Physical Biosciences Division, Lawrence Berkeley National Laboratories, One Cyclotron Road, Berkeley, CA 94720, USA.
J Struct Biol. 2012 Oct;180(1):226-34. doi: 10.1016/j.jsb.2012.05.011. Epub 2012 Jun 1.
Small angle X-ray scattering (SAXS) experiments are widely applied in structural biology. The SAXS experiments yield one-dimensional profile that needs further analysis to reveal structural information. The pair distance distribution function (PDDF), P(r), can provide molecular structures more intuitively, and it can be used to guide ab initio model reconstructions, making it a critical step to derive P(r) from experimental SAXS profiles. To calculate the P(r) curves, a new method based on a specially designed parametric functional form is developed, and implemented in pregxs. This method is tested against both synthetic and experimental data, the estimated P(r) functions are in good agreement with correct or known P(r). The method can also predict the molecular size. In summary, the pregxs method is robust and accurate in P(r) determination from SAXS profiles. The pregxs source code and an online server are available at http://www.sastbx.als.lbl.gov.
小角 X 射线散射（SAXS）实验在结构生物学中得到了广泛应用。SAXS 实验产生的一维谱需要进一步分析才能揭示结构信息。对距离分布函数（PDDF），P(r)，可以更直观地提供分子结构，它可以用来指导从头模型重建，因此从实验 SAXS 谱中导出 P(r)是一个关键步骤。为了计算 P(r)曲线，开发了一种基于特殊设计的参数函数形式的新方法，并在 pregxs 中实现。该方法针对合成数据和实验数据进行了测试，估计的 P(r)函数与正确或已知的 P(r)吻合较好。该方法还可以预测分子大小。总之，pregxs 方法在从 SAXS 谱中确定 P(r)方面具有稳健性和准确性。pregxs 的源代码和在线服务器可在 http://www.sastbx.als.lbl.gov 获得。
