Abstract:
:We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the molecular electrostatic potential, whose three-dimensional coordinates have been either experimentally or theoretically determined. Thus we achieve a reduction of the initial three-dimensional information on the molecular surface to the one-dimensional information on pairs of points at a fixed scale apart. Consequently, the similarity search in our method is computationally less demanding and significantly faster than shape comparison methods. As proof of principle, we applied our method to a training set of viral proteins that are involved in major diseases such as Hepatitis C, Dengue fever, Yellow fever, Bovine viral diarrhea and West Nile fever. The training set contains proteins of four different protein families, as well as a mammalian representative enzyme. We found that the power spectrum successfully assigns a unique signature to each protein included in our training set, thus providing a direct probe of functional similarity among proteins. The results agree with established biological data from conventional structural biochemistry analyses.
journal_name
PeerJjournal_title
PeerJauthors
Carvalho CS,Vlachakis D,Tsiliki G,Megalooikonomou V,Kossida Sdoi
10.7717/peerj.185subject
Has Abstractpub_date
2013-10-22 00:00:00pages
e185issn
2167-8359pii
185journal_volume
1pub_type
杂志文章相关文献
PeerJ文献大全abstract:BACKGROUND:The purpose of this study is to provide a report on scientific production during the period 2010-2014 in order to identify the major topics as well as the predominant actors (journals, countries, continents) involved in the field of eye disease. METHODS:A PubMed search was carried out to extract articles re...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.1557
更新日期:2016-01-07 00:00:00
abstract::Climatic variables have been the main predictors employed in ecological niche modeling and species distribution modeling, although biotic interactions are known to affect species' spatial distributions via mechanisms such as predation, competition, and mutualism. Biotic interactions can affect species' responses to ab...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6052
更新日期:2018-12-05 00:00:00
abstract:Background:Overweight (OW) is considered a risk for various metabolic diseases. However, its effects as a mechanism that alters the metabolite profiles remain unclear. The purpose of this study is to investigate the effects that OW has on the lipid and metabolite profiles in young adults. Methods:The serum metabolite ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.7137
更新日期:2019-06-20 00:00:00
abstract::Small interference RNA has been widely used to suppress gene expression. Three different short hairpin RNAs (shRNAs) against dopamine D1 receptor (Drd1), driven by mouse U6 promoter in self-complementary AAV8 vector (scAAV8), were used to silence mouse striatal Drd1 expression. Transduction of mouse striatum with all ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.3905
更新日期:2017-10-31 00:00:00
abstract::Eggplant (Solanum melongena L.) is an important vegetable cultivated in Asia, Africa and southern Europe and, following tomato and pepper, ranks as the third most important solanaceous vegetable crop. The Dof (DNA-binding with one finger) family is a group of plant-specific transcription factors that play important ro...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.4481
更新日期:2018-03-06 00:00:00
abstract::Synaptic exocytosis requires the assembly of syntaxin 1A and SNAP-25 on the plasma membrane and synaptobrevin 2 (VAMP2) on the vesicular membrane to bridge the two opposite membranes. It is believed that the three SNARE proteins assemble in steps along the dynamic assembly pathway. The C-terminus of SNAP-25 is known t...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.1065
更新日期:2015-06-30 00:00:00
abstract::The most intense commercial harvest of marine aquarium species in North America occurs in the coastal waters surrounding Florida, yet very often little information exists on the life histories, population dynamics, or reproductive characteristics of these organisms. The peppermint shrimp Lysmata boggessi is one such s...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.8231
更新日期:2020-01-23 00:00:00
abstract:Background and Purpose:Several studies have proposed that the advanced lung cancer inflammation index (ALI), a new inflammation-related index, can be used for the prognosis assessment of various malignancies. However, few studies have reported its prognostic value in colorectal cancer (CRC). Therefore, this study explo...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.10100
更新日期:2020-10-08 00:00:00
abstract::Rhynchosauria is a group of archosauromorph reptiles abundant in terrestrial ecosystems of the Middle Triassic. Mesosuchus is one of the earliest and basalmost rhynchosaurs, playing an important role not only for the understanding of the evolution of the group as a whole, but also of archosauromorphs in general. The b...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6798
更新日期:2019-05-22 00:00:00
abstract::A new species of Scutalus Albers, 1850 (Gastropoda: Bulimulidae), Scutalus chango sp. n., is described from a coastal area of northern Chile. Empty shells of this new species were found buried in sand and under boulders and rocks in the foothills of the Chilean Coastal Range at Paposo, Región de Antofagasta. This new ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.3538
更新日期:2017-07-05 00:00:00
abstract::The structural and material properties of insect cuticle remain largely unexplored, even though they comprise the majority (approximately 80%) of animals. Insect cuticle serves many functions, including protection against predatory attacks, which is especially beneficial to species failing to employ effective running ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.501
更新日期:2014-07-31 00:00:00
abstract:Background:The influenza virus can cause seasonal infections with mild to severe symptoms, circulating worldwide, and it can affect people in any age group. Therefore, this infection is a serious public health problem that causes severe illness and death in high-risk populations. Every year, 0.5% of the world's populat...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.5716
更新日期:2018-10-26 00:00:00
abstract:Background and Purpose:Oxidative stress is involved in normal and pathological functioning of skeletal muscle. Protection of myoblasts from oxidative stress may improve muscle contraction and delay aging. Here we studied the effect of R. coriaria sumac fruit extract on human myoblasts and zebrafish embryos in condition...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.4144
更新日期:2017-12-12 00:00:00
abstract::Koalas (Phascolarctos cinereus) are highly specialized herbivorous marsupials that feed almost exclusively on Eucalyptus leaves, which are known to contain varying concentrations of many different toxic chemical compounds. The literature suggests that Lonepinella koalarum, a bacterium in the Pasteurellaceae family, ca...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.10177
更新日期:2020-10-20 00:00:00
abstract:Background:Silkworm pupae is the main by-product of the sericulture industry with an interesting nutritional profile, especially in terms of proteins. In consideration of its possible use as a food or food ingredient in Western countries, a comparative proteomic experiment has been performed to investigate the differen...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6723
更新日期:2019-06-12 00:00:00
abstract::Among helminth parasites, Paragonimus (zoonotic lung fluke) gains considerable importance from veterinary and medical points of view because of its diversified effect on its host. Nearly fifty species of Paragonimus have been described across the globe. It is estimated that more than 20 million people are infected wor...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.484
更新日期:2014-08-12 00:00:00
abstract::Purpose. People with stroke living in the community have an increased prevalence of depression and lower quality of life than healthy older adults. This cross-sectional observational study investigated whether participation in regular exercise was associated with improved mood and quality of life. Methods. We recruite...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.331
更新日期:2014-03-27 00:00:00
abstract:Background:KIAA1199 is a recently identified novel gene that is upregulated in various human cancers with poor survival, but its role and the underlying mechanisms in laryngeal squamous cell carcinoma (LSCC) remain unknown. Here, we collected tissues from 105 cases of LSCC to investigate the relationships between KIAA1...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.9637
更新日期:2020-09-07 00:00:00
abstract:Background:Sexual development in Flammulina velutipes is controlled by two different mating type loci (HD and PR). The HD locus contains homeodomain (Hd) genes on two separate HD subloci: HD-a and HD-b. While the functionality of the HD-b sublocus has been largely confirmed, the status and content of the HD-a sublocus ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6292
更新日期:2019-02-22 00:00:00
abstract:Objective:The N-methyl-D-aspartate subtype glutamate receptor antagonist ketamine has rapid antidepressant and antisuicidal effects in treating treatment-resistant bipolar depression (TRBD). The neurocognitive effects of repeated ketamine infusions in TRBD are not known. Methods:Six intravenous infusions of ketamine (...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.10208
更新日期:2020-11-03 00:00:00
abstract::Histone deacetylases (HDACs) are key epigenetic factors in regulating chromatin structure and gene expression in multiple aspects of plant growth, development, and response to abiotic or biotic stresses. Many studies on systematic analysis and molecular function of HDACs in Arabidopsis and rice have been conducted. Ho...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.8539
更新日期:2020-02-12 00:00:00
abstract:Background:Vitamin D 1α-hydroxylase CYP27B1 is the key factor in the vitamin D pathway. Previously, we analyzed the expression of CYP27B1 in human gingival fibroblasts in vitro. In the present study, we analyzed the gingival expression of CYP27B1 in vivo. Methods:Forty-two patients with periodontitis Stage IV Grade C ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.10279
更新日期:2021-01-04 00:00:00
abstract::Multidrug and toxic compound extrusion (MATE) transporters contribute to multidrug resistance and play major determinants of aluminum (Al) tolerance in plants. Alfalfa (Medicago sativa L.) is the most extensively cultivated forage crop in the world, yet most alfalfa cultivars are not Al tolerant. The basic knowledge o...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6302
更新日期:2019-01-31 00:00:00
abstract::The main objective of this research was to test central assumptions from the Self-centeredness/Selflessness Happiness Model. According to this model, while self-centered psychological functioning induces fluctuating happiness, authentic-durable happiness results from selflessness. Distinct mediating processes are supp...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.3306
更新日期:2017-05-11 00:00:00
abstract:Background:In horses and ponies numerous medical conditions are known to be linked with inflammation in different tissues, especially in the liver. Besides affecting other metabolic pathways such as the expression of certain interleukins (IL), inflammation is associated with stress of the endoplasmic reticulum (ER). In...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.8053
更新日期:2019-11-12 00:00:00
abstract::Changes in behavior are often the proximate response of animals to human disturbance, with variability in tolerance levels leading some species to exhibit striking shifts in life history, fitness, and/or survival. Thus, elucidating the effects of disturbance on animal behavior, and how this varies among taxonomically ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6956
更新日期:2019-06-07 00:00:00
abstract:Background:Over the last two decades, there has been a constant increase in prescription rates of antidepressants. In parallel, neuroactive pharmaceuticals are making their way into aquatic environments at increasing concentrations. Among the antidepressants detected in the environment citalopram, a selective serotonin...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.8765
更新日期:2020-03-12 00:00:00
abstract::Histone lysine modifications are important epigenetic modifications in early embryonic development. JARID2, which is a member of the jumonji demethylase protein family, is a regulator of early embryonic development and can regulate mouse development and embryonic stem cell (ESC) differentiation by modifying histone ly...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.4189
更新日期:2017-12-21 00:00:00
abstract:Background:Conserving both biodiversity and ecosystem services is a major goal of the Convention on Biological Diversity. Hotspots for biodiversity in the Andes significantly overlap with areas with dense human populations that sustain their economy through agricultural production. Therefore, developing management form...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6207
更新日期:2019-02-13 00:00:00
abstract:Background:Fibroblast growth factor 2 (FGF2) is a highly pleiotropic cytokine with antifibrotic activity in wound healing. During the process of wound healing and fibrosis, fibroblasts are the key players. Although accumulating evidence has suggested the antagonistic effects of FGF2 in the activation process of fibrobl...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.10671
更新日期:2021-01-15 00:00:00