receptors for more complex instances. The results show how the nVidia's Tesla C2050 GPU was utilized to enable the generation of complex agonists effectively. In fact, eight of the 1, 809 molecules designed for LXRs are found in the ZINC database of commercially available compounds.","PeriodicalId":38959,"journal":{"name":"IPSJ Transactions on Bioinformatics","volume":"5 1","pages":"7-17"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2197/IPSJTBIO.5.7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68502862","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

Distance-based Factor Graph Linearization and Sampled Max-sum Algorithm for Efficient 3D Potential Decoding of Macromolecules 基于距离的因子图线性化和采样最大和算法的大分子三维高效电位解码

IPSJ Transactions on Bioinformatics Pub Date : 2011-09-06 DOI: 10.2197/IPSJTBIO.4.34

T. Shinozaki, Toshinao Iwaki, Shiqiao Du, M. Sekijima, S. Furui

{"title":"Distance-based Factor Graph Linearization and Sampled Max-sum Algorithm for Efficient 3D Potential Decoding of Macromolecules","authors":"T. Shinozaki, Toshinao Iwaki, Shiqiao Du, M. Sekijima, S. Furui","doi":"10.2197/IPSJTBIO.4.34","DOIUrl":"https://doi.org/10.2197/IPSJTBIO.4.34","url":null,"abstract":"Three-dimensional structure prediction of a molecule can be modeled as a minimum energy search problem in a potential landscape. Popular ab initio structure prediction approaches based on this formalization are the Monte Carlo methods represented by the Metropolis method. However, their prediction performance degrades for larger molecules such as proteins since the search space is exponential to the number of atoms. In order to search the exponential space more efficiently, we propose a new method modeling the potential landscape as a factor graph. The key ideas are slicing the factor graph based on the maximum distance of bonded atoms to convert it to a linear structured graph, and the utilization of the max-sum search algorithm combined with samplings. It is referred to as Slice Chain Max-Sum and it has an advantage that the search is efficient because the graph is linear. Experiments are performed using polypeptides having 50 to 300 amino acid residues. It has been shown that the proposed method is computationally more efficient than the Metropolis method for large molecules.","PeriodicalId":38959,"journal":{"name":"IPSJ Transactions on Bioinformatics","volume":"4 1","pages":"34-44"},"PeriodicalIF":0.0,"publicationDate":"2011-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2197/IPSJTBIO.4.34","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68501989","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

Hypothesis Ranking Based on Semantic Event Similarities 基于语义事件相似度的假设排序

IPSJ Transactions on Bioinformatics Pub Date : 2011-01-01 DOI: 10.2197/IPSJTBIO.4.9

Taiki Miyanishi, Kazuhiro Seki, K. Uehara

引用次数: 1

A Web Server for Multi-objective Pairwise RNA Sequence Alignment with an Index for Selecting Accurate Alignments 多目标配对RNA序列比对的Web服务器与选择精确比对的索引

IPSJ Transactions on Bioinformatics Pub Date : 2011-01-01 DOI: 10.2197/IPSJTBIO.4.2

A. Taneda

{"title":"A Web Server for Multi-objective Pairwise RNA Sequence Alignment with an Index for Selecting Accurate Alignments","authors":"A. Taneda","doi":"10.2197/IPSJTBIO.4.2","DOIUrl":"https://doi.org/10.2197/IPSJTBIO.4.2","url":null,"abstract":"The importance of non-coding RNAs and their informatics tools has grown for a decade due to a drastic increase of known non-coding RNAs. RNA sequence alignment is one of the most important technologies in such informatics tools. Recently, we have proposed a multi-objective genetic algorithm, Cofolga2mo, for obtaining an approximate set of weak Pareto optimal solutions for global pairwise RNA sequence alignment, where a sequence similarity and a secondary structure contribution are taken into account as objective functions. In the present study, we have developed a web server for obtaining RNA sequence alignments by Cofolga2mo and for assisting the decision making from the alignments. Furthermore, we introduced an index for reducing the number of alignments output by Cofolga2mo. As a result, we successfully reduced the maximum number of alignments for an input RNA sequence pair from fifty to ten without a significant loss of accurate alignments. By using the BRAliBase 2.1 benchmark dataset, we show that a set of alignments output by Cofolga2mo for an input RNA sequence pair, which has at most ten alignments, includes an accurate alignment compared to those of the previous mono-objective RNA sequence alignment programs.","PeriodicalId":38959,"journal":{"name":"IPSJ Transactions on Bioinformatics","volume":"4 1","pages":"2-8"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2197/IPSJTBIO.4.2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68502345","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

Algebraic Approaches to Underdetermined Experiments in Biology 生物学中欠定实验的代数方法

IPSJ Transactions on Bioinformatics Pub Date : 2010-12-01 DOI: 10.2197/IPSJTBIO.3.62

H. Yoshida, Kinji Kimura, Naoki Yoshida, Junko Tanaka, Y. Miwa

引用次数: 3

Differentially Aberrant Region Detection in Array CGH Data Based on Nearest Neighbor Classification Performance 基于最近邻分类性能的阵列CGH数据差异异常区域检测

IPSJ Transactions on Bioinformatics Pub Date : 2010-10-13 DOI: 10.2197/IPSJTBIO.3.70

Yuta Ishikawa, I. Takeuchi

引用次数: 0

Monte Carlo-based Mouse Nuclear Receptor Superfamily Gene Regulatory Network Prediction: Stochastic Dynamical System on Graph with Zipf Prior 基于蒙特卡罗的小鼠核受体超家族基因调控网络预测:基于Zipf先验图的随机动力系统

IPSJ Transactions on Bioinformatics Pub Date : 2010-03-15 DOI: 10.2197/IPSJTBIO.3.24

Y. Kitamura, Tomomi Kimiwada, J. Maruyama, T. Kaburagi, Takashi Matsumoto, K. Wada

引用次数: 0