International Journal of Computational Biology and Drug Design最新文献_第7页

Plant defence model revisions through iterative minimisation of constraint violations. 植物防御模型修订通过迭代最小化约束违反。

International Journal of Computational Biology and Drug Design Pub Date : 2014-01-01 Epub Date: 2014-01-09 DOI: 10.1504/IJCBDD.2014.058588

Dragana Miljkovic, Matjaž Depolli, Tjaša Stare, Igor Mozetič, Marko Petek, Kristina Gruden, Nada Lavrač

{"title":"Plant defence model revisions through iterative minimisation of constraint violations.","authors":"Dragana Miljkovic, Matjaž Depolli, Tjaša Stare, Igor Mozetič, Marko Petek, Kristina Gruden, Nada Lavrač","doi":"10.1504/IJCBDD.2014.058588","DOIUrl":"https://doi.org/10.1504/IJCBDD.2014.058588","url":null,"abstract":"Biologists have been investigating plant defence response to virus infections; however, a comprehensive mathematical model of this complex process has not been developed. One obstacle in developing a dynamic model, useful for simulation, is the lack of kinetic data from which the model parameters could be determined. We address this problem by proposing a methodology for iterative improvement of the model parameters until the simulation results come close to the expectation of biology experts. These expectations are formalised in the form of constraints to be satisfied by the model simulations. In three iterative steps the model converged to satisfy the biology experts. There are two results of our approach: individual simulations and optimised model parameters, which provide a deeper insight into the biological system. Our constraint-driven optimisation approach allows for an efficient exploration of the dynamic behaviour of biological models and, at the same time, increases their reliability. ","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"7 1","pages":"61-79"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2014.058588","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32033453","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: 2

Adaptive tree-based search for stochastic simulation algorithm. 基于自适应树的随机模拟搜索算法。

International Journal of Computational Biology and Drug Design Pub Date : 2014-01-01 Epub Date: 2014-12-25 DOI: 10.1504/IJCBDD.2014.066542

Vo Hong Thanh, Roberto Zunino

引用次数: 19

A new iterative method to reduce workload in systematic review process. 减少系统审查过程工作量的新迭代法。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-02-21 DOI: 10.1504/IJCBDD.2013.052198

Siddhartha Jonnalagadda, Diana Petitti

引用次数: 0

A contrast enhancement filter for improving stent visibility in interventional X-ray fluoroscopy: an initial study. 用于提高介入x线透视支架可视性的对比增强滤光片:初步研究。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-07-30 DOI: 10.1504/IJCBDD.2013.055458

Yuhao Jiang, Ling-Hsiao Chang

引用次数: 2

Performance of chemical shift-based water-fat separation with self-calibrated fat spectrum is sensitive to echo times. 基于自校准脂肪谱的化学位移水脂肪分离对回波次数敏感。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-07-30 DOI: 10.1504/IJCBDD.2013.055461

Xinwei Shi, Hua Guo

{"title":"Performance of chemical shift-based water-fat separation with self-calibrated fat spectrum is sensitive to echo times.","authors":"Xinwei Shi, Hua Guo","doi":"10.1504/IJCBDD.2013.055461","DOIUrl":"https://doi.org/10.1504/IJCBDD.2013.055461","url":null,"abstract":"Chemical shift-based water-fat separation method utilises water-fat resonance frequency difference to decompose signals into water and fat partitions in magnetic resonance imaging (MRI) on a pixel-wise basis. It provides an effective way to measure fat fraction, or to suppress fat signal which might obscure underlying pathology. IDEAL (Iterative decomposition of water and fat with echo asymmetry and least-squares estimation) algorithm with multi-peak fat spectral modelling has been developed. Recent studies have discussed the performance of this algorithm assuming that the frequencies and relative amplitudes of fat peaks are constant among all subjects. However, the fat spectra vary in different tissues, thus a self-calibration method which estimates the fat spectrum directly from the data provides more accurate results. In this work, we analyse the performance of multi-peak IDEAL algorithm with self-calibrated fat spectrum by theoretical calculation, simulation, and experiments, and find optimal echo time increments which provide reliable water-fat separation. ","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"6 3","pages":"244-54"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2013.055461","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31620029","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

Gene Co-expression analysis predicts genetic aberration loci associated with colon cancer metastasis. 基因共表达分析预测与结肠癌转移相关的基因畸变位点。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-02-21 DOI: 10.1504/IJCBDD.2013.052202

Jie Zhang, Shiwei Ni, Yang Xiang, Jeffrey D Parvin, Yufeng Yang, Yongjian Zhou, Kun Huang

引用次数: 12

Gene interaction networks based on kernel correlation metrics. 基于核相关度量的基因互作网络。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-02-21 DOI: 10.1504/IJCBDD.2013.052203

Lijun Cheng, K Khorasani, Yongsheng Ding, Xihong Guo

引用次数: 1

Multidrug resistance protein P-gp interaction with nanoparticles (fullerenes and carbon nanotube) to assess their drug delivery potential: a theoretical molecular docking study. 多药耐药蛋白P-gp与纳米颗粒(富勒烯和碳纳米管)相互作用以评估其药物传递潜力:理论分子对接研究。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-09-30 DOI: 10.1504/IJCBDD.2013.056801

Sergey Shityakov, Carola Förster

{"title":"Multidrug resistance protein P-gp interaction with nanoparticles (fullerenes and carbon nanotube) to assess their drug delivery potential: a theoretical molecular docking study.","authors":"Sergey Shityakov, Carola Förster","doi":"10.1504/IJCBDD.2013.056801","DOIUrl":"https://doi.org/10.1504/IJCBDD.2013.056801","url":null,"abstract":"P-glycoprotein (P-gp)-mediated efflux system plays an important role to maintain chemical balance in mammalian cells for endogenous and exogenous chemical compounds. However, despite the extensive characterisation of P-gp potential interaction with drug-like molecules, the interaction of carbon nanoparticles with this type of protein molecule is poorly understood. Thus, carbon nanoparticles were analysed, such as buckminsterfullerenes (C20, C60, C70), capped armchair single-walled carbon nanotube (SWCNT or C168), and P-gp interactions using different molecular docking techniques, such as gradient optimisation algorithm (ADVina), Lamarckian genetic algorithm (FastDock), and shape-based approach (PatchDock) to estimate the binding affinities between these structures. The theoretical results represented in this work show that fullerenes might be P-gp binders because of low levels of Gibbs free energy of binding (ΔG) and potential of mean force (PMF) values. Furthermore, the SWCNT binding is energetically unfavourable, leading to a total decrease in binding affinity by elevation of the residual area (Ares), which also affects the π-π stacking mechanisms. Further, the obtained data could potentially call experimental studies using carbon nanostructures, such as SWCNT for development of drug delivery vehicles, to administer and assess drug-like chemical compounds to the target cells since organisms probably did not develop molecular sensing elements to detect these types of carbon molecules. ","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"6 4","pages":"343-57"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2013.056801","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31777250","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: 27

Effects of key parameters of impulse noise on prediction of the auditory hazard using AHAAH model. 脉冲噪声关键参数对AHAAH模型听觉危害预测的影响。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-07-30 DOI: 10.1504/IJCBDD.2013.055457

Qing Wu, Jun Qin

引用次数: 13

Characterisation of the flexibility of substrate binding loop in the binding of direct InhA inhibitors. 直接InhA抑制剂结合的底物结合环的柔韧性表征。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-09-30 DOI: 10.1504/IJCBDD.2013.056795

Vivek Kumar, M Elizabeth Sobhia

{"title":"Characterisation of the flexibility of substrate binding loop in the binding of direct InhA inhibitors.","authors":"Vivek Kumar, M Elizabeth Sobhia","doi":"10.1504/IJCBDD.2013.056795","DOIUrl":"https://doi.org/10.1504/IJCBDD.2013.056795","url":null,"abstract":"The substrate binding loop (SBL) of inhA shows conformational changes on binding of direct inhA inhibitors (DIIs). The knowledge of conformational changes and its importance in binding of DII to inhA has not been explored before. This study initially focused on studying the conformational changes of SBL in selected inhA crystal structures. These conformational changes are measured as angle of rotation for SBL from the static hinge region, Ile194, in the crystal structures. The maximal angle difference of ∼41° was observed between most open and closed conformation of SBL. To gain insights into these conformational changes, comparative molecular dynamics simulations of inhA bound with a direct inhibitor (Genz10850) and apoprotein were performed. A considerable variation in the angle of rotation (∼24° to ∼12°) for the SBL which led to the closed conformation was observed during binding of Genz10850 with a consistent increase in electrostatic energy, whereas no change was observed in apoprotein. Hence, conformational changes in the SBL under the influence of inhibitor can be utilised as a parameter for enhanced binding inhibitor with inhA to screen the potent DIIs. ","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"6 4","pages":"318-42"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2013.056795","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31777249","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: 8