Chem-Bio Informatics Journal最新文献_第5页

An Interaction-based Approach for Affinity Prediction between Antigen Peptide and Human Leukocyte Antigen Using COMBINE Analysis 结合分析抗原肽与人白细胞抗原亲和预测的相互作用方法

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Chem-Bio Informatics Journal Pub Date : 2017-09-06 DOI: 10.1273/CBIJ.17.93

Shinya Nakamura, Rie Ohmura, I. Nakanishi

引用次数: 2

Myths in Modern Science: The Hydrogen Bond and its Surroundings. Part 1. The Hydrogen-Bond-Myth 现代科学中的神话:氢键及其周围环境。第1部分。的Hydrogen-Bond-Myth

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Chem-Bio Informatics Journal Pub Date : 2017-08-24 DOI: 10.1273/CBIJ.17.85

M. Nishio

引用次数: 0

Explicit solvation of a single-stranded DNA, a binding protein, and their complex: a suitable protocol for fragment molecular orbital calculation 单链DNA，结合蛋白及其复合物的显式溶剂化:片段分子轨道计算的合适方案

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Chem-Bio Informatics Journal Pub Date : 2017-07-30 DOI: 10.1273/CBIJ.17.72

Yuto Komeij, Yoshio Okiyama, Y. Mochizuki, Kaori Fukuzawa

引用次数: 6

Using A Priori Knowledge after Genetic Network Inference: Integrating Multiple Kinds of Knowledge 遗传网络推理后的先验知识利用:多知识集成

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Chem-Bio Informatics Journal Pub Date : 2017-06-17 DOI: 10.1273/CBIJ.17.53

Shuhei Kimura, Koji Kitazawa, M. Tokuhisa, M. Okada‐Hatakeyama

{"title":"Using A Priori Knowledge after Genetic Network Inference: Integrating Multiple Kinds of Knowledge","authors":"Shuhei Kimura, Koji Kitazawa, M. Tokuhisa, M. Okada‐Hatakeyama","doi":"10.1273/CBIJ.17.53","DOIUrl":"https://doi.org/10.1273/CBIJ.17.53","url":null,"abstract":"Several researchers have focused on the inference of genetic networks as a process for extracting useful information from gene expression data. Their work has led to the proposal of a number of methods for genetic network inference. Yet the genetic networks inferred by these methods often contain large numbers of false-positive regulations along with the true-positives. One effective way to reduce the number of erroneous regulations is to apply inference methods that use a priori knowledge on the properties of the genetic networks. The existing inference methods adopting this approach generally use a priori knowledge and the observed gene expression data simultaneously to determine whether or not the target genetic network actually contains each of the candidate regulations. In this study, we establish a new framework for “using a priori knowledge after genetic network inference.” The framework uses a priori knowledge only to modify the genetic network that has already been inferred by the other inference method. Based on this framework, we propose a new inference method that uses multiple kinds of a priori knowledge about genetic networks. The proposed method effectively combines multiple kinds of knowledge and computes the confidence values of regulations. Here, we confirm the effectiveness of the proposed method by applying it to artificial and actual genetic network inference problems. While only a small improvement is gained from the use of multiple kinds of a priori knowledge, we can improve the performance of many other existing inference methods by combining them with the method we propose here.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"113 1","pages":"53-71"},"PeriodicalIF":0.3,"publicationDate":"2017-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85374991","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

Prediction of the site of CYP3A4 metabolism of tolterodine by molecular dynamics simulation from multiple initial structures of the CYP3A4-tolterodine complex 基于CYP3A4-托特罗定复合物多个初始结构的分子动力学模拟预测CYP3A4对托特罗定的代谢位点

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Chem-Bio Informatics Journal Pub Date : 2017-05-31 DOI: 10.1273/CBIJ.17.38

A. Sato, Hitomi Yuki, C. Watanabe, J. Saito, A. Konagaya, T. Honma

引用次数: 2

Competitive fragment assay for the selective inhibitor of WNKs kinase WNKs激酶选择性抑制剂的竞争性片段分析

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Chem-Bio Informatics Journal Pub Date : 2017-04-08 DOI: 10.1273/CBIJ.17.34

Nae Saito, Y. Tada, T. Okabe, T. Nagano

引用次数: 0

Docking simulation of fragment library compounds to find new leads for specific WNK kinase inhibitors 对接模拟片段文库化合物，寻找特异性WNK激酶抑制剂的新线索

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Chem-Bio Informatics Journal Pub Date : 2017-03-30 DOI: 10.1273/CBIJ.17.30

Nae Saito, Y. Tada, T. Okabe, T. Nagano

引用次数: 1

SBDDとclassical QSAR 解析によるチミジンホスホリラーゼ阻害薬の分子設計 SBDD和classical QSAR分析的噻嗪磷酸化酶抑制剂的分子设计

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Chem-Bio Informatics Journal Pub Date : 2017-03-24 DOI: 10.1273/CBIJ.17.19

Y. Tada, H. Kazuno, Tsutomu Sato, N. Suzuki, Tomohiro Emura, S. Yano

引用次数: 0

A Novel Fragment Recommendation Workflow using Direct and Indirect Transfer of SAR According to Integrated Similarities of Scaffold Motifs and SAR Trends: Application to Identifying Factor Xa Inhibitors 基于支架基序和SAR趋势的直接和间接SAR转移的新片段推荐工作流:在识别因子Xa抑制剂中的应用

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Chem-Bio Informatics Journal Pub Date : 2017-03-04 DOI: 10.1273/CBIJ.17.1

T. Ishihara, K. Mori, R. Munakata, Ayako Moritomo

{"title":"A Novel Fragment Recommendation Workflow using Direct and Indirect Transfer of SAR According to Integrated Similarities of Scaffold Motifs and SAR Trends: Application to Identifying Factor Xa Inhibitors","authors":"T. Ishihara, K. Mori, R. Munakata, Ayako Moritomo","doi":"10.1273/CBIJ.17.1","DOIUrl":"https://doi.org/10.1273/CBIJ.17.1","url":null,"abstract":"Here we report a new drug design workflow that facilitates the transfer of structure-activity relationships (SARs) and recommends alternative fragments from SAR databases. We first prepare two collections of matched molecular series (MMS) comprising a query set of compounds with their SARs and a set derived from reference SAR databases. The second step detects MMS from the reference SAR sources, which identifies profiles similar to a query MMS according to integrated similarities of scaffold shapes and SAR trends. The third step enumerates new compounds with improved activity profiles compared with a query compound computed using a collaborative filtering algorithm. Our workflow detected direct and latent relationships between a query MMS and those derived from the reference SAR sources. Retrospective application of this workflow to the identification of factor Xa inhibitors yielded recommendations with higher predictive accuracy than a conventional quantitative SAR technique. Moreover, potent S1 binding elements were identified using SAR knowledge independent of information about ligand-protein complexes.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":"28 3 1","pages":"1-18"},"PeriodicalIF":0.3,"publicationDate":"2017-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91337036","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

Population Pharmacokinetic Parameter Estimates using a Limited Sampling Design: Analysis of Blood Alcohol Levels 使用有限抽样设计的人群药代动力学参数估计:血液酒精水平分析

IF 0.3

Chem-Bio Informatics Journal Pub Date : 2016-12-10 DOI: 10.1273/CBIJ.16.25

Asuka Nemoto, Masaaki Matsuura, K. Yamaoka

引用次数: 0