Abstract:
:In drug development, preclinical safety and pharmacokinetics assessments of candidate drugs to ensure the safety profile are a must. While in vivo and in vitro tests are traditionally used, experimental determinations have disadvantages, as they are usually time-consuming and costly. In silico predictions of these preclinical endpoints have each been developed in the past decades. However, only a few web-based tools have integrated different models to provide a simple one-step platform to help researchers thoroughly evaluate potential drug candidates. To efficiently achieve this approach, a platform for preclinical evaluation must not only predict key ADMET (absorption, distribution, metabolism, excretion and toxicity) properties but also provide some guidance on structural modifications to improve the undesired properties. In this review, we organized and compared several existing integrated web servers that can be adopted in preclinical drug development projects to evaluate the subject of interest. We also introduced our new web server, Virtual Rat, as an alternative choice to profile the properties of drug candidates. In Virtual Rat, we provide not only predictions of important ADMET properties but also possible reasons as to why the model made those structural predictions. Multiple models were implemented into Virtual Rat, including models for predicting human ether-a-go-go-related gene (hERG) inhibition, cytochrome P450 (CYP) inhibition, mutagenicity (Ames test), blood-brain barrier penetration, cytotoxicity and Caco-2 permeability. Virtual Rat is free and has been made publicly available at https://virtualrat.cmdm.tw/.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Hsiao Y,Su BH,Tseng YJdoi
10.1093/bib/bbaa160subject
Has Abstractpub_date
2020-08-07 00:00:00eissn
1467-5463issn
1477-4054pii
5881374pub_type
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journal_title:Briefings in bioinformatics
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doi:10.1093/bib/bbz037
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journal_title:Briefings in bioinformatics
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abstract::Data from the SEER reports reveal that the occurrence rate of a cancer type generally follows a unimodal distribution over age, peaking at an age that is cancer-type specific and ranges from 30+ through 70+. Previous studies attribute such bell-shaped distributions to the reduced proliferative potential in senior year...
journal_title:Briefings in bioinformatics
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更新日期:2020-12-30 00:00:00
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pub_type: 杂志文章,评审
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更新日期:2017-05-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2016-09-01 00:00:00
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pub_type: 杂志文章,评审
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
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更新日期:2018-09-28 00:00:00
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pub_type: 杂志文章
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更新日期:2019-07-19 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
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更新日期:2013-01-01 00:00:00
abstract::Rapidly evolving sequencing technologies produce data on an unparalleled scale. A central challenge to the analysis of this data is sequence alignment, whereby sequence reads must be compared to a reference. A wide variety of alignment algorithms and software have been subsequently developed over the past two years. I...
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pub_type: 杂志文章,评审
doi:10.1093/bib/bbq015
更新日期:2010-09-01 00:00:00
abstract::Mediation analysis has been a useful tool for investigating the effect of mediators that lie in the path from the independent variable to the outcome. With the increasing dimensionality of mediators such as in (epi)genomics studies, high-dimensional mediation model is needed. In this work, we focus on epigenetic studi...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa113
更新日期:2020-07-01 00:00:00
abstract::CyanoPATH is a database that curates and analyzes the common genomic functional repertoire for cyanobacteria harmful algal blooms (CyanoHABs) in eutrophic waters. Based on the literature of empirical studies and genome/protein databases, it summarizes four types of information: common biological functions (pathways) d...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa375
更新日期:2020-12-16 00:00:00
abstract::In view of great difficulties in the pathogenesis analysis of Alzheimer's disease (AD) presently, profiling the modifiable risk factors is crucial for early detection and intervention of AD. However, the causal associations among them have yet to be identified, and the effective integration and application of these da...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa213
更新日期:2020-09-21 00:00:00
abstract::Synonymous mutations do not change the encoded amino acids but may alter the structure or function of an mRNA in ways that impact gene function. Advances in next generation sequencing technologies have detected numerous synonymous mutations in the human genome. Several computational models have been proposed to predic...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz047
更新日期:2020-05-21 00:00:00
abstract::Systems pharmacology is an emerging field that integrates systems biology and pharmacology to advance the process of drug discovery, development and the understanding of therapeutic mechanisms. The aim of the present work is to highlight the role that the systems pharmacology plays across the traditional herbal medici...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbt035
更新日期:2014-09-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa183
更新日期:2020-08-25 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bby028
更新日期:2019-03-25 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbs049
更新日期:2014-01-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa109
更新日期:2020-06-10 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbv116
更新日期:2017-01-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbs053
更新日期:2013-11-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2020-07-15 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2020-12-15 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
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更新日期:2015-03-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2020-05-21 00:00:00
abstract:MOTIVATION:Long noncoding RNAs (lncRNAs) correspond to a eukaryotic noncoding RNA class that gained great attention in the past years as a higher layer of regulation for gene expression in cells. There is, however, a lack of specific computational approaches to reliably predict lncRNA in plants, which contrast the vari...
journal_title:Briefings in bioinformatics
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更新日期:2019-03-25 00:00:00
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更新日期:2019-11-27 00:00:00
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