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Inferring multi-target QSAR models with taxonomy-based multi-task learning.
Rosenbaum L, Dörr A, Bauer MR, Boeckler FM, Zell A. Rosenbaum L, et al. J Cheminform. 2013 Jul 11;5(1):33. doi: 10.1186/1758-2946-5-33. J Cheminform. 2013. PMID: 23842210 Free PMC article.
CONCLUSIONS: Multi-task learning is a valuable approach for inferring multi-target QSAR models for lead optimization. The application of multi-task learning is most beneficial if knowledge can be transferred from a similar task with a lot of in-domain knowled …
CONCLUSIONS: Multi-task learning is a valuable approach for inferring multi-target QSAR models for lead optimization. The application …
Optimization and visualization of the edge weights in optimal assignment methods for virtual screening.
Rosenbaum L, Jahn A, Dörr A, Zell A. Rosenbaum L, et al. BioData Min. 2013 Mar 26;6(1):7. doi: 10.1186/1756-0381-6-7. BioData Min. 2013. PMID: 23531368 Free PMC article.
BACKGROUND: Ligand-based virtual screening plays a fundamental part in the early drug discovery stage. In a virtual screening, a chemical library is searched for molecules with similar properties to a query molecule by means of a similarity func …
BACKGROUND: Ligand-based virtual screening plays a fundamental part in the early drug discovery stage. In a virtual screening, …
A ranking method for the concurrent learning of compounds with various activity profiles.
Dörr A, Rosenbaum L, Zell A. Dörr A, et al. J Cheminform. 2015 Jan 16;7(1):2. doi: 10.1186/s13321-014-0050-6. eCollection 2015. J Cheminform. 2015. PMID: 25643067 Free PMC article.
BACKGROUND: In this study, we present a SVM-based ranking algorithm for the concurrent learning of compounds with different activity profiles and their varying prioritization. To this end, a specific labeling of each compound was elaborated in order to infer virtual …
BACKGROUND: In this study, we present a SVM-based ranking algorithm for the concurrent learning of compounds with different activity …
SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology.
Dörr A, Keller R, Zell A, Dräger A. Dörr A, et al. Computation (Basel). 2014 Dec;2(4):246-257. doi: 10.3390/computation2040246. Epub 2014 Dec 18. Computation (Basel). 2014. PMID: 32211200 Free PMC article.
The identification of suitable model parameters for biochemical reactions has been recognized as a quite difficult endeavor. ...In a parameter estimation study based on a published model and artificial data we demonstrate the capability of SBMLsimulator to id …
The identification of suitable model parameters for biochemical reactions has been recognized as a quite difficult endeavor. ...In …
The systems biology simulation core algorithm.
Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Le Novère N, Hiroi N, Planatscher H, Zell A, Dräger A. Keller R, et al. BMC Syst Biol. 2013 Jul 5;7:55. doi: 10.1186/1752-0509-7-55. BMC Syst Biol. 2013. PMID: 23826941 Free PMC article.
We begin our consideration with a formal representation of the mathematical form of the models and explain all parts of the algorithm in detail, including several preprocessing steps. We provide a flexible reference implementation as part of the Systems Biology Simu …
We begin our consideration with a formal representation of the mathematical form of the models and explain all parts of the algorithm …
JSBML: a flexible Java library for working with SBML.
Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, Zell A, Hucka M. Dräger A, et al. Bioinformatics. 2011 Aug 1;27(15):2167-8. doi: 10.1093/bioinformatics/btr361. Epub 2011 Jun 22. Bioinformatics. 2011. PMID: 21697129 Free PMC article.
In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. ...JSBML also supports modules that can facilitate the devel …
In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java programming language, and can the …
pROC-Chemotype Plots Enhance the Interpretability of Benchmarking Results in Structure-Based Virtual Screening.
Ibrahim TM, Bauer MR, Dörr A, Veyisoglu E, Boeckler FM. Ibrahim TM, et al. J Chem Inf Model. 2015 Nov 23;55(11):2297-307. doi: 10.1021/acs.jcim.5b00475. Epub 2015 Oct 21. J Chem Inf Model. 2015. PMID: 26434782
Recently, we have reported a systematic comparison of molecular preparation protocols (using MOE or Maestro) in combination with two docking tools (GOLD or Glide), employing our DEKOIS 2.0 benchmark sets. ...
Recently, we have reported a systematic comparison of molecular preparation protocols (using MOE or Maestro) in combination with two …
Oxidative stress ecology on Pacific oyster Crassostrea gigas from lagoon and offshore Italian sites.
Elia AC, Burioli E, Magara G, Pastorino P, Caldaroni B, Menconi V, Dörr AJM, Colombero G, Abete MC, Prearo M. Elia AC, et al. Among authors: dorr ajm. Sci Total Environ. 2020 Jun 3;739:139886. doi: 10.1016/j.scitotenv.2020.139886. Online ahead of print. Sci Total Environ. 2020. PMID: 32554117
Oxidative stress ecology in brook trout (Salvelinus fontinalis) from a high-mountain lake (Cottian Alps).
Pastorino P, Elia AC, Caldaroni B, Menconi V, Abete MC, Brizio P, Bertoli M, Zaccaroni A, Gabriele M, Dörr AJM, Pizzul E, Prearo M. Pastorino P, et al. Among authors: dorr ajm. Sci Total Environ. 2020 May 1;715:136946. doi: 10.1016/j.scitotenv.2020.136946. Epub 2020 Jan 25. Sci Total Environ. 2020. PMID: 32007898
Human and mouse essentiality screens as a resource for disease gene discovery.
Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LMJ, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu CW, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon AM, Lloyd KCK, Brown SDM, Parkinson H, Meehan TF, Smedley D; Genomics England Research Consortium; International Mouse Phenotyping Consortium. Cacheiro P, et al. Nat Commun. 2020 Jan 31;11(1):655. doi: 10.1038/s41467-020-14284-2. Nat Commun. 2020. PMID: 32005800 Free PMC article.
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