Perspective on a large-scale ligand structure characterization

An introduction to a set of three related papers in this issue describing 216 ligand-bound fatty acid-binding protein structure determinations and the pitfalls that can arise in such a study.

Probabilistic single-particle cryo-EM ab initio 3D reconstruction in SIMPLE

We introduce a new approach to probabilistic multi-volume single-particle cryo-EM ab initio 3D reconstruction for simultaneous estimation of the relative particle 3D orientations and partitioning of the particles into groups with distinct structural states.

Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps

Q-scores are calculated for atomic models derived from 3D electron microscopy maps, measure how well the model fits the map and reflect the quality of the map itself. Here, we develop a statistical model for Q-scores applied to many maps and models in the EMDB and PDB, respectively, and show how it can be used to assess the reliability of entire models as well as their subcomponents.

A high-resolution data set of fatty acid-binding protein structures. I. Dynamics of FABP4 and ligand binding

NMR studies on human FABP4 in solution and bound to micelles and bicelles delineate its dynamics in a ligand-dependent fashion. Residual ligands are co-purified with the protein, which may negatively influence binding studies with low-affinity ligands.

A high-resolution data set of fatty acid-binding protein structures. II. Crystallographic overview, ligand classes and binding pose

A high-quality set of 229 crystal structures of various isoforms of human and mouse fatty acid-binding proteins in apo and ligand-bound forms is presented. Many ligands have associated affinity data, which may help in the development of affinity- and pose-predicting algorithms.

A high-resolution data set of fatty acid-binding protein structures. III. Unexpectedly high occurrence of wrong ligands

Very high-resolution fatty acid-binding protein structures identified a substantial number of ligands that differ strongly from their expected structure. If different ligand chemistry is a potentially overlooked problem in other, lower resolution, crystal structures of protein–ligand complexes, it has repercussions for any study using such structures, particularly when training machine-learning algorithms.

Time-Resolved Methods in Structural Biology, Methods in Enzymology Volume 709

Rolf Peter Hilgenfeld (1954–2025)

Rolf Hilgenfeld lived a life in the fast lane, devoted entirely to science, in which he absorbed a wealth of knowledge, conscientiously created new knowledge and passionately passed it on to his students.