Abstract：
:The accurate prediction of the impact of an amino acid substitution on the thermal stability of a protein is a central issue in protein science, and is of key relevance for the rational optimization of various bioprocesses that use enzymes in unusual conditions. Here we present one of the first computational tools to predict the change in melting temperature ΔTm upon point mutations, given the protein structure and, when available, the melting temperature Tm of the wild-type protein. The key ingredients of our model structure are standard and temperature-dependent statistical potentials, which are combined with the help of an artificial neural network. The model structure was chosen on the basis of a detailed thermodynamic analysis of the system. The parameters of the model were identified on a set of more than 1,600 mutations with experimentally measured ΔTm. The performance of our method was tested using a strict 5-fold cross-validation procedure, and was found to be significantly superior to that of competing methods. We obtained a root mean square deviation between predicted and experimental ΔTm values of 4.2 °C that reduces to 2.9 °C when ten percent outliers are removed. A webserver-based tool is freely available for non-commercial use at soft.dezyme.com.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Pucci F,Bourgeas R,Rooman Mdoi
10.1038/srep23257subject
Has Abstractpub_date
2016-03-18 00:00:00pages
23257issn
2045-2322pii
srep23257journal_volume
6pub_type
杂志文章abstract：:Although habitat transformation is one of the main causes of biodiversity loss, there are many examples of species successfully occupying and even proliferating in highly human-modified habitats such are the cities. Thus, there is an increasing interest in understanding the drivers favoring urban life for some species...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-03853-z
更新日期：2017-06-14 00:00:00
abstract：:Cell penetrating peptides (CPPs) are peptides that can be translocated into cells and used as a carrier platform for the intracellular uptake of cargo molecules. Subject to the source of CPP sequences and their positively charged nature, the cytotoxicity and immunogenicity of conventional CPPs needs to be optimized to...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep11719
更新日期：2015-06-26 00:00:00
abstract：:Pachychoroid spectrum diseases have attracted increasing attention, though their pathophysiology has yet to be fully elucidated. In this study, we assessed the vascular diameters of vortex veins in pachychoroid spectrum diseases such as central serous chorioretinopathy (CSC), pachychoroid neovasculopathy without polyp...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-75789-w
更新日期：2020-11-11 00:00:00
abstract：:In biological tissues, radiation causes the formation of reactive oxygen species (ROS), some of which lead to sequential oxidation of certain protein cysteine residues. Resultant cysteinyl radicals are subject to post-translational modification through S-glutathionylation. The present clinical trial was designed to de...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-50288-9
更新日期：2019-09-24 00:00:00
abstract：:A clinical study was designed to record a wide range of physiological values from patients undergoing haemodialysis treatment in the Renal Unit of the Churchill Hospital in Oxford. Video was recorded for a total of 84 dialysis sessions from 40 patients during the course of 1 year, comprising an overall video recording...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-75152-z
更新日期：2020-10-28 00:00:00
abstract：:This retrospective study was undertaken to provide more modern data of real-life management of non-metastatic rectal cancer, to compare therapeutic strategies, and to identify prognostic factors of overall survival (OS) in a large cohort of patients. Data on efficacy and on acute/late toxicity were retrospectively col...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-29040-2
更新日期：2018-07-16 00:00:00
abstract：:Ultrafast ultrasound imaging is used to capture driven spinal vibrations as a new method for non-invasive spinal testing in living subjects. Previously, it has been shown that accelerometer-based vibration testing in cadaveric models can reveal the presence, location and magnitude of spinal pathology. However, this pr...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-27816-0
更新日期：2018-06-25 00:00:00
abstract：:Mechanical forces are critical to modulate cell spreading, contractility, gene expression, and even stem cell differentiation. Yet, existing tools that can apply controllable subcellular forces to a large number of single cells simultaneously are still limited. Here we report a novel ultrasound tweezing cytometry util...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep02176
更新日期：2013-01-01 00:00:00
abstract：:The coal fires, a global catastrophe for hundreds of years, have been proved extremely difficult to control, and hit almost every coal-bearing area globally. Meanwhile, underground coal fires contain tremendous reservoir of geothermal energy. Approximately one billion tons of coal burns underground annually in the wor...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-05622-4
更新日期：2017-07-13 00:00:00
abstract：:The present study investigated when emotion modulates working memory from the perspective of neural activation. Using fMRI, we measured brain activity during the encoding and retrieval phases of a reading span test (RST) that used emotional contexts. The emotional RST required participants to read sentences that elici...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep01375
更新日期：2013-01-01 00:00:00
abstract：:We propose a new efficient algorithm to simulate magnetic structures numerically. It contains a generative model using a complex-valued neural network to generate k-space information. The output information is hermitized and transformed into real-space spin configurations through an inverse fast Fourier transform. The...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-53411-y
更新日期：2019-11-13 00:00:00
abstract：:Organic nanofibers have found various applications in optoelectronic devices. In such devices, exciton diffusion is a major aspect concerning their efficiency. In the case of singlet excitons, Förster transfer is the mechanism responsible for this process. Temperature and morphology are factors known to influence exci...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-32232-5
更新日期：2018-09-19 00:00:00
abstract：:An effective method, involving time and frequency domains was developed to interpret seismic precursors by comparing groundwater-level fluctuations recorded immediately and long before the occurrence of a known earthquake. The proposed method, consisting of the pre-processing (3-point filtering, band-pass filtering, a...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-64586-0
更新日期：2020-05-12 00:00:00
abstract：:Receptor-mediated endocytosis is an essential process in signalling pathways for activation of intracellular signalling cascades. One example is the Wnt signalling pathway that seems to depend on endocytosis of the ligand-receptor complex for initiation of Wnt signal transduction. To date, the roles of different endoc...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-49082-4
更新日期：2019-09-10 00:00:00
abstract：:Microalgae identification is extremely difficult. The efficiency of DNA barcoding in microalgae identification involves ideal gene markers and approaches employed, which however, is still under the way. Although Scenedesmus has obtained much research in producing lipids its identification is difficult. Here we present...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep36822
更新日期：2016-11-09 00:00:00
abstract：:The Anfinsen hypothesis, the demonstration of which led to the Nobel prize in Chemistry, posits that all information required to determine a proteins' three dimensional structure is contained within its amino acid sequence. This suggests that it should be possible, in theory, to fold any protein in vitro. In practice,...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep18906
更新日期：2016-01-19 00:00:00
abstract：:Sporadic outbreaks caused by coxsackievirus A4 (CV-A4) have been reported worldwide. To further elucidate the detailed genetic characteristics and evolutionary recombination events of CV-A4, virus samples from nationwide hand, foot and mouth disease (HFMD) surveillance, encompassing 27 out of the 31 provinces in China...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-49859-7
更新日期：2019-09-20 00:00:00
abstract：:Current preclinical screening methods do not adequately detect cardiotoxicity. Using human induced pluripotent stem cell-derived cardiomyocytes (iPS-CMs), more physiologically relevant preclinical or patient-specific screening to detect potential cardiotoxic effects of drug candidates may be possible. However, one of ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep11817
更新日期：2015-07-03 00:00:00
abstract：:There is a huge request for the development of low dielectric constant polymeric materials for microelectronic applications. In thisstudy, polymer blends based on PVA:POZ with low dielectric constant has been fabricated. The results of XRD indicate that crystalline domain is enhanced at higher POZ concentration. Brill...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-49715-8
更新日期：2019-09-11 00:00:00
abstract：:An inexpensive and compact frequency multi-mode diode laser enables a compact two-photon polarization entanglement source via the continuous wave broadband pumped spontaneous parametric down-conversion (SPDC) process. Entanglement degradation caused by polarization mode dispersion (PMD) is one of the critical issues i...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep25846
更新日期：2016-05-13 00:00:00
abstract：:The anatomic and functional combinations of cusps and lophs (ridges) define the tooth shape of rodent molars, which distinguishes species. The species-specific cusp patterns result from the spatiotemporal induction of enamel knots (EKs), which require precisely controlled cellular behavior to control the epithelial in...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep37828
更新日期：2016-11-28 00:00:00
abstract：:Gas-filled hollow-core fiber (HCF) pulse post-compressors generating few- to single-cycle pulses are a key enabling tool for attosecond science and ultrafast spectroscopy. Achieving optimum performance in this regime can be extremely challenging due to the ultra-broad bandwidth of the pulses and the need of an adequat...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-20580-1
更新日期：2018-02-02 00:00:00
abstract：:Network analysis is an important tool to analyze the structure of complex systems such as tropical forests. Here, we infer spatial proximity networks in tropical forests by using network science. First, we focus on tree neighborhoods to derive spatial tree networks from forest inventory data. In a second step, we cons...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-70052-8
更新日期：2020-08-06 00:00:00
abstract：:Twenty-six imprinted genes were quantified in bovine in vivo produced oocytes and embryos using RNA-seq. Eighteen were detectable and their transcriptional patterns were: largely decreased (MEST and PLAGL1); first decreased and then increased (CDKN1C and IGF2R); peaked at a specific stage (PHLDA2, SGCE, PEG10, PEG3, G...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep17898
更新日期：2015-12-07 00:00:00
abstract：:Influenza virus evolves constantly in an unpredictable fashion, making it necessary to vaccinate people annually for effective prevention and control of influenza. In general, however, during the first wave of an influenza outbreak caused by a newly emerging virus strain, influenza morbidity and mortality have been ob...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep28729
更新日期：2016-06-29 00:00:00
abstract：:We have studied differentially regulated nuclear proteome of the clinical tissue specimens of glioblastoma (GBM, WHO Grade IV) and lower grades of gliomas (Grade II and III) using high resolution mass spectrometry- based quantitative proteomics approach. The results showed altered expression of many regulatory protein...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-47360-9
更新日期：2019-07-29 00:00:00
abstract：:A two step excitation scheme in hot atomic sodium vapor is experimentally investigated. The observed effects reflect a coupling between the 32S, 32P and the 32D states. We present the relative dependence on detuning of the two utilized lasers around λ = 589 nm and 819 nm. Unlike expected, we achieve a higher detuning ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-12089-w
更新日期：2017-09-18 00:00:00
abstract：:Oxide heterointerfaces are ideal for investigating strong correlation effects to electron transport, relevant for oxide-electronics. Using hot-electrons, we probe electron transport perpendicular to the La₀.₇Sr₀.₃MnO₃ (LSMO)- Nb-doped SrTiO₃ (Nb:STO) interface and find the characteristic hot-electron attenuation lengt...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep01274
更新日期：2013-01-01 00:00:00
abstract：:The physiological, biochemical and functional differences between oxidative and glycolytic muscles play important roles in human metabolic health and in animal meat quality. To explore these differences, we determined the genome-wide landscape of DNA methylomes and their relationship with the mRNA and miRNA transcript...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep32186
更新日期：2016-08-26 00:00:00
abstract：:Werner syndrome (WS) is the canonical adult human progeroid ('premature aging') syndrome. Patients with this autosomal recessive Mendelian disorder display constitutional genomic instability and an elevated risk of important age-associated diseases including cancer. Remarkably few analyses of WS patient tissue and tum...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep32038
更新日期：2016-08-25 00:00:00
