Atomic structures of protein-ligand complexes can aid scientists in therapeutic discovery through structure-based drug design and the understanding of biological processes in disease. X-ray crystallography is one way to obtain accurate, high-resolution structures of these complexes. X-ray solution scattering (XSS) is a complimentary method that yields lower resolution structural information but is advantageous due to it being high throughput at modern X-ray sources and applicable to a wide range of targets including soluble and membrane proteins and RNA/DNA. DENSS is a unique algorithm that utilizes solution scattering data to perform ab-initio three-dimensional electron density reconstruction of these targets. A common application of XSS is often for screening different conditions, such as a protein bound to a ligand followed by a protein in its unbound state. For these experiments, the scattering profile of the unbound state is subtracted from the bound state to generate a XSS difference profile. It is often the case in these types of experiments that the target protein structure is well characterized; however, the bound state of a small molecule remains unknown. Here, we present our latest developments of DENSS, where we provide known structural density of a protein coupled with an XSS difference scattering profile to increase the resolution of the reconstructed electron density of protein-ligand complexes. We demonstrate multiple cases where DENSS performs ab-initio reconstruction of ligand density at high-resolution and the ability to discern between small molecules from information within XSS difference profiles. Overall, these developments along with the capability to perform XSS at room temperature and in high throughput lead to the advancement of methods in structural biology and therapeutic discovery.
Chamberlain et al. (2026) studied this question.