Abstract:
:Cryo-electron microscopy (cryo-EM) has become a leading technology for determining protein structures. Recent advances in this field have allowed for atomic resolution. However, predicting the backbone trace of a protein has remained a challenge on all but the most pristine density maps (<2.5 Å resolution). Here we introduce a deep learning model that uses a set of cascaded convolutional neural networks (CNNs) to predict Cα atoms along a protein's backbone structure. The cascaded-CNN (C-CNN) is a novel deep learning architecture comprised of multiple CNNs, each predicting a specific aspect of a protein's structure. This model predicts secondary structure elements (SSEs), backbone structure, and Cα atoms, combining the results of each to produce a complete prediction map. The cascaded-CNN is a semantic segmentation image classifier and was trained using thousands of simulated density maps. This method is largely automatic and only requires a recommended threshold value for each protein density map. A specialized tabu-search path walking algorithm was used to produce an initial backbone trace with Cα placements. A helix-refinement algorithm made further improvements to the α-helix SSEs of the backbone trace. Finally, a novel quality assessment-based combinatorial algorithm was used to effectively map protein sequences onto Cα traces to obtain full-atom protein structures. This method was tested on 50 experimental maps between 2.6 Å and 4.4 Å resolution. It outperformed several state-of-the-art prediction methods including Rosetta de-novo, MAINMAST, and a Phenix based method by producing the most complete predicted protein structures, as measured by percentage of found Cα atoms. This method accurately predicted 88.9% (mean) of the Cα atoms within 3 Å of a protein's backbone structure surpassing the 66.8% mark achieved by the leading alternate method (Phenix based fully automatic method) on the same set of density maps. The C-CNN also achieved an average root-mean-square deviation (RMSD) of 1.24 Å on a set of 50 experimental density maps which was tested by the Phenix based fully automatic method. The source code and demo of this research has been published at https://github.com/DrDongSi/Ca-Backbone-Prediction.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Si D,Moritz SA,Pfab J,Hou J,Cao R,Wang L,Wu T,Cheng Jdoi
10.1038/s41598-020-60598-ysubject
Has Abstractpub_date
2020-03-09 00:00:00pages
4282issue
1issn
2045-2322pii
10.1038/s41598-020-60598-yjournal_volume
10pub_type
杂志文章abstract::Lentiviral vectors (LVs) are excellent tools to promote gene transfer and stable gene expression. Their potential has been already demonstrated in gene therapy clinical trials for the treatment of diverse disorders. For large scale LV production, a stable producer system is desirable since it allows scalable and cost-...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-23593-y
更新日期:2018-03-27 00:00:00
abstract::Are cooperative decisions typically made more quickly or slowly than non-cooperative decisions? While this question has attracted considerable attention in recent years, most research has focused on one-shot interactions. Yet it is repeated interactions that characterize most important real-world social interactions. ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep29622
更新日期:2016-07-20 00:00:00
abstract::Fatty liver (FL) disease is the most common type of chronic liver disease. We hypothesized that liver's response to the process where large droplets of triglyceride fat accumulate in liver cells is reflected also in gene pathway expression in blood. Peripheral blood genome wide gene expression analysis and ultrasonic ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-28563-y
更新日期:2018-07-09 00:00:00
abstract::A child with Down syndrome, like any other child, may benefit from interacting with memory stimuli, but needs additional support and help. The use of special teaching methods, which add playfulness and use of the computer, can enhance the memory processes of these children. In this work, we present the virtual environ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-60014-5
更新日期:2020-02-21 00:00:00
abstract::Annually averaged solar radiation in the McMurdo Dry Valleys, Antarctica has varied by over 20 W m-2 during the past three decades; however, the drivers of this variability are unknown. Because small differences in radiation are important to water availability and ecosystem functioning in polar deserts, determining th...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-23390-7
更新日期:2018-03-22 00:00:00
abstract::Plasmonics offer an exciting way to mediate the interaction between light and matter, allowing strong field enhancement and confinement, large absorption and scattering at resonance. However, simultaneous realization of ultra-narrow band perfect absorption and electromagnetic field enhancement is challenging due to th...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep24063
更新日期:2016-04-05 00:00:00
abstract::The indirect interactions between insect vectors, such as whiteflies, and the viruses they transmit, such as begomoviruses, via host plants may produce a range of outcome depending on the species/strain of each of the three organisms involved, and the mechanisms underlying the variations are not well understood. Here,...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-00692-w
更新日期:2017-04-03 00:00:00
abstract::To understand the impact of PIK3CA mutations on clinical characteristics and treatment response to epidermal growth factor tyrosine kinase inhibitors (EGFR TKIs) of lung adenocarcinoma, we examined PIK3CA and EGFR mutations in lung adenocarcinoma patients, and analyzed their clinical outcomes. Surgically excised tumor...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep35249
更新日期:2016-10-13 00:00:00
abstract::Cyanobacteria are photosynthetic prokaryotes that make major contributions to the production of the oxygen in the Earth atmosphere. The photosynthetic machinery in cyanobacterial cells is housed in flattened membrane structures called thylakoids. The structural organization of cyanobacterial cells and the arrangement ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep19627
更新日期:2016-01-21 00:00:00
abstract::While carbon-based materials have spearheaded numerous breakthroughs in biomedicine, they also have procreated many logical concerns on their overall toxicity. Carbon dots (CDs) as a respectively new member have been extensively explored in nucleus directed delivery and bioimaging due to their intrinsic fluorescence p...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-70796-3
更新日期:2020-08-17 00:00:00
abstract::By means of extensive ab initio calculations, a new two-dimensional (2D) atomic material tin selenide monolayer (coined as tinselenidene) is predicted to be a semiconductor with an indirect gap (~1.45 eV) and a high hole mobility (of order 10000 cm(2)V(-1)S(-1)), and will bear an indirect-direct gap transition under a...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep19830
更新日期:2016-02-01 00:00:00
abstract::Systemic lupus erythematosus (SLE) flares elicit progressive organ damage, leading to disability and early mortality. This study evaluated clinical and immunologic factors associated with impending flare in the Biomarkers of Lupus Disease study. Autoantibodies and 32 soluble mediators were measured by multiplex assays...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-45135-w
更新日期:2019-06-13 00:00:00
abstract::Heterodonty is one of the hallmarks of mammals. It has been suggested that, homeobox genes, differentially expressed in the ectomesenchyme of the jaw primordium along the distal-proximal axis, would determine the tooth classes (homeobox code model) based on mouse studies. Because mouse has highly specialized tooth pat...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-49116-x
更新日期:2019-09-06 00:00:00
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
更新日期:2017-03-02 00:00:00
abstract::A Late Cretaceous-aged multi-taxon nesting site from Romania preserved in three dimensions reveals the earliest example of nest site sharing yet known from the vertebrate fossil record. Eggshell and osteological evidence combined in this single accumulation demonstrate that at least four vertebrate taxa including enan...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-36305-3
更新日期:2019-02-13 00:00:00
abstract::A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper. ...
journal_title:Scientific reports
pub_type: 已发布勘误
doi:10.1038/s41598-019-39022-7
更新日期:2019-05-03 00:00:00
abstract::To attach reliably on various inclined rough surfaces, many insects have evolved both claws and adhesive pads on their feet. However, the interaction between these organs still remains unclear. Here we designed an artificial attachment device, which mimics the structure and function of claws and adhesive pads, and tes...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep26219
更新日期:2016-05-20 00:00:00
abstract::Light-inducible gene regulation has great potential for remote and noninvasive control of the fate and function of target cells. One method to achieve such control is delivery of heat shock protein (HSP) promoter-driven protein expression vectors and photothermal heaters into the cells, followed by activation by illum...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-04912-1
更新日期:2017-07-05 00:00:00
abstract::In situ HfB2-SiC-VSi2 composite was fabricated by reactive pressureless sintering at the temperature of 2150 °C for 4 h under a vacuum atmosphere. In situ SiC and VSi2 reinforcements were formed using VC and Si powders as starting materials according to the following reaction: VC + 3Si = SiC + VSi2. Microstructural st...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-73295-7
更新日期:2020-10-06 00:00:00
abstract::In insects, the transition from juvenile development to the adult stage is controlled by juvenile hormone (JH) synthesized from the corpora allata (CA) glands. Whereas a JH-free period during the last juvenile instar triggers metamorphosis and the end of the growth period, the reappearance of this hormone after the im...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep40234
更新日期:2017-01-11 00:00:00
abstract::Potassium channel tetramerization domain containing 12 (KCTD12), the auxiliary GABAB receptor subunit, is identified as a susceptibility gene for bipolar I (BPI) disorder in the Han Chinese population. Moreover, the single-nucleotide polymorphism (SNP) rs17026688 in glutamate decarboxylase-like protein 1 (GADL1) is sh...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-46655-1
更新日期:2019-07-16 00:00:00
abstract::The population of hepatitis B combined with a number of metabolic disorders is increasing significantly. Resveratrol (RSV) has been used as a preclinical drug for the treatment of the metabolic disorders. However, the impact of RSV on HBV replication remains unknown. In this study, the HBV-expressing hepatocelluar car...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep24744
更新日期:2016-04-21 00:00:00
abstract::A visible light active Bi0.9Ho0.1FeO3 nanoparticles/TiO2 composite thin films with different mol.% of Bi0.9Ho0.1FeO3 were successfully prepared via non-aqueous sol-gel method. The incorporation of 5, 10 and 20 mol.% Bi0.9Ho0.1FeO3 nanoparticles in the precursor solution of TiO2 brings modifications in the functional p...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-41570-x
更新日期:2019-03-26 00:00:00
abstract::Teleportation plays an important role in the communication of quantum information between the nodes of a quantum network and is viewed as an essential ingredient for long-distance Quantum Cryptography. We describe a method to teleport the quantum information carried by a photon in a superposition of a number d of ligh...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep03548
更新日期:2013-12-19 00:00:00
abstract::Disease associated genetic variations often cause intracellular enzyme inactivation, dysregulation and instability. However, allosteric communication of mutational effects to distant functional sites leading to loss-of-function remains poorly understood. We characterize here interdomain site-to-site communication by w...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep44532
更新日期:2017-03-14 00:00:00
abstract::Cardiac resynchronization therapy (CRT) threw lights on heart failure treatment, however, parts of patients showed nonresponse to CRT. Unfortunately, it lacks effective parameters to predict CRT non-response. In present study, we try to seek effective electro-echocardiographic predictors on CRT non-response. This is a...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep44009
更新日期:2017-03-10 00:00:00
abstract::Plasma dipeptidyl-peptidase-4 activity (DPP4a) is inversely associated with left ventricular function in patients with heart failure (HF) or diabetes. However, the association between DPP4a and left ventricular function in ST-segment elevation myocardial infarction (STEMI) patients has not been reported. We studied th...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-06514-3
更新日期:2017-07-21 00:00:00
abstract::The prion protein (PrP) evolved from the subbranch of ZIP metal ion transporters comprising ZIPs 5, 6 and 10, raising the prospect that the study of these ZIPs may reveal insights relevant for understanding the function of PrP. Building on data which suggested PrP and ZIP6 are critical during epithelial-to-mesenchymal...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep40313
更新日期:2017-01-18 00:00:00
abstract::Personalized medicine is a promising tool not only for prevention, screening and development of more efficient treatment strategies, but also for diminishing the side effects caused by current therapies. Deciphering gene regulation pathways provides a reliable prognostic analysis to elucidate the origin of grave disea...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep41368
更新日期:2017-01-25 00:00:00
abstract::Ovarian cancer is a highly aggressive disease and novel treatments are required. Thyroid hormones binding to αvβ3 integrin produced growth-promoting activities in ovarian cancer and we hypothesized that natural thyroid hormone derivatives may antagonize these actions. The effect of three antagonists, tetraiodoacetic a...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-16593-x
更新日期:2017-11-28 00:00:00