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WAXSiS：一个基于显式溶剂分子动力学计算小角X射线散射/广角X射线散射曲线的网络服务器。

WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics.

作者信息

Knight Christopher J, Hub Jochen S

机构信息

Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.

Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany

出版信息

Nucleic Acids Res. 2015 Jul 1;43(W1):W225-30. doi: 10.1093/nar/gkv309. Epub 2015 Apr 8.

DOI:10.1093/nar/gkv309
PMID:25855813
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4489308/
Abstract

Small- and wide-angle X-ray scattering (SWAXS) has evolved into a powerful tool to study biological macromolecules in solution. The interpretation of SWAXS curves requires their accurate predictions from structural models. Such predictions are complicated by scattering contributions from the hydration layer and by effects from thermal fluctuations. Here, we describe the new web server WAXSiS (WAXS in solvent) that computes SWAXS curves based on explicit-solvent all-atom molecular dynamics (MD) simulations (http://waxsis.uni-goettingen.de/). The MD simulations provide a realistic model for both the hydration layer and the excluded solvent, thereby avoiding any solvent-related fitting parameters, while naturally accounting for thermal fluctuations.

摘要

小角和广角X射线散射（SWAXS）已发展成为研究溶液中生物大分子的强大工具。对SWAXS曲线的解释需要从结构模型对其进行准确预测。由于水化层的散射贡献和热涨落的影响，这种预测变得复杂。在这里，我们描述了新的网络服务器WAXSiS（溶剂中的WAXS），它基于显式溶剂全原子分子动力学（MD）模拟来计算SWAXS曲线（http://waxsis.uni-goettingen.de/）。MD模拟为水化层和排除溶剂提供了一个现实的模型，从而避免了任何与溶剂相关的拟合参数，同时自然地考虑了热涨落。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9173/4489308/b1c8b63102e6/gkv309fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9173/4489308/e24ce935bee6/gkv309fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9173/4489308/be2f6727753a/gkv309fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9173/4489308/b1c8b63102e6/gkv309fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9173/4489308/e24ce935bee6/gkv309fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9173/4489308/be2f6727753a/gkv309fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9173/4489308/b1c8b63102e6/gkv309fig3.jpg

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