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

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

authors： Bartel J,Krumsiek J,Theis FJ

更新日期：2013-03-22 00:00:00

abstract：:The emergence of recent SARS-CoV-2 has become a global health issue. This single-stranded positive-sense RNA virus is continuously spreading with increasing morbidities and mortalities. The proteome of this virus contains four structural and sixteen nonstructural proteins that ensure the replication of the virus in th...

journal_title：Computational and structural biotechnology journal

authors： Khan A,Tahir Khan M,Saleem S,Junaid M,Ali A,Shujait Ali S,Khan M,Wei DQ

更新日期：2020-01-01 00:00:00

abstract：:Across the eubacteria, antigenic variation has emerged as a strategy to evade host immunity. However, phenotypic variation in some of these antigens also allows the bacteria to exploit variable host niches as well. The specific mechanisms are not shared-derived characters although there is considerable convergent evol...

journal_title：Computational and structural biotechnology journal

authors： Foley J

更新日期：2015-07-26 00:00:00

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

authors： Kronbichler A,Harrison EM,Wagner J

更新日期：2020-12-27 00:00:00

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

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

abstract：:The challenging task of studying and modeling complex dynamics of biological systems in order to describe various human diseases has gathered great interest in recent years. Major biological processes are mediated through protein interactions, hence there is a need to understand the chaotic network that forms these pr...

journal_title：Computational and structural biotechnology journal

authors： Sevimoglu T,Arga KY

更新日期：2014-09-03 00:00:00

abstract：:Allosteric modulation provides an effective avenue for selective and potent enzyme inhibition. Here, we summarize and critically discuss recent advances on the mechanisms of allosteric partial agonists for three representative signalling enzymes activated by cyclic nucleotides: the cAMP-dependent protein kinase (PKA),...

journal_title：Computational and structural biotechnology journal

authors： Byun JA,VanSchouwen B,Akimoto M,Melacini G

更新日期：2020-11-11 00:00:00

abstract：:Interactions between their transmembrane domains (TMDs) frequently support the assembly of single-pass membrane proteins to non-covalent complexes. Yet, the TMD-TMD interactome remains largely uncharted. With a view to predicting homotypic TMD-TMD interfaces from primary structure, we performed a systematic analysis o...

journal_title：Computational and structural biotechnology journal

authors： Xiao Y,Zeng B,Berner N,Frishman D,Langosch D,George Teese M

更新日期：2020-10-07 00:00:00

abstract：:Appropriate development of the intestinal microbiota during infancy is known to be important for human health. In fact, aberrant alterations of the microbial composition during childhood may cause short- and/or long-term negative health effects. Many factors influence the initial assembly and subsequent progression of...

journal_title：Computational and structural biotechnology journal

authors： Mancabelli L,Tarracchini C,Milani C,Lugli GA,Fontana F,Turroni F,van Sinderen D,Ventura M

更新日期：2020-09-15 00:00:00

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

authors： Agany DDM,Pietri JE,Gnimpieba EZ

更新日期：2020-06-25 00:00:00

abstract：:Biased agonism, the ability of agonists to differentially activate downstream signaling pathways by stabilizing specific receptor conformations, is a key issue for G protein-coupled receptor (GPCR) signaling. The C-terminal domain might influence this functional selectivity of GPCRs as it engages G proteins, GPCR kina...

journal_title：Computational and structural biotechnology journal

authors： Navarro G,Gonzalez A,Campanacci S,Rivas-Santisteban R,Reyes-Resina I,Casajuana-Martin N,Cordomí A,Pardo L,Franco R

更新日期：2020-09-24 00:00:00

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

authors： Tam B,Sinha S,Wang SM

更新日期：2020-12-02 00:00:00

abstract：:Runs of Homozygosity (RoHs) are popular among geneticists as the footprint of demographic processes, evolutionary forces and inbreeding in shaping our genome, and are known to confer risk of Mendelian and complex diseases. Notwithstanding growing interest in their study, there is unmet need for reliable and rapid meth...

journal_title：Computational and structural biotechnology journal

authors： Magi A,Giangregorio T,Semeraro R,Carangelo G,Palombo F,Romeo G,Seri M,Pippucci T

更新日期：2020-07-14 00:00:00

abstract：:MicroRNAs (miRNAs) are well-studied small noncoding RNAs involved in post-transcriptional gene regulation in a wide range of organisms, including mammals. Their function is mediated by base pairing with their target RNAs. Although many features required for miRNA-mediated repression have been described, the identifica...

journal_title：Computational and structural biotechnology journal

authors： Schäfer M,Ciaudo C

更新日期：2020-03-05 00:00:00

abstract：:The use of herbs to treat various human diseases has been recorded for thousands of years. In Asia's current medical system, numerous herbal formulas have been repeatedly verified to confirm their effectiveness in different periods, which is a great resource for drug innovation and discovery. Through the mining of the...

journal_title：Computational and structural biotechnology journal

authors： Bu D,Xia Y,Zhang J,Cao W,Huo P,Wang Z,He Z,Ding L,Wu Y,Zhang S,Gao K,Yu H,Liu T,Ding X,Gu X,Zhao Y

更新日期：2020-12-04 00:00:00

abstract：:The COVID-19 pandemic has substantially stressed health care systems globally, subsequently reducing cancer care services and delaying treatments. Pediatric populations infected by COVID-19 have shown mild clinical symptoms compared to adults, perhaps due to decreased susceptibility. Several scientific societies and g...

journal_title：Computational and structural biotechnology journal

authors： Capozza MA,Triarico S,Attinà G,Romano A,Mastrangelo S,Maurizi P,Frassanito P,Bianchi F,Verdolotti T,Gessi M,Balducci M,Massimi L,Tamburrini G,Ruggiero A,Gemelli Pediatric Neuro-Oncology Tumor Board.

更新日期：2021-01-12 00:00:00

abstract：:One of the long-standing challenges in biology is to understand how non-synonymous single nucleotide polymorphisms (nsSNPs) change protein structure and further affect their function. While it is impractical to solve all the mutated protein structures experimentally, it is quite feasible to model the mutated structure...

journal_title：Computational and structural biotechnology journal

authors： Wang D,Song L,Singh V,Rao S,An L,Madhavan S

更新日期：2015-09-30 00:00:00

abstract：:Although the potential advantages of clinical germline genome editing (GGE) over currently available methods are limited, the implementation of GGE in the clinic has been proposed and discussed. Ethical issues related to such an application have been extensively debated, meanwhile, seemingly less attention has been pa...

journal_title：Computational and structural biotechnology journal

authors： Niemiec E,Howard HC

更新日期：2020-03-21 00:00:00

abstract：:Traditional Chinese Medicine (TCM) has a long history of widespread clinical applications, especially in East Asia, and is becoming frequently used in Western countries. However, owing to extreme complicacy in both chemical ingredients and mechanism of action, a deep understanding of TCM is still difficult. To acceler...

journal_title：Computational and structural biotechnology journal

authors： Li B,Ma C,Zhao X,Hu Z,Du T,Xu X,Wang Z,Lin J

更新日期：2018-11-23 00:00:00

abstract：:With omics data being generated at an unprecedented rate, genome-scale modelling has become pivotal in its organisation and analysis. However, machine learning methods have been gaining ground in cases where knowledge is insufficient to represent the mechanisms underlying such data or as a means for data curation prio...

journal_title：Computational and structural biotechnology journal

authors： Antonakoudis A,Barbosa R,Kotidis P,Kontoravdi C

更新日期：2020-10-16 00:00:00

abstract：:Compounds that inhibit the catalytic function of lysine-specific demethylase 1 (LSD1) are interesting as therapeutic agents. Recently, we identified three lysine-phenylcyclopropylamine conjugates, NCD18, NCD25, and NCD41, which are potent LSD1 inactivators. However, in our previous study, because we tested those compo...

journal_title：Computational and structural biotechnology journal

authors： Itoh Y,Ogasawara D,Ota Y,Mizukami T,Suzuki T

更新日期：2014-02-15 00:00:00

abstract：:Numerous bioactive natural products are synthesised by modular polyketide synthases. These compounds can be made in high yield by native multienzyme assembly lines. However, formation of analogues by genetically engineered systems is often considerably less efficient. Biochemical studies on intact polyketide synthase ...

journal_title：Computational and structural biotechnology journal

authors： Caffrey P

更新日期：2012-11-17 00:00:00

abstract：:Recent years have witnessed a spurt of activities in the elucidation of the molecular function of a class of proteins with great potential in biomass degradation. GH61 proteins are of fungal origin and were originally classified in family 61 of the glycoside hydrolases. From the beginning they were strongly suspected ...

journal_title：Computational and structural biotechnology journal

authors： Lo Leggio L,Welner D,De Maria L

更新日期：2012-11-30 00:00:00

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

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

更新日期：2019-03-26 00:00:00

abstract：:Coronaviruses are a group of enveloped RNA viruses that are diversely found in humans and now declared a global pandemic by the World Health Organization in March 2020. The population's susceptibility to these highly pathogenic coronaviruses has contributed to large outbreaks, evolved into public health events, and ra...

journal_title：Computational and structural biotechnology journal

authors： Singh DD,Han I,Choi EH,Yadav DK

更新日期：2020-01-01 00:00:00

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

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

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

authors： Varmuza K,Filzmoser P,Dehmer M

更新日期：2013-03-02 00:00:00

abstract：:Lung cancer is the leading worldwide cause of cancer mortality, however, neither curative treatments nor substantial prolonged survival has been achieved, highlighting the need for investigating new proteins responsible for its development and progression. IKKα is an essential protein for cell survival and differentia...

journal_title：Computational and structural biotechnology journal

authors： Page A,Ortega A,Alameda JP,Navarro M,Paramio JM,Saiz-Pardo M,Almeida EI,Hernández P,Fernández-Aceñero MJ,García-Fernández RA,Casanova ML

更新日期：2019-02-07 00:00:00

abstract：:As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molec...

journal_title：Computational and structural biotechnology journal

authors： Zhang X,Zhang Q,Liu Y,Wang B,Zhou S

更新日期：2020-08-06 00:00:00

abstract：:Recent high-throughput structure-sensitive genome-wide sequencing-based assays have enabled large-scale studies of RNA structure, and robust transcriptome-wide computational prediction of individual RNA structures across RNA classes from these assays has potential to further improve the prediction accuracy. Here, we d...

journal_title：Computational and structural biotechnology journal

authors： Kuksa PP,Li F,Kannan S,Gregory BD,Leung YY,Wang LS

更新日期：2020-06-08 00:00:00