Small-angle X-ray scattering from RNA, proteins, and protein complexes

J Lipfert, S Doniach - Annu. Rev. Biophys. Biomol. Struct., 2007 - annualreviews.org
Small-angle X-ray scattering (SAXS) is increasingly used to characterize the structure and
interactions of biological macromolecules and their complexes in solution. Although still a …

Integrating diverse data for structure determination of macromolecular assemblies

F Alber, F Förster, D Korkin, M Topf… - Annu. Rev. Biochem., 2008 - annualreviews.org
To understand the cell, we need to determine the macromolecular assembly structures,
which may consist of tens to hundreds of components. First, we review the varied …

Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies

F Förster, B Webb, KA Krukenberg, H Tsuruta… - Journal of molecular …, 2008 - Elsevier
A major challenge in structural biology is to determine the configuration of domains and
proteins in multidomain proteins and assemblies, respectively. All available data should be …

[图书][B] Proteins: energy, heat and signal flow

DM Leitner, JE Straub - 2009 - taylorfrancis.com
Computational modeling can provide a wealth of insight into how energy flow in proteins
mediates protein function. Computational methods can also address fundamental questions …

A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein …

S Yang, S Park, L Makowski, B Roux - Biophysical journal, 2009 - cell.com
We present a coarse residue-based computational method to rapidly compute the solution
scattering profile from a protein with dynamical fluctuations. The method is built upon a …

A new method for coarse-grained elastic normal-mode analysis

M Lu, B Poon, J Ma - Journal of chemical theory and computation, 2006 - ACS Publications
In this paper, we report a new method for coarse-grained elastic normal-mode analysis. The
purpose is to overcome a long-standing problem in the conventional analysis called the tip …

Improving coarse-grained protein force fields with small-angle X-ray scattering data

AP Latham, B Zhang - The Journal of Physical Chemistry B, 2019 - ACS Publications
Small-angle X-ray scattering (SAXS) experiments provide valuable structural data for
biomolecules in solution. We develop a highly efficient maximum entropy approach to fit …

OPUS‐Ca: A knowledge‐based potential function requiring only Cα positions

Y Wu, M Lu, M Chen, J Li, J Ma - Protein science, 2007 - Wiley Online Library
In this paper, we report a knowledge‐based potential function, named the OPUS‐Ca
potential, that requires only Cα positions as input. The contributions from other atomic …

Structural analysis of flexible proteins in solution by small angle X-ray scattering combined with crystallography

SE Tsutakawa, GL Hura, KA Frankel, PK Cooper… - Journal of structural …, 2007 - Elsevier
In the last few years, SAXS of biological materials has been rapidly evolving and promises to
move structural analysis to a new level. Recent innovations in SAXS data analysis allow ab …

Accurate flexible fitting of high-resolution protein structures to small-angle x-ray scattering data using a coarse-grained model with implicit hydration shell

W Zheng, M Tekpinar - Biophysical journal, 2011 - cell.com
Small-angle x-ray scattering (SAXS) is a powerful technique widely used to explore
conformational states and transitions of biomolecular assemblies in solution. For accurate …