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  • 1
    Online Resource
    Online Resource
    Institute of Electrical and Electronics Engineers (IEEE) ; 2017
    In:  IEEE Transactions on Electron Devices Vol. 64, No. 9 ( 2017-9), p. 3690-3695
    In: IEEE Transactions on Electron Devices, Institute of Electrical and Electronics Engineers (IEEE), Vol. 64, No. 9 ( 2017-9), p. 3690-3695
    Type of Medium: Online Resource
    ISSN: 0018-9383 , 1557-9646
    Language: Unknown
    Publisher: Institute of Electrical and Electronics Engineers (IEEE)
    Publication Date: 2017
    detail.hit.zdb_id: 2028088-9
    detail.hit.zdb_id: 241634-7
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  • 2
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2021
    In:  Nucleic Acids Research Vol. 49, No. W1 ( 2021-07-02), p. W237-W241
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 49, No. W1 ( 2021-07-02), p. W237-W241
    Abstract: Protein–protein interactions play crucial roles in diverse biological processes, including various disease progressions. Atomistic structural details of protein–protein interactions may provide important information that can facilitate the design of therapeutic agents. GalaxyHeteromer is a freely available automatic web server (http://galaxy.seoklab.org/heteromer) that predicts protein heterodimer complex structures from two subunit protein sequences or structures. When subunit structures are unavailable, they are predicted by template- or distance-prediction-based modelling methods. Heterodimer complex structures can be predicted by both template-based and ab initio docking, depending on the template's availability. Structural templates are detected from the protein structure database based on both the sequence and structure similarities. The templates for heterodimers may be selected from monomer and homo-oligomer structures, as well as from hetero-oligomers, owing to the evolutionary relationships of heterodimers with domains of monomers or subunits of homo-oligomers. In addition, the server employs one of the best ab initio docking methods when heterodimer templates are unavailable. The multiple heterodimer structure models and the associated scores, which are provided by the web server, may be further examined by user to test or develop functional hypotheses or to design new functional molecules.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2022
    In:  Nature Methods Vol. 19, No. 1 ( 2022-01), p. 13-14
    In: Nature Methods, Springer Science and Business Media LLC, Vol. 19, No. 1 ( 2022-01), p. 13-14
    Type of Medium: Online Resource
    ISSN: 1548-7091 , 1548-7105
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2163081-1
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Wiley ; 2019
    In:  Journal of Computational Chemistry Vol. 40, No. 27 ( 2019-10-15), p. 2413-2417
    In: Journal of Computational Chemistry, Wiley, Vol. 40, No. 27 ( 2019-10-15), p. 2413-2417
    Abstract: Protein–protein docking methods are spotlighted for their roles in providing insights into protein–protein interactions in the absence of full structural information by experiment. GalaxyTongDock is an ab initio protein–protein docking web server that performs rigid‐body docking just like ZDOCK but with improved energy parameters. The energy parameters were trained by iterative docking and parameter search so that more native‐like structures are selected as top rankers. GalaxyTongDock performs asymmetric docking of two different proteins (GalaxyTongDock_A) and symmetric docking of homo‐oligomeric proteins with C n and D n symmetries (GalaxyTongDock_C and GalaxyTongDock_D). Performance tests on an unbound docking benchmark set for asymmetric docking and a model docking benchmark set for symmetric docking showed that GalaxyTongDock is better or comparable to other state‐of‐the‐art methods. Experimental and/or evolutionary information on binding interfaces can be easily incorporated by using block and interface options. GalaxyTongDock web server is freely available at http://galaxy.seoklab.org/tongdock . © 2019 Wiley Periodicals, Inc.
    Type of Medium: Online Resource
    ISSN: 0192-8651 , 1096-987X
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 1479181-X
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  • 5
    Online Resource
    Online Resource
    Frontiers Media SA ; 2023
    In:  Frontiers in Pediatrics Vol. 11 ( 2023-6-27)
    In: Frontiers in Pediatrics, Frontiers Media SA, Vol. 11 ( 2023-6-27)
    Abstract: Non-pharmaceutical interventions (NPIs), such as social distancing and hand washing, have been associated with a decline in the preterm birth rate worldwide. We aimed to evaluate whether the preterm birth rate in Korea during the coronavirus disease 2019 lockdown has changed compared to that in previous years. Method A birth registry from the Korea Statistical Information Service, which is a nationwide official database, was used to include all births claimed to have occurred between 2011 and 2020. Newborns with gestational age (GA) less than 22 weeks and birth weight less than 220 g were excluded. The pre-NPI period was designated as January 2011 to January 2020, and the NPI period was defined as February 2020 to December 2020. We assessed the effect of NPI on the incidence of prematurity per 100 births using an interrupted time-series quasi-experimental design and implementing an autoregressive integrated moving average (ARIMA) model. Results From 2011 to 2020, a total of 3,931,974 live births were registered, among which 11,416 were excluded. Consequently, the final study population included 3,920,558 live births (both singleton and multiple births) among which 275,009 (7.0%) were preterm. The preterm birth rate was significantly higher during the NPI period (8.68%) compared to that in the pre-NPI period (6.92%) ( P  & lt; 0.001). The ARIMA model showed that in all singleton and multiple births, except those in July (observed 9.24, expected 8.54, [95% prediction interval {PI} 8.13–8.96], percent difference 7.81%), September (observed 7.89, expected 8.35, [95% PI 7.93–8.76] , percent difference −5.66%), and December (observed 9.90, expected 9.40, [95% PI 8.98–9.82], percent difference 5.2%), most observed values were within the 95% PI of the expected values and showed an increasing trend. Conclusion In this nationwide observational study, the trend in premature birth rate did not significantly change due to NPI implementation in Korea, as it had been increasing since 2011. The trend of Korea's birth rate appears to be unaffected by the implementation of NPIs; however, further studies with a longer follow-up period are needed.
    Type of Medium: Online Resource
    ISSN: 2296-2360
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2711999-3
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  • 6
    Online Resource
    Online Resource
    Wiley ; 2001
    In:  American Journal of Hematology Vol. 67, No. 4 ( 2001-08), p. 270-272
    In: American Journal of Hematology, Wiley, Vol. 67, No. 4 ( 2001-08), p. 270-272
    Abstract: Ubiquitin‐ and proteasome‐mediated protein degradation is involved in many intracellular processes, including cell cycle regulation, transcriptional activation, and signal transduction in all eukaryotes. Novel subfamily members of the ubp superfamily, DUB‐1 and DUB‐2, are known to be immediate–early genes and are specifically expressed in B‐lymphocytes and T‐lymphocytes, respectively. With the site‐directed mutagenesis in four conserved amino acids (Cys60, Asp133, His298, and His307) and a series of deletion in the carboxy‐terminal region, we demonstrate that these conserved amino acids are critical, but not the C‐terminus, for the deubiquitinating activity of DUB‐2. Am. J. Hematol. 67:270–272, 2001. © 2001 Wiley‐Liss, Inc.
    Type of Medium: Online Resource
    ISSN: 0361-8609 , 1096-8652
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2001
    detail.hit.zdb_id: 1492749-4
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  • 7
    Online Resource
    Online Resource
    Wiley ; 2019
    In:  Proteins: Structure, Function, and Bioinformatics Vol. 87, No. 12 ( 2019-12), p. 1351-1360
    In: Proteins: Structure, Function, and Bioinformatics, Wiley, Vol. 87, No. 12 ( 2019-12), p. 1351-1360
    Abstract: Scoring model structure is an essential component of protein structure prediction that can affect the prediction accuracy tremendously. Users of protein structure prediction results also need to score models to select the best models for their application studies. In Critical Assessment of techniques for protein Structure Prediction (CASP), model accuracy estimation methods have been tested in a blind fashion by providing models submitted by the tertiary structure prediction servers for scoring. In CASP13, model accuracy estimation results were evaluated in terms of both global and local structure accuracy. Global structure accuracy estimation was evaluated by the quality of the models selected by the global structure scores and by the absolute estimates of the global scores. Residue‐wise, local structure accuracy estimations were evaluated by three different measures. A new measure introduced in CASP13 evaluates the ability to predict inaccurately modeled regions that may be improved by refinement. An intensive comparative analysis on CASP13 and the previous CASPs revealed that the tertiary structure models generated by the CASP13 servers show very distinct features. Higher consensus toward models of higher global accuracy appeared even for free modeling targets, and many models of high global accuracy were not well optimized at the atomic level. This is related to the new technology in CASP13, deep learning for tertiary contact prediction. The tertiary model structures generated by deep learning pose a new challenge for EMA (estimation of model accuracy) method developers. Model accuracy estimation itself is also an area where deep learning can potentially have an impact, although current EMA methods have not fully explored that direction.
    Type of Medium: Online Resource
    ISSN: 0887-3585 , 1097-0134
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 1475032-6
    SSG: 12
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  • 8
    In: Proteins: Structure, Function, and Bioinformatics, Wiley, Vol. 87, No. 12 ( 2019-12), p. 1200-1221
    Abstract: We present the results for CAPRI Round 46, the third joint CASP‐CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo‐oligomers and 6 heterocomplexes. Eight of the homo‐oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher‐order assemblies. These were more difficult to model, as their prediction mainly involved “ab‐initio” docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance “gap” was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template‐based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.
    Type of Medium: Online Resource
    ISSN: 0887-3585 , 1097-0134
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 1475032-6
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    Wiley ; 2017
    In:  Proteins: Structure, Function, and Bioinformatics Vol. 85, No. 3 ( 2017-03)
    In: Proteins: Structure, Function, and Bioinformatics, Wiley, Vol. 85, No. 3 ( 2017-03)
    Type of Medium: Online Resource
    ISSN: 0887-3585 , 1097-0134
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 1475032-6
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    Wiley ; 2018
    In:  Proteins: Structure, Function, and Bioinformatics Vol. 86, No. S1 ( 2018-03), p. 257-273
    In: Proteins: Structure, Function, and Bioinformatics, Wiley, Vol. 86, No. S1 ( 2018-03), p. 257-273
    Abstract: We present the quality assessment of 5613 models submitted by predictor groups from both CAPRI and CASP for the total of 15 most tractable targets from the second joint CASP‐CAPRI protein assembly prediction experiment. These targets comprised 12 homo‐oligomers and 3 hetero‐complexes. The bulk of the analysis focuses on 10 targets (of CAPRI Round 37), which included all 3 hetero‐complexes, and whose protein chains or the full assembly could be readily modeled from structural templates in the PDB. On average, 28 CAPRI groups and 10 CASP groups (including automatic servers), submitted models for each of these 10 targets. Additionally, about 16 groups participated in the CAPRI scoring experiments. A range of acceptable to high quality models were obtained for 6 of the 10 Round 37 targets, for which templates were available for the full assembly. Poorer results were achieved for the remaining targets due to the lower quality of the templates available for the full complex or the individual protein chains, highlighting the unmet challenge of modeling the structural adjustments of the protein components that occur upon binding or which must be accounted for in template‐based modeling. On the other hand, our analysis indicated that residues in binding interfaces were correctly predicted in a sizable fraction of otherwise poorly modeled assemblies and this with higher accuracy than published methods that do not use information on the binding partner. Lastly, the strengths and weaknesses of the assessment methods are evaluated and improvements suggested.
    Type of Medium: Online Resource
    ISSN: 0887-3585 , 1097-0134
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 1475032-6
    SSG: 12
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