当前位置： SCI文献检索 > Computational and Structural Biotechnology Journal期刊下所有文献 > Current computational methods for predicting protein interactions of natural products.

Current computational methods for predicting protein interactions of natural products.

Abstract：

:Natural products (NPs) are an indispensable source of drugs and they have a better coverage of the pharmacological space than synthetic compounds, owing to their high structural diversity. The prediction of their interaction profiles with druggable protein targets remains a major challenge in modern drug discovery. Experimental (off-)target predictions of NPs are cost- and time-consuming, whereas computational methods, on the other hand, are much faster and cheaper. As a result, computational predictions are preferentially used in the first instance for NP profiling, prior to experimental validations. This review covers recent advances in computational approaches which have been developed to aid the annotation of unknown drug-target interactions (DTIs), by focusing on three broad classes, namely: ligand-based, target-based, and target-ligand-based (hybrid) approaches. Computational DTI prediction methods have the potential to significantly advance the discovery and development of novel selective drugs exhibiting minimal side effects. We highlight some inherent caveats of these methods which must be overcome to enable them to realize their full potential, and a future outlook is given.

journal_name

Comput Struct Biotechnol J

journal_title

Computational and structural biotechnology journal

authors

Moumbock AFA,Li J,Mishra P,Gao M,Günther S

doi

10.1016/j.csbj.2019.08.008

subject

Has Abstract

pub_date

2019-10-28 00:00:00

pages

1367-1376

issn

2001-0370

pii

S2001-0370(19)30105-9

journal_volume

17

pub_type

杂志文章,评审

相关文献

Computational and Structural Biotechnology Journal文献大全
  • Assessment of automated analyses of cell migration on flat and nanostructured surfaces.

    abstract：:Motility studies of cells often rely on computer software that analyzes time-lapse recorded movies and establishes cell trajectories fully automatically. This raises the question of reproducibility of results, since different programs could yield significantly different results of such automated analysis. The fact tha...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.5936/csbj.201207004

    authors： Grădinaru C,Lopacińska JM,Huth J,Kestler HA,Flyvbjerg H,Mølhave K

    更新日期：2012-11-21 00:00:00

  • Nasal microbiome research in ANCA-associated vasculitis: Strengths, limitations, and future directions.

    abstract：:The human nasal microbiome is characterized by biodiversity and undergoes changes during the span of life. In granulomatosis with polyangiitis (GPA), the persistent nasal colonization by Staphylococcus aureus (S. aureus) assessed by culture-based detection methods has been associated with increased relapse frequency. ...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2020.12.031

    authors： Kronbichler A,Harrison EM,Wagner J

    更新日期：2020-12-27 00:00:00

  • Taxonomy and evolution of Aspergillus, Penicillium and Talaromyces in the omics era - Past, present and future.

    abstract：:Aspergillus, Penicillium and Talaromyces are diverse, phenotypically polythetic genera encompassing species important to the environment, economy, biotechnology and medicine, causing significant social impacts. Taxonomic studies on these fungi are essential since they could provide invaluable information on their evol...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2018.05.003

    authors： Tsang CC,Tang JYM,Lau SKP,Woo PCY

    更新日期：2018-05-31 00:00:00

  • Both intra and inter-domain interactions define the intrinsic dynamics and allosteric mechanism in DNMT1s.

    abstract：:DNA methyltransferase 1 (DNMT1), a large multidomain enzyme, is believed to be involved in the passive transmission of genomic methylation patterns via methylation maintenance. Yet, the molecular mechanism of interaction networks underlying DNMT1 structures, dynamics, and its biological significance has yet to be full...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.03.016

    authors： Liang Z,Zhu Y,Long J,Ye F,Hu G

    更新日期：2020-03-23 00:00:00

  • Increasing European Support for Neglected Infectious Disease Research.

    abstract：:Neglected infectious diseases (NIDs) are a persistent cause of death and disability in low-income countries. Currently available drugs and vaccines are often ineffective, costly or associated with severe side-effects. Although the scale of research on NIDs does not reflect their disease burden, there are encouraging s...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2017.01.007

    authors： Olesen OF,Ackermann M

    更新日期：2017-01-19 00:00:00

  • Effect of mutations on the thermostability of Aspergillus aculeatus β-1,4-galactanase.

    abstract：:New variants of β-1,4-galactanase from the mesophilic organism Aspergillus aculeatus were designed using the structure of β-1,4-galactanase from the thermophile organism Myceliophthora thermophila as a template. Some of the variants were generated using PROPKA 3.0, a validated pKa prediction tool, to test its usefulne...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2015.03.010

    authors： Torpenholt S,De Maria L,Olsson MH,Christensen LH,Skjøt M,Westh P,Jensen JH,Lo Leggio L

    更新日期：2015-04-09 00:00:00

  • Assessment of vector-host-pathogen relationships using data mining and machine learning.

    abstract：:Infectious diseases, including vector-borne diseases transmitted by arthropods, are a leading cause of morbidity and mortality worldwide. In the era of big data, addressing broad-scale, fundamental questions regarding the complex dynamics of these diseases will increasingly require the integration of diverse datasets ...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2020.06.031

    authors： Agany DDM,Pietri JE,Gnimpieba EZ

    更新日期：2020-06-25 00:00:00

  • Computational drug repurposing for inflammatory bowel disease using genetic information.

    abstract：:As knowledge of the genetics behind inflammatory bowel disease (IBD) has continually improved, there has been a demand for methods that can use this data in a clinically significant way. Genome-wide association analyses for IBD have identified 232 risk genetic loci for the disorder. While identification of these risk ...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2019.01.001

    authors： Grenier L,Hu P

    更新日期：2019-01-07 00:00:00

  • Constructing knowledge graphs and their biomedical applications.

    abstract：:Knowledge graphs can support many biomedical applications. These graphs represent biomedical concepts and relationships in the form of nodes and edges. In this review, we discuss how these graphs are constructed and applied with a particular focus on how machine learning approaches are changing these processes. Biomed...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2020.05.017

    authors： Nicholson DN,Greene CS

    更新日期：2020-06-02 00:00:00

  • ASJA: A Program for Assembling Splice Junctions Analysis.

    abstract：:RNA splicing may generate different kinds of splice junctions, such as linear, back-splice and fusion junctions. Only a limited number of programs are available for detection and quantification of splice junctions. Here, we present Assembling Splice Junctions Analysis (ASJA), a software package that identifies and cha...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2019.08.001

    authors： Zhao J,Li Q,Li Y,He X,Zheng Q,Huang S

    更新日期：2019-08-07 00:00:00

  • Protein electrostatics: From computational and structural analysis to discovery of functional fingerprints and biotechnological design.

    abstract：:Computationally driven engineering of proteins aims to allow them to withstand an extended range of conditions and to mediate modified or novel functions. Therefore, it is crucial to the biotechnological industry, to biomedicine and to afford new challenges in environmental sciences, such as biocatalysis for green che...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2020.06.029

    authors： Vascon F,Gasparotto M,Giacomello M,Cendron L,Bergantino E,Filippini F,Righetto I

    更新日期：2020-06-30 00:00:00

  • Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity.

    abstract：:SARS-CoV-2 is a novel highly virulent pathogen which gains entry to human cells by binding with the cell surface receptor - angiotensin converting enzyme (ACE2). We computationally contrasted the binding interactions between human ACE2 and coronavirus spike protein receptor binding domain (RBD) of the 2002 epidemic-ca...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.09.019

    authors： Chowdhury R,Boorla VS,Maranas CD

    更新日期：2020-01-01 00:00:00

  • Computational Enzyme Design: Advances, hurdles and possible ways forward.

    abstract：:This mini review addresses recent developments in computational enzyme design. Successful protocols as well as known issues and limitations are discussed from an energetic perspective. It will be argued that improved results can be obtained by including a dynamic treatment in the design protocol. Finally, a molecular ...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.5936/csbj.201209009

    authors： Linder M

    更新日期：2012-10-23 00:00:00

  • The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses.

    abstract：:The viromes of the mammalian lower gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballu...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.10.036

    authors： Babenko VV,Millard A,Kulikov EE,Spasskaya NN,Letarova MA,Konanov DN,Belalov IS,Letarov AV

    更新日期：2020-11-10 00:00:00

  • Treatment According to Molecular Profiling in Relapsed/Refractory Cancer Patients: A Review Focusing on Latest Profiling Studies.

    abstract：:In this review we aim to summarize studies investigating the impact of a molecular profiling (MP)-guided treatment approach in heavily pretreated cancer patients. In summary, many independent single- and multicenter studies showed a significant benefit of MP-guided treatment regarding response rates and survival. Howe...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2019.03.012

    authors： Zimmer K,Kocher F,Spizzo G,Salem M,Gastl G,Seeber A

    更新日期：2019-03-26 00:00:00

  • News in livestock research - use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals.

    abstract：:Technical progress in the field of next-generation sequencing, mass spectrometry and bioinformatics facilitates the study of highly complex biological samples such as taxonomic and functional characterization of microbial communities that virtually colonize all present ecological niches. Compared to the structural inf...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2014.12.005

    authors： Deusch S,Tilocca B,Camarinha-Silva A,Seifert J

    更新日期：2014-12-24 00:00:00

  • Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing.

    abstract：:Alternative splicing contributes to the majority of protein diversity in higher eukaryotes by allowing one gene to generate multiple distinct protein isoforms. It adds another regulation layer of gene expression. Up to 95% of human multi-exon genes undergo alternative splicing to encode proteins with different functio...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2020.12.009

    authors： Jiang W,Chen L

    更新日期：2020-12-24 00:00:00

  • Combining Ramachandran plot and molecular dynamics simulation for structural-based variant classification: Using TP53 variants as model.

    abstract：:The wide application of new DNA sequencing technologies is generating vast quantities of genetic variation data at unprecedented speed. Developing methodologies to decode the pathogenicity of the variants is imperatively demanding. We hypothesized that as deleterious variants may function through disturbing structural...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.11.041

    authors： Tam B,Sinha S,Wang SM

    更新日期：2020-12-02 00:00:00

  • BOG: R-package for Bacterium and virus analysis of Orthologous Groups.

    abstract：:BOG (Bacterium and virus analysis of Orthologous Groups) is a package for identifying groups of differentially regulated genes in the light of gene functions for various virus and bacteria genomes. It is designed to identify Clusters of Orthologous Groups (COGs) that are enriched among genes that have gone through sig...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2015.05.002

    authors： Park J,Taslim C,Lin S

    更新日期：2015-05-21 00:00:00

  • Structure-based discovery of neoandrographolide as a novel inhibitor of Rab5 to suppress cancer growth.

    abstract：:Rab5 is a small GTPase that plays a crucial role in oncogenic signal transduction, which was considered as an attractive target for cancer therapy. Rapid GDP/GTP exchange in the packet of Rab5 sustains its high activity for promoting cancer progression. However, Rab5 currently remains undruggable due to the lack of sp...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.11.033

    authors： Zhang J,Sun Y,Zhong LY,Yu NN,Ouyang L,Fang RD,Wang Y,He QY

    更新日期：2020-11-30 00:00:00

  • Network analysis of human post-mortem microarrays reveals novel genes, microRNAs, and mechanistic scenarios of potential importance in fighting huntington's disease.

    abstract：:Huntington's disease is a progressive neurodegenerative disorder characterized by motor disturbances, cognitive decline, and neuropsychiatric symptoms. In this study, we utilized network-based analysis in an attempt to explore and understand the underlying molecular mechanism and to identify critical molecular players...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2016.02.001

    authors： Chandrasekaran S,Bonchev D

    更新日期：2016-02-10 00:00:00

  • Identification and characterisation of putative drug binding sites in human ATP-binding cassette B5 (ABCB5) transporter.

    abstract：:The human ATP-binding cassette B5 (ABCB5) transporter, a member of the ABC transporter superfamily, is linked to chemoresistance in tumour cells by drug effluxion. However, little is known about its structure and drug-binding sites. In this study, we generated an atomistic model of the full-length human ABCB5 transpor...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.12.042

    authors： Tangella LP,Arooj M,Deplazes E,Gray ES,Mancera RL

    更新日期：2020-12-30 00:00:00

  • A bird's-eye view of deep learning in bioimage analysis.

    abstract：:Deep learning of artificial neural networks has become the de facto standard approach to solving data analysis problems in virtually all fields of science and engineering. Also in biology and medicine, deep learning technologies are fundamentally transforming how we acquire, process, analyze, and interpret data, with ...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2020.08.003

    authors： Meijering E

    更新日期：2020-08-07 00:00:00

  • Multivariate linear QSPR/QSAR models: Rigorous evaluation of variable selection for PLS.

    abstract：:Basic chemometric methods for making empirical regression models for QSPR/QSAR are briefly described from a user's point of view. Emphasis is given to PLS regression, simple variable selection and a careful and cautious evaluation of the performance of PLS models by repeated double cross validation (rdCV). A demonstra...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.5936/csbj.201302007

    authors： Varmuza K,Filzmoser P,Dehmer M

    更新日期：2013-03-02 00:00:00

  • Statistical methods for the analysis of high-throughput metabolomics data.

    abstract：:Metabolomics is a relatively new high-throughput technology that aims at measuring all endogenous metabolites within a biological sample in an unbiased fashion. The resulting metabolic profiles may be regarded as functional signatures of the physiological state, and have been shown to comprise effects of genetic regul...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.5936/csbj.201301009

    authors： Bartel J,Krumsiek J,Theis FJ

    更新日期：2013-03-22 00:00:00

  • Deep learning predicts microbial interactions from self-organized spatiotemporal patterns.

    abstract：:Microbial communities organize into spatial patterns that are largely governed by interspecies interactions. This phenomenon is an important metric for understanding community functional dynamics, yet the use of spatial patterns for predicting microbial interactions is currently lacking. Here we propose supervised dee...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.05.023

    authors： Lee JY,Sadler NC,Egbert RG,Anderton CR,Hofmockel KS,Jansson JK,Song HS

    更新日期：2020-05-29 00:00:00

  • Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass.

    abstract：:Understanding the pathogenesis of disease is instrumental in delineating its progression mechanisms and for envisioning ways to counteract it. In the process, animal models represent invaluable tools for identifying disease-related loci and their genetic components. Amongst them, the laboratory rat is used extensively...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2015.11.006

    authors： Petri V,Hayman GT,Tutaj M,Smith JR,Laulederkind S,Wang SJ,Nigam R,De Pons J,Shimoyama M,Dwinell MR

    更新日期：2015-11-26 00:00:00

  • Transcriptome and proteome analyses reveal the regulatory networks and metabolite biosynthesis pathways during the development of Tolypocladium guangdongense.

    abstract：:Tolypocladium guangdongense has a similar metabolite profile to Ophiocordyceps sinensis, a highly regarded fungus used for traditional Chinese medicine with high nutritional and medicinal value. Although the genome sequence of T. guangdongense has been reported, relatively little is known about the regulatory networks...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.07.014

    authors： Wang G,Li M,Zhang C,Cheng H,Gao Y,Deng W,Li T

    更新日期：2020-07-25 00:00:00

  • Identity, Structure and Compositional Analysis of Aluminum Phosphate Adsorbed Pediatric Quadrivalent and Pentavalent Vaccines.

    abstract：Purpose:The goal of this study is to set an empirical baseline to map the structure-function relation of the antigens from the commercialized vaccine products. Methods:To study the structural changes of protein antigens after adsorption several analytical tools including DLS, FTIR, Fluorescence, LD, and SEM have been ...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2018.11.006

    authors： Kalbfleisch K,Deshmukh S,Mei C,Ore M,Williams W,Durowoju I,Duprez J,Morin S,Carpick B,Kirkitadze M

    更新日期：2018-11-29 00:00:00

  • On fusion methods for knowledge discovery from multi-omics datasets.

    abstract：:Recent years have witnessed the tendency of measuring a biological sample on multiple omics scales for a comprehensive understanding of how biological activities on varying levels are perturbed by genetic variants, environments, and their interactions. This new trend raises substantial challenges to data integration a...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2020.02.011

    authors： Baldwin E,Han J,Luo W,Zhou J,An L,Liu J,Zhang HH,Li H

    更新日期：2020-03-05 00:00:00