Different protein-protein interface patterns predicted by different machine learning methods.

Abstract:

:Different types of protein-protein interactions make different protein-protein interface patterns. Different machine learning methods are suitable to deal with different types of data. Then, is it the same situation that different interface patterns are preferred for prediction by different machine learning methods? Here, four different machine learning methods were employed to predict protein-protein interface residue pairs on different interface patterns. The performances of the methods for different types of proteins are different, which suggest that different machine learning methods tend to predict different protein-protein interface patterns. We made use of ANOVA and variable selection to prove our result. Our proposed methods taking advantages of different single methods also got a good prediction result compared to single methods. In addition to the prediction of protein-protein interactions, this idea can be extended to other research areas such as protein structure prediction and design.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Wang W,Yang Y,Yin J,Gong X

doi

10.1038/s41598-017-16397-z

subject

Has Abstract

pub_date

2017-11-22 00:00:00

pages

16023

issue

1

issn

2045-2322

pii

10.1038/s41598-017-16397-z

journal_volume

7

pub_type

杂志文章
  • Association of leukocyte telomere length and the risk of age-related hearing impairment in Chinese Hans.

    abstract::Age-related hearing loss (ARHI) is the most common sensory disorder in the elderly. Although telomere attrition has been shown as a determinant in the pathobiology of various age-related diseases, it remains unknown whether telomere length is associated with ARHI. We hypothesized that decreased leukocyte telomere leng...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-10680-9

    authors: Liu H,Luo H,Yang T,Wu H,Chen D

    更新日期:2017-08-31 00:00:00

  • Wells provide a distorted view of life in the aquifer: implications for sampling, monitoring and assessment of groundwater ecosystems.

    abstract::When compared to surface ecosystems, groundwater sampling has unique constraints, including limited access to ecosystems through wells. In order to monitor groundwater, a detailed understanding of groundwater biota and what biological sampling of wells truly reflects, is paramount. This study aims to address this unce...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep40702

    authors: Korbel K,Chariton A,Stephenson S,Greenfield P,Hose GC

    更新日期:2017-01-19 00:00:00

  • Characterization of Chinese liquor aroma components during aging process and liquor age discrimination using gas chromatography combined with multivariable statistics.

    abstract::Chinese liquor aroma components were characterized during the aging process using gas chromatography (GC). Principal component and cluster analysis (PCA, CA) were used to discriminate the Chinese liquor age which has a great economic value. Of a total of 21 major aroma components identified and quantified, 13 componen...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep39671

    authors: Xu ML,Yu Y,Ramaswamy HS,Zhu SM

    更新日期:2017-01-06 00:00:00

  • Whispering Gallery Mode Enabled Efficiency Enhancement: Defect and Size Controlled CdSe Quantum Dot Sensitized Whisperonic Solar Cells.

    abstract::A synergetic approach of employing smooth mesoporous TiO2 microsphere (SμS-TiO2)-nanoparticulate TiO2 (np-TiO2) composite photoanode, and size and defect controlled CdSe quantum dots (QD) to achieve high efficiency (η) in a modified Grätzel solar cell, quantum dot sensitized whisperonic solar cells (QDSWSC), is report...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-27969-y

    authors: Das TK,Ilaiyaraja P,Sudakar C

    更新日期:2018-06-26 00:00:00

  • Optofluidic UV-Vis spectrophotometer for online monitoring of photocatalytic reactions.

    abstract::On-chip integration of optical detection units into the microfluidic systems for online monitoring is highly desirable for many applications and is also well in line with the spirit of optofluidics technology-fusion of optics and microfluidics for advanced functionalities. This paper reports the construction of a UV-V...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep28928

    authors: Wang N,Tan F,Zhao Y,Tsoi CC,Fan X,Yu W,Zhang X

    更新日期:2016-06-29 00:00:00

  • Predictors of impending acute chest syndrome in patients with sickle cell anaemia.

    abstract::Acute chest syndrome (ACS) is a major complication of sickle cell anaemia (SCA) and a leading cause for hospital admissions and death. We aimed to study the spectrum of clinical and laboratory features of ACS and to assess the predisposing factors and predictors of severity. A retrospective case-control cohort was stu...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-59258-y

    authors: Alkindi S,Al-Busaidi I,Al-Salami B,Raniga S,Pathare A,Ballas SK

    更新日期:2020-02-12 00:00:00

  • Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype.

    abstract::Genes with similar roles in the cell cluster on chromosomes, thus benefiting from coordinated regulation. This allows gene function to be inferred by transferring annotations from genomic neighbors, following the guilt-by-association principle. We performed a systematic search for co-occurrence of >1000 gene functions...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-55984-0

    authors: Mihelčić M,Šmuc T,Supek F

    更新日期:2019-12-20 00:00:00

  • Synapse-specific expression of mu opioid receptor long-term depression in the dorsomedial striatum.

    abstract::The dorsal striatum is a brain region involved in action control, with dorsomedial striatum (DMS) mediating goal-directed actions and dorsolateral striatum (DLS) mediating habitual actions. Presynaptic long-term synaptic depression (LTD) plasticity at glutamatergic inputs to dorsal striatum mediates many dorsal striat...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-64203-0

    authors: Muñoz B,Haggerty DL,Atwood BK

    更新日期:2020-04-29 00:00:00

  • Differential photosynthetic and morphological adaptations to low light affect depth distribution of two submersed macrophytes in lakes.

    abstract::To evaluate the relative importance of photosynthetic versus morphological adaptations of submersed macrophytes to low light intensity in lakes, rapid light curves (RLCs), morphological parameters, relative growth rate (RGR), clonal reproduction and abundance of two submersed macrophytes (Potamogeton maackianus and Va...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep34028

    authors: Chen J,Cao T,Zhang X,Xi Y,Ni L,Jeppesen E

    更新日期:2016-10-03 00:00:00

  • Transient effects of chemotherapy for testicular cancer on mouse behaviour.

    abstract::The treatment of testicular cancer includes unilateral orchiectomy and chemotherapy and is curative for most patients. However, observational studies revealed an association with depression, anxiety and cognitive impairment. It is unclear whether these side effects are caused by chemotherapy, hemicastration or the dis...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-67081-8

    authors: Borbélyová V,Renczés E,Chovanec M,Mego M,Celec P

    更新日期:2020-06-23 00:00:00

  • Sevoflurane Pre-conditioning Ameliorates Diabetic Myocardial Ischemia/Reperfusion Injury Via Differential Regulation of p38 and ERK.

    abstract::Diabetes mellitus (DM) significantly increases myocardial ischemia/reperfusion (MI/R) injury. During DM, cardioprotection induced by conventional pre-conditioning (PreCon) is decreased due to impaired AMP-activated protein kinase (AMPK) signaling. The current study investigated whether PreCon with inhaled anesthetic s...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-56897-8

    authors: Xie D,Zhao J,Guo R,Jiao L,Zhang Y,Lau WB,Lopez B,Christopher T,Gao E,Cao J,Ma X,Wang Y

    更新日期:2020-01-08 00:00:00

  • Maternally expressed NLRP2 links the subcortical maternal complex (SCMC) to fertility, embryogenesis and epigenetic reprogramming.

    abstract::Mammalian parental genomes contribute differently to early embryonic development. Before activation of the zygotic genome, the maternal genome provides all transcripts and proteins required for the transition from a highly specialized oocyte to a pluripotent embryo. Depletion of these maternally-encoded transcripts fr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep44667

    authors: Mahadevan S,Sathappan V,Utama B,Lorenzo I,Kaskar K,Van den Veyver IB

    更新日期:2017-03-20 00:00:00

  • Characterization of Discrete Phosphopantetheinyl Transferases in Streptomyces tsukubaensis L19 Unveils a Complicate Phosphopantetheinylation Network.

    abstract::Phosphopantetheinyl transferases (PPTases) play essential roles in both primary metabolisms and secondary metabolisms via post-translational modification of acyl carrier proteins (ACPs) and peptidyl carrier proteins (PCPs). In this study, an industrial FK506 producing strain Streptomyces tsukubaensis L19, together wit...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep24255

    authors: Wang YY,Zhang XS,Luo HD,Ren NN,Jiang XH,Jiang H,Li YQ

    更新日期:2016-04-07 00:00:00

  • Enduring rules of care within pairs - how blue tit parents resume provisioning behaviour after experimental disturbance.

    abstract::Sexual conflict over parental investment can result in suboptimal reproductive output. A recent hypothesis suggests that equality in investment, and hence conflict resolution, may be reached via coordination of parental activities like alternating nest visits. However, how robust patterns of care within couples are ag...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-39139-9

    authors: Iserbyt A,Griffioen M,Eens M,Müller W

    更新日期:2019-02-26 00:00:00

  • On the near-wall accumulation of injectable particles in the microcirculation: smaller is not better.

    abstract::Although most nanofabrication techniques can control nano/micro particle (NMP) size over a wide range, the majority of NMPs for biomedical applications exhibits a diameter of ~100 nm. Here, the vascular distribution of spherical particles, from 10 to 1,000 nm in diameter, is studied using intravital microscopy and com...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep02079

    authors: Lee TR,Choi M,Kopacz AM,Yun SH,Liu WK,Decuzzi P

    更新日期:2013-01-01 00:00:00

  • Classification of naturally evoked compound action potentials in peripheral nerve spatiotemporal recordings.

    abstract::Peripheral neural signals have the potential to provide the necessary motor, sensory or autonomic information for robust control in many neuroprosthetic and neuromodulation applications. However, developing methods to recover information encoded in these signals is a significant challenge. We introduce the idea of usi...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-47450-8

    authors: Koh RGL,Nachman AI,Zariffa J

    更新日期:2019-07-31 00:00:00

  • Potassium depletion induces cellular conversion in the outer medullary collecting duct altering Notch signaling pathway.

    abstract::Potassium depletion affects AQP2 expression and the cellular composition of the kidney collecting duct. This, in turn, contributes to the development of a secondary form of nephrogenic diabetes insipidus and hypokalemic nephropathy. Here we show that after 14 days of potassium depletion, the cellular fraction of A-typ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-61882-7

    authors: Iervolino A,Prosperi F,De La Motte LR,Petrillo F,Spagnuolo M,D'Acierno M,Siccardi S,Perna AF,Christensen BM,Frische S,Capasso G,Trepiccione F

    更新日期:2020-03-31 00:00:00

  • FGF21 signaling in glutamatergic neurons is required for weight loss associated with dietary protein dilution.

    abstract::Alterations in macronutrient intake can have profound effects on energy intake and whole-body metabolism. For example, reducing protein intake increases energy expenditure, increases insulin sensitivity and decreases body weight in rodents. Fibroblast growth factor 21 (FGF21) signaling in the brain is necessary for th...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-76593-2

    authors: Flippo KH,Jensen-Cody SO,Claflin KE,Potthoff MJ

    更新日期:2020-11-11 00:00:00

  • Beneficial mutation-selection dynamics in finite asexual populations: a free boundary approach.

    abstract::Using a free boundary approach based on an analogy with ice melting models, we propose a deterministic PDE framework to describe the dynamics of fitness distributions in the presence of beneficial mutations with non-epistatic effects on fitness. Contrarily to most approaches based on deterministic models, our framewor...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-17212-5

    authors: Roques L,Garnier J,Martin G

    更新日期:2017-12-19 00:00:00

  • HAPPENN is a novel tool for hemolytic activity prediction for therapeutic peptides which employs neural networks.

    abstract::The growing prevalence of resistance to antibiotics motivates the search for new antibacterial agents. Antimicrobial peptides are a diverse class of well-studied membrane-active peptides which function as part of the innate host defence system, and form a promising avenue in antibiotic drug research. Some antimicrobia...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-67701-3

    authors: Timmons PB,Hewage CM

    更新日期:2020-07-02 00:00:00

  • Long-term isolation at a low effective population size greatly reduced genetic diversity in Gulf of California fin whales.

    abstract::The Gulf of California, Mexico is home to many cetacean species, including a presumed resident population of fin whales, Balaenoptera physalus. Past studies reported very low levels of genetic diversity among Gulf of California fin whales and a significant level of genetic differentiation from con-specifics in the eas...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-48700-5

    authors: Rivera-León VE,Urbán J,Mizroch S,Brownell RL Jr,Oosting T,Hao W,Palsbøll PJ,Bérubé M

    更新日期:2019-08-27 00:00:00

  • Remote control of resistive switching in TiO2 based resistive random access memory device.

    abstract::We report on the magnetic field control of a bipolar resistive switching in Ag/TiO2/FTO based resistive random access memory device through I-V characteristics. Essentially, in the presence of magnetic field and in the low resistance state, an abrupt change in the resistance of the device demands higher voltage, hinti...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-17607-4

    authors: Sahu DP,Jammalamadaka SN

    更新日期:2017-12-08 00:00:00

  • Efficacy of Losartan in the management of Post-Dialysis Euvolemic Hypertension (HELD-Trial): A Single-Blind Randomized Control Trial.

    abstract::To assess the effectiveness of losartan 50 mg on post dialysis euvolemic hypertensive patients against standard antihypertensive pharmacotherapy. A multicentre, prospective, randomized, single-blind trial was conducted to assess the effect of losartan 50 mg every other day (EOD), once a morning (OM) among post-dialysi...

    journal_title:Scientific reports

    pub_type: 杂志文章,多中心研究,随机对照试验

    doi:10.1038/srep36592

    authors: Aftab RA,Khan AH,Adnan AS,Sulaiman SAS,Khan TM

    更新日期:2016-12-06 00:00:00

  • The possible role of Dickkopf-1, Golgi protein- 73 and Midkine as predictors of hepatocarcinogenesis: a review and an Egyptian study.

    abstract::Hepatocellular carcinoma (HCC) is the second most common cause of cancer-related death worldwide. The use of alpha fetoprotein (AFP) alone was not an accurate biomarker for HCC despite its high specificity. Therefore, we assessed the possible role of serum biomarkers that have been mentioned briefly in previous studie...

    journal_title:Scientific reports

    pub_type: 杂志文章,评审

    doi:10.1038/s41598-020-62051-6

    authors: N Zekri AR,El Kassas M,Salam ESE,Hassan RM,Mohanad M,Gabr RM,M Lotfy M,Abdel-Zaher RAT,Bahnassy AA,Ahmed OS

    更新日期:2020-03-20 00:00:00

  • A Phospholipid Profile at 4 Months Predicts the Onset of Celiac Disease in at-Risk Infants.

    abstract::Celiac disease (CeD) is a multifactorial disease influenced by both genetic and environmental risk factors. CeD genetic components are mainly due to HLA class II genes, which account for approximately 40% of the disease heritability. The environmental factor is linked to gliadin ingestion. Despite genetic and epigenet...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-50735-7

    authors: Auricchio R,Galatola M,Cielo D,Amoresano A,Caterino M,De Vita E,Illiano A,Troncone R,Greco L,Ruoppolo M

    更新日期:2019-10-04 00:00:00

  • Destination of apyrene sperm following migration from the bursa copulatrix in the monandrous swallowtail butterfly Byasa alcinous.

    abstract::Most male lepidopterans produce fertile eupyrene sperm and non-fertile apyrene sperm, both of which are transferred to the female in a spermatophore during mating. Apyrene sperm outnumbers eupyrene sperm and both sperm types migrate from the bursa copulatrix to the spermatheca after mating. While eupyrene sperm are ma...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-77683-x

    authors: Konagaya T,Idogawa N,Watanabe M

    更新日期:2020-12-01 00:00:00

  • Triggering of major eruptions recorded by actively forming cumulates.

    abstract::Major overturn within a magma chamber can bring together felsic and mafic magmas, prompting de-volatilisation and acting as the driver for Plinian eruptions. Until now identification of mixing has been limited to analysis of lavas or individual crystals ejected during eruptions. We have recovered partially developed c...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep00731

    authors: Stock MJ,Taylor RN,Gernon TM

    更新日期:2012-01-01 00:00:00

  • Nematicidal and insecticidal activities of halogenated indoles.

    abstract::Parasite death via ion channel activations is the hallmark of anthelmintic and antiparasitic drugs. Glutamate gated chloride channel (GluCl) is a prominent targets for drug selection and design in parasitology. We report several iodine-fluorine based lead activators of GluCl by computational studies and structure-acti...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-38561-3

    authors: Rajasekharan SK,Lee JH,Ravichandran V,Kim JC,Park JG,Lee J

    更新日期:2019-02-14 00:00:00

  • Prediction of age-related macular degeneration disease using a sequential deep learning approach on longitudinal SD-OCT imaging biomarkers.

    abstract::We propose a hybrid sequential prediction model called "Deep Sequence", integrating radiomics-engineered imaging features, demographic, and visual factors, with a recursive neural network (RNN) model in the same platform to predict the risk of exudation within a future time-frame in non-exudative AMD eyes. The propose...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-72359-y

    authors: Banerjee I,de Sisternes L,Hallak JA,Leng T,Osborne A,Rosenfeld PJ,Gregori G,Durbin M,Rubin D

    更新日期:2020-09-22 00:00:00

  • Insights into Population Health Management Through Disease Diagnoses Networks.

    abstract::The increasing availability of electronic health care records has provided remarkable progress in the field of population health. In particular the identification of disease risk factors has flourished under the surge of available data. Researchers can now access patient data across a broad range of demographics and g...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep30465

    authors: Feldman K,Stiglic G,Dasgupta D,Kricheff M,Obradovic Z,Chawla NV

    更新日期:2016-07-27 00:00:00