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- 저자 : Ehlen, Asa (검색결과 2 건)
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Hoobas: A highly object-oriented builder for molecular dynamics
Girard, Martin,Ehlen, Ali,Shakya, Anisha,Bereau, Tristan,de la Cruz, Monica Olvera Elsevier 2019 Computational materials science Vol.167 No.-
<P><B>Abstract</B></P> <P>Polydispersity and random sequences are ubiquitous features of polymers, and molecular dynamics simulations can help elucidate the impact of disorder in polymer systems. However, currently available packages for building polymer topologies do not enable the user to include randomness in a straightforward fashion. Here, we introduce Hoobas, a molecular builder package that easily handles polydispersity using a prototype-builder design pattern. This enables fast and easy building of systems comprised of thousands of distinct objects. It is written in the Python programming language, which ensures compatibility with a wide range of molecular dynamics packages and tools, as well as easy integration into most workflows.</P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>
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<i>BRCA2</i> Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer
Shimelis, Hermela,Mesman, Romy L.S.,Von Nicolai, Catharina,Ehlen, Asa,Guidugli, Lucia,Martin, Charlotte,Callé,ja, Fabienne M.G.R.,Meeks, Huong,Hallberg, Emily,Hinton, Jamie,Lilyquist, Jenna,Hu, American Association for Cancer Research 2017 Cancer Research Vol.77 No.11
<P>These results show how BRCA2 missense variants that partially influence protein function can confer clinically relevant increased risks of breast cancer, with potential implications for risk management of women who harbor specific variants.</P><P>Breast cancer risks conferred by many germline missense variants in the <I>BRCA1</I> and <I>BRCA2</I> genes, often referred to as variants of uncertain significance (VUS), have not been established. In this study, associations between 19 BRCA1 and 33 BRCA2 missense substitution variants and breast cancer risk were investigated through a breast cancer case–control study using genotyping data from 38 studies of predominantly European ancestry (41,890 cases and 41,607 controls) and nine studies of Asian ancestry (6,269 cases and 6,624 controls). The BRCA2 c.9104A>C, p.Tyr3035Ser (OR = 2.52; <I>P</I> = 0.04), and BRCA1 c.5096G>A, p.Arg1699Gln (OR = 4.29; <I>P</I> = 0.009) variant were associated with moderately increased risks of breast cancer among Europeans, whereas BRCA2 c.7522G>A, p.Gly2508Ser (OR = 2.68; <I>P</I> = 0.004), and c.8187G>T, p.Lys2729Asn (OR = 1.4; <I>P</I> = 0.004) were associated with moderate and low risks of breast cancer among Asians. Functional characterization of the BRCA2 variants using four quantitative assays showed reduced BRCA2 activity for p.Tyr3035Ser compared with wild-type. Overall, our results show how BRCA2 missense variants that influence protein function can confer clinically relevant, moderately increased risks of breast cancer, with potential implications for risk management guidelines in women with these specific variants. <I>Cancer Res; 77(11); 2789–99. ©2017 AACR</I>.</P>
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