From plant genomes to protein families: computational tools.

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

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

abstract：:We report a study of the interaction between internalin A (inlA) and human or murine E-cadherin (Ecad). inlA is used by Listeria monocytogenes to internalize itself into host cell, but the bacterium is unable to invade murine cells, which has been attributed to the difference in sequence between hEcad and mEcad. Using...

journal_title：Computational and structural biotechnology journal

authors： Genheden S,Eriksson LA

更新日期：2013-12-15 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：: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：: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

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

更新日期：2018-05-31 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：: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：: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：:Functional annotation transfer across multi-gene family orthologs can lead to functional misannotations. We hypothesised that co-expression network will help predict functional orthologs amongst complex homologous gene families. To explore the use of transcriptomic data available in public domain to identify functiona...

journal_title：Computational and structural biotechnology journal

authors： Reyes PFL,Michoel T,Joshi A,Devailly G

更新日期：2017-08-26 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：: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 field of dentistry lacks satisfactory tools to help visualize planned procedures and their potential results to patients. Dentists struggle to provide an effective image in their patient's mind of the end results of the planned treatment only through verbal explanations. Thus, verbal explanations alone often canno...

journal_title：Computational and structural biotechnology journal

authors： Canbazoglu E,Salman YB,Yildirim ME,Merdenyan B,Ince IF

更新日期：2016-06-29 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：: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：:RNA-Seq was used to examine the microbial, eukaryotic, and viral communities in water catchments ('tanks') formed by tropical bromeliads from Costa Rica. In total, transcripts with taxonomic affiliation to a wide array of bacteria, archaea, and eukaryotes, were observed, as well as RNA-viruses that appeared related to...

journal_title：Computational and structural biotechnology journal

authors： Goffredi SK,Jang GE,Haroon MF

更新日期：2014-12-13 00:00:00

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

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

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：: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

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

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. Ex...

journal_title：Computational and structural biotechnology journal

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

更新日期：2019-10-28 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：:Vascular calcification (VC), an unpredictable pathophysiological process and critical event in patients with cardiovascular diseases (CVDs), is the leading cause of morbi-mortality and disability in chronic kidney disease (CKD) patients worldwide. Currently, no diagnostic method is available for identifying patients a...

journal_title：Computational and structural biotechnology journal

authors： Alique M,Bodega G,Corchete E,García-Menéndez E,de Sequera P,Luque R,Rodríguez-Padrón D,Marqués M,Portolés J,Carracedo J,Ramírez R

更新日期：2020-04-09 00:00:00

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

authors： Olesen OF,Ackermann M

更新日期：2017-01-19 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：: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：:Buried active sites of enzymes are connected to the bulk solvent through a network of hydrophobic channels. We developed a discretized model that can accurately predict ligand transport along hydrophobic channels up to six orders of magnitude faster than any other existing method. The non-dimensional nature of the mod...

journal_title：Computational and structural biotechnology journal

authors： Escalante DE,Aksan A

更新日期：2019-06-11 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 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：:Bacteria can migrate towards more suitable environments by rotating flagella that are under the control of sensory signal transduction networks. The bacterial flagellum is composed of the long helical filament functioning as a propeller, the flexible hook as a universal joint and the basal body as a rotary motor power...

journal_title：Computational and structural biotechnology journal

authors： Terahara N,Namba K,Minamino T

更新日期：2020-10-15 00:00:00

abstract：:Target based chemical screens are a mainstay of modern drug discovery, but the effectiveness of this reductionist approach is being questioned in light of declines in pharmaceutical R & D efficiency. In recent years, phenotypic screens have gained increasing acceptance as a complementary/alternative approach to early ...

journal_title：Computational and structural biotechnology journal

authors： Williams CH,Hong CC

更新日期：2016-09-18 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