Observation selection bias in contact prediction and its implications for structural bioinformatics.

Abstract:

:Next Generation Sequencing is dramatically increasing the number of known protein sequences, with related experimentally determined protein structures lagging behind. Structural bioinformatics is attempting to close this gap by developing approaches that predict structure-level characteristics for uncharacterized protein sequences, with most of the developed methods relying heavily on evolutionary information collected from homologous sequences. Here we show that there is a substantial observational selection bias in this approach: the predictions are validated on proteins with known structures from the PDB, but exactly for those proteins significantly more homologs are available compared to less studied sequences randomly extracted from Uniprot. Structural bioinformatics methods that were developed this way are thus likely to have over-estimated performances; we demonstrate this for two contact prediction methods, where performances drop up to 60% when taking into account a more realistic amount of evolutionary information. We provide a bias-free dataset for the validation for contact prediction methods called NOUMENON.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Orlando G,Raimondi D,Vranken WF

doi

10.1038/srep36679

subject

Has Abstract

pub_date

2016-11-18 00:00:00

pages

36679

issn

2045-2322

pii

srep36679

journal_volume

6

pub_type

杂志文章
  • Metabolomics Identifies Biomarker Pattern for Early Diagnosis of Hepatocellular Carcinoma: from Diethylnitrosamine Treated Rats to Patients.

    abstract::Early diagnosis of hepatocellular carcinoma (HCC) remains challenging to date. Characteristic metabolic deregulations of HCC may enable novel biomarkers discovery for early diagnosis. A capillary electrophoresis-time of flight mass spectrometry (CE-TOF/MS)-based metabolomics approach was performed to discover and vali...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep16101

    authors: Zeng J,Huang X,Zhou L,Tan Y,Hu C,Wang X,Niu J,Wang H,Lin X,Yin P

    更新日期:2015-11-03 00:00:00

  • Use of Ultrasonic Device in Cervical and Thoracic Laminectomy: a Retrospective Comparative Study and Technical Note.

    abstract::Multilevel severe compressive myelopathy is a challenging disorder for the surgeons, the aim of this study is to assess the efficacy and safety of a newly designed ultrasonic burr as an assistant tool to the ultrasonic scalpel in laminectomy for this disease. This is a retrospective comparative study, the included sub...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-22454-y

    authors: Chen Y,Chang Z,Yu X,Song R,Huang W

    更新日期:2018-03-05 00:00:00

  • Clinicopathological features and surgical treatment of cervical oesophageal cancer.

    abstract::Cervical oesophageal cancer (CEC) is a relatively uncommon malignancy. The biological behaviour and treatment have not been well studied. This retrospective study reviewed the clinicopathological features of 28 patients with CEC who underwent surgical resection to investigate the biological behaviour, treatment and pr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-03593-0

    authors: Chen SB,Yang XH,Weng HR,Liu DT,Li H,Chen YP

    更新日期:2017-06-12 00:00:00

  • High rate of drug resistance among tuberculous meningitis cases in Shaanxi province, China.

    abstract::The clinical and mycobacterial features of tuberculous meningitis (TBM) cases in China are not well described; especially in western provinces with poor tuberculosis control. We prospectively enrolled patients in whom TBM was considered in Shaanxi Province, northwestern China, over a 2-year period (September 2010 to D...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep25251

    authors: Wang T,Feng GD,Pang Y,Liu JY,Zhou Y,Yang YN,Dai W,Zhang L,Li Q,Gao Y,Chen P,Zhan LP,Marais BJ,Zhao YL,Zhao G

    更新日期:2016-05-04 00:00:00

  • Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fiber production.

    abstract::After domestication in the Near East around 10,000 years ago several founder crops, flax included, spread to European latitudes. On reaching northerly latitudes the architecture of domesticated flax became more suitable to fiber production over oil, with longer stems, smaller seeds and fewer axillary branches. Latitud...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-37086-5

    authors: Gutaker RM,Zaidem M,Fu YB,Diederichsen A,Smith O,Ware R,Allaby RG

    更新日期:2019-01-30 00:00:00

  • Applications of chitosan (CHI)-reduced graphene oxide (rGO)-polyaniline (PAni) conducting composite electrode for energy generation in glucose biofuel cell.

    abstract::A glassy carbon electrode (GC) immobilized with chitosan (CHI)@reduced graphene (rGO)-polyaniline (PAni)/ferritin (Frt)/glucose oxidase (GOx) bioelectrode was prepared. The prepared electrode was characterized by using cyclic voltammetry (CV), linear sweep voltammetry (LSV) and electrochemical impedance spectroscopy (...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-67253-6

    authors: Haque SU,Nasar A,Inamuddin,Rahman MM

    更新日期:2020-06-26 00:00:00

  • Experimental study of the nonreciprocal effective interactions between microparticles in an anisotropic plasma.

    abstract::There is a variety of cases in nature when the action-reaction symmetry is broken. In particular, suitable conditions for this are realized in colloidal suspensions and complex plasmas. Since the first theories and simulations of the nonreciprocal effective interactions between microparticles in complex plasmas were p...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-70441-z

    authors: Lisin EA,Petrov OF,Sametov EA,Vaulina OS,Statsenko KB,Vasiliev MM,Carmona-Reyes J,Hyde TW

    更新日期:2020-08-12 00:00:00

  • The effect of nanometre-scale V-pits on electronic and optical properties and efficiency droop of GaN-based green light-emitting diodes.

    abstract::The development of efficient green light-emitting diodes (LEDs) is of paramount importance for the realization of colour-mixing white LEDs with a high luminous efficiency. While the insertion of an InGaN/GaN superlattice (SL) with a lower In content before the growth of InGaN/GaN multiple quantum wells (MQWs) is known...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-29440-4

    authors: Zhou S,Liu X,Yan H,Gao Y,Xu H,Zhao J,Quan Z,Gui C,Liu S

    更新日期:2018-07-23 00:00:00

  • Altered Gut Microbiota Profiles in Sows and Neonatal Piglets Associated with Porcine Epidemic Diarrhea Virus Infection.

    abstract::Porcine epidemic diarrhea virus (PEDV) is a devastating cause of diarrhea in pigs worldwide. Most of studies have focused on molecular and pathogenic characterization of PEDV, whereas there were limited studies in understanding the role of gut microbiota (GM) in viral-associated diarrhea. Here, using the Illumina MiSe...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-17830-z

    authors: Song D,Peng Q,Chen Y,Zhou X,Zhang F,Li A,Huang D,Wu Q,Ye Y,He H,Wang L,Tang Y

    更新日期:2017-12-12 00:00:00

  • Neural basis of uncertain cue processing in trait anxiety.

    abstract::Individuals with high trait anxiety form a non-clinical group with a predisposition for an anxiety-related bias in emotional and cognitive processing that is considered by some to be a prerequisite for psychiatric disorders. Anxious individuals tend to experience more worry under uncertainty, and processing uncertain ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep21298

    authors: Zhang M,Ma C,Luo Y,Li J,Li Q,Liu Y,Ding C,Qiu J

    更新日期:2016-02-19 00:00:00

  • Synergistic Antibacterial Activity and Wound Healing Properties of Selenium-Chitosan-Mupirocin Nanohybrid System: An in Vivo Study on Rat Diabetic Staphylococcus aureus Wound Infection Model.

    abstract::The current study aimed to formulate Selenium-Chitosan-Mupirocin (M-SeNPs-CCH) complex. The nanohybrid system was prepared using chitosan-cetyltrimethylammonium bromide (CTAB)-based hydrogel (CCH) that entrapped mupirocin (M) and selenium nanoparticles (SeNPs). The in vitro studies were performed by evaluation of the ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-59510-5

    authors: Golmohammadi R,Najar-Peerayeh S,Tohidi Moghadam T,Hosseini SMJ

    更新日期:2020-02-18 00:00:00

  • A random Q-switched fiber laser.

    abstract::Extensive studies have been performed on random lasers in which multiple-scattering feedback is used to generate coherent emission. Q-switching and mode-locking are well-known routes for achieving high peak power output in conventional lasers. However, in random lasers, the ubiquitous random cavities that are formed b...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep09338

    authors: Tang Y,Xu J

    更新日期:2015-03-23 00:00:00

  • Traditional Chinese medicine xin-mai-jia recouples endothelial nitric oxide synthase to prevent atherosclerosis in vivo.

    abstract::Endothelial dysfunction, which is caused by endothelial nitric oxide synthase (eNOS) uncoupling, is an initial step in atherosclerosis. This study was designed to explore whether Chinese medicine xin-mai-jia (XMJ) recouples eNOS to exert anti-atherosclerotic effects. Pretreatment of XMJ (25, 50, 100 μg/ml) for 30 minu...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep43508

    authors: Yin YL,Zhu ML,Wan J,Zhang C,Pan GP,Lu JX,Ping S,Chen Y,Zhao FR,Yu HY,Guo T,Jian X,Liu LY,Zhang JN,Wan GR,Wang SX,Li P

    更新日期:2017-03-02 00:00:00

  • Cluster analysis: a new approach for identification of underlying risk factors for coronary artery disease in essential hypertensive patients.

    abstract::Grading of essential hypertension according to blood pressure (BP) level may not adequately reflect clinical heterogeneity of hypertensive patients. This study was carried out to explore clinical phenotypes in essential hypertensive patients using cluster analysis. This study recruited 513 hypertensive patients and ev...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep43965

    authors: Guo Q,Lu X,Gao Y,Zhang J,Yan B,Su D,Song A,Zhao X,Wang G

    更新日期:2017-03-07 00:00:00

  • Deficient Vitamin E Uptake During Development Impairs Neural Tube Closure in Mice Lacking Lipoprotein Receptor SR-BI.

    abstract::SR-BI is the main receptor for high density lipoproteins (HDL) and mediates the bidirectional transport of lipids, such as cholesterol and vitamin E, between these particles and cells. During early development, SR-BI is expressed in extraembryonic tissue, specifically in trophoblast giant cells in the parietal yolk sa...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-05422-w

    authors: Santander N,Lizama C,Parga MJ,Quiroz A,Pérez D,Echeverría G,Ulloa L,Palma V,Rigotti A,Busso D

    更新日期:2017-07-12 00:00:00

  • Immunization against an IL-6 peptide induces anti-IL-6 antibodies and modulates the Delayed-Type Hypersensitivity reaction in cynomolgus monkeys.

    abstract::Interleukin-6 (IL-6) overproduction has been involved in the pathogenesis of several chronic inflammatory diseases and the administration of an anti-IL-6 receptor monoclonal antibody has been proven clinically efficient to treat them. However, the drawbacks of monoclonal antibodies have led our group to develop an inn...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep19549

    authors: Desallais L,Bouchez C,Mouhsine H,Moreau G,Ratsimandresy R,Montes M,Do H,Quintin-Colonna F,Zagury JF

    更新日期:2016-01-19 00:00:00

  • Spring maize yield, soil water use and water use efficiency under plastic film and straw mulches in the Loess Plateau.

    abstract::To compare the soil water balance, yield and water use efficiency (WUE) of spring maize under different mulching types in the Loess Plateau, a 7-year field experiment was conducted in the Changwu region of the Loess Plateau. Three treatments were used in this experiment: straw mulch (SM), plastic film mulch (PM) and c...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep38995

    authors: Lin W,Liu W,Xue Q

    更新日期:2016-12-15 00:00:00

  • The non-Newtonian maxwell nanofluid flow between two parallel rotating disks under the effects of magnetic field.

    abstract::The main feature of the present numerical model is to explore the behavior of Maxwell nanoliquid moving within two horizontal rotating disks. The disks are stretchable and subjected to a magnetic field in axial direction. The time dependent characteristics of thermal conductivity have been considered to scrutinize the...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-74096-8

    authors: Ahmadian A,Bilal M,Khan MA,Asjad MI

    更新日期:2020-10-13 00:00:00

  • Atomic interaction mechanism for designing the interface of W/Zr-based bulk metallic glass composites.

    abstract::The interaction between active element Zr and W damages the W fibers and the interface and decreases the mechanical properties, especially the tensile strength of the W fibers reinforced Zr-based bulk metallic glass composites (BMGCs). From the viewpoint of atomic interaction, the W-Zr interaction can be restrained by...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep08967

    authors: Li ZK,Fu HM,Sha PF,Zhu ZW,Wang AM,Li H,Zhang HW,Zhang HF,Hu ZQ

    更新日期:2015-03-11 00:00:00

  • mTORC1 inhibitor rapamycin and ER stressor tunicamycin induce differential patterns of ER-mitochondria coupling.

    abstract::Efficient mitochondrial Ca2+ uptake takes place at contact points between the ER and mitochondria, and represents a key regulator of many cell functions. In a previous study with HeLa cells, we showed that ER-to-mitochondria Ca2+ transfer increases during the early phase of ER stress induced by tunicamycin as an adapt...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep36394

    authors: Bravo-Sagua R,López-Crisosto C,Parra V,Rodriguez-Peña M,Rothermel BA,Quest AF,Lavandero S

    更新日期:2016-11-03 00:00:00

  • Lipid indices as simple and clinically useful surrogate markers for insulin resistance in the U.S. population.

    abstract::This study aimed to compare the accuracy of novel lipid indices, including the visceral adiposity index (VAI), lipid accumulation product (LAP), triglycerides and glucose (TyG) index, TyG-body mass index (TyG-BMI), and TyG-waist circumference (TyG-WC), in identifying insulin resistance and establish valid cutoff value...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-021-82053-2

    authors: Lee J,Kim B,Kim W,Ahn C,Choi HY,Kim JG,Kim J,Shin H,Kang JG,Moon S

    更新日期:2021-01-27 00:00:00

  • Associations of Plasma FGF2 Levels and Polymorphisms in the FGF2 Gene with Obesity Phenotypes in Han Chinese Population.

    abstract::Obesity is highly heritable, but the specific genes influencing obesity related traits are largely unknown. Fibroblast growth factor 2 (FGF2) could influence adipocyte differentiation. However, the association of FGF2 polymorphisms and obesity remains unclear. This study aimed to investigate the associations of both t...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep19868

    authors: Hao RH,Guo Y,Dong SS,Weng GZ,Yan H,Zhu DL,Chen XF,Chen JB,Yang TL

    更新日期:2016-02-16 00:00:00

  • Classification of skin phenotypes caused by diabetes mellitus using complex scattering parameters in the millimeter-wave frequency range.

    abstract::The pathological skin phenotype caused by hyperglycemia is an important indicator for the progress of diabetes mellitus. An early detection of diabetes assures an early intervention to regulate the carbohydrate metabolism. In this publication a non-invasive detection principle based on the measurement of complex scatt...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-06034-0

    authors: Dornuf F,Martín-Mateos P,Duarte B,Hils B,Bonilla-Manrique OE,Larcher F,Acedo P,Krozer V

    更新日期:2017-07-19 00:00:00

  • Achieving sub-wavelength imaging through a flat hyperlens in a modified anodic aluminum oxide template.

    abstract::Constrained by the diffraction limit, a lens can only resolve features larger than half of the incident wavelength owing to the decaying nature of evanescent waves. Several novel devices have been proposed, for example, superlenses and hyperlenses to break this limit. In this work, we present a flat hyperlens composed...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-62243-0

    authors: Tao CW,Yen TJ,Huang TY

    更新日期:2020-03-24 00:00:00

  • A combined method for synthesis of superconducting Cu doped Bi2Se3.

    abstract::We present a two-step technique for the synthesis of superconducting CuxBi2Se3. Cu0.15Bi2Se3 single crystals were synthesized using the melt-growth method. Although these samples are non-superconducting, they can be employed to generate high quality superconducting samples if used as precursors in the following electr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep22713

    authors: Wang M,Song Y,You L,Li Z,Gao B,Xie X,Jiang M

    更新日期:2016-03-03 00:00:00

  • Minority and Majority Charge Carrier Mobility in Cu2ZnSnSe4 revealed by Terahertz Spectroscopy.

    abstract::The mobilities of electrons and holes determine the applicability of any semiconductor, but their individual measurement remains a major challenge. Here, we show that time-resolved terahertz spectroscopy (TRTS) can distinguish the mobilities of minority and majority charge carriers independently of the doping-type and...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-32695-6

    authors: Hempel H,Hages CJ,Eichberger R,Repins I,Unold T

    更新日期:2018-09-27 00:00:00

  • Role of agonistic autoantibodies against type-1 angiotensin II receptor in the pathogenesis of retinopathy in preeclampsia.

    abstract::To investigate the mechanism underlying AT1-AA-induced retinopathy in severe preeclampsia by measuring the positive rate and titer of AT1-AA in plasma from women with severe preeclampsia and normal pregnant women to see whether AT1-AA titer was correlated with the grade of retinopathy. A preeclampsia rat model was als...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep29036

    authors: Liu F,Wang Y,Wang X,Zheng Y,Jin Z,Zhi J

    更新日期:2016-07-06 00:00:00

  • L-proline: a highly effective cryoprotectant for mouse oocyte vitrification.

    abstract::Recent studies have shown that L-proline is a natural osmoprotectant and an antioxidant to protect cells from injuries such as that caused by freezing and thawing in many species including plant, ram sperm and human endothelial cells. Nevertheless, this nontoxic cryoprotectant has not yet been applied to mammalian ooc...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep26326

    authors: Zhang L,Xue X,Yan J,Yan LY,Jin XH,Zhu XH,He ZZ,Liu J,Li R,Qiao J

    更新日期:2016-07-14 00:00:00

  • Chaotic time series prediction for glucose dynamics in type 1 diabetes mellitus using regime-switching models.

    abstract::In patients with type 1 diabetes mellitus (T1DM), glucose dynamics are influenced by insulin reactions, diet, lifestyle, etc., and characterized by instability and nonlinearity. With the objective of a dependable decision support system for T1DM self-management, we aim to model glucose dynamics using their nonlinear c...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-06478-4

    authors: Frandes M,Timar B,Timar R,Lungeanu D

    更新日期:2017-07-24 00:00:00

  • Leu8 and Pro8 oxytocin agonism differs across human, macaque, and marmoset vasopressin 1a receptors.

    abstract::Oxytocin (OXT) is an important neuromodulator of social behaviors via activation of both oxytocin receptors (OXTR) and vasopressin (AVP) 1a receptors (AVPR1a). Marmosets are neotropical primates with a modified OXT ligand (Pro8-OXT), and this ligand shows significant coevolution with traits including social monogamy a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-52024-9

    authors: Mustoe A,Schulte NA,Taylor JH,French JA,Toews ML

    更新日期:2019-10-29 00:00:00