Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, United States.
Methods Enzymol. 2023;678:145-192. doi: 10.1016/bs.mie.2022.09.018. Epub 2022 Nov 3.
Ab initio modeling methods have proven to be powerful means of interpreting solution scattering data. In the absence of atomic models, or complementary to them, ab initio modeling approaches can be used for generating low-resolution particle envelopes using only solution scattering profiles. Recently, a new ab initio reconstruction algorithm has been introduced to the scientific community, called DENSS. DENSS is unique among ab initio modeling algorithms in that it solves the inverse scattering problem, i.e., the 1D scattering intensities are directly used to determine the 3D particle density. The reconstruction of particle density has several advantages over conventional uniform density modeling approaches, including the ability to reconstruct a much wider range of particle types and the ability to visualize low-resolution density fluctuations inside the particle envelope. In this chapter we will discuss the theory behind this new approach, how to use DENSS, and how to interpret the results. Several examples with experimental and simulated data will be provided.
从头计算建模方法已被证明是解释溶液散射数据的有力手段。在没有原子模型的情况下,或者作为其补充,从头计算建模方法可用于仅使用溶液散射曲线来生成低分辨率的粒子包络。最近,一种新的从头计算重构算法已被引入科学界,称为 DENSS。与其他从头计算建模算法相比,DENSS 具有独特性,它可以解决逆散射问题,即直接使用一维散射强度来确定三维粒子密度。与传统的均匀密度建模方法相比,粒子密度重构具有多个优势,包括能够重构更广泛的粒子类型和能够可视化粒子包络内的低分辨率密度波动。在本章中,我们将讨论该新方法的理论、如何使用 DENSS 以及如何解释结果。将提供几个带有实验和模拟数据的示例。