Estimation of the protein–ligand interaction energy for model building and validation

The use of the protein–ligand interaction energy as an additional parameter for the automated identification of crystallographic ligands and its applicability to structure validation are described.

Tools for ligand validation in Coot

The current tools of Coot for ligand validation and comparison in are presented. The user-selected ligand is assessed by ligand-distortion and map-correlation metrics, and compared with those of ligands of the wwPDB to create a percentile rank.

Twilight reloaded: the peptide experience

The potential causes of the misinterpretation of peptide density in a significant number of protein–peptide complex structures are analyzed, together with suggestions for good practice and specific education aimed at minimizing overinterpretation and mistakes in protein–peptide complex structure models.

CheckMyMetal: a macromolecular metal-binding validation tool

The metal-site validation tool CheckMyMetal is described, with examples to follow.

Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis

A guide to how the Cambridge Structural Database can be used to aid macromolecular crystallography.

The use of small-molecule structures to complement protein–ligand crystal structures in drug discovery

Small-molecule crystal structures are of tremendous value in understanding protein–ligand complexes, both individually and as a collection.

Gentle, fast and effective crystal soaking by acoustic dispensing

A high-throughput method is described for crystal soaking using acoustic droplet ejection, and its effectiveness is demonstrated.

Proper modelling of ligand binding requires an ensemble of bound and unbound states

The importance of modelling the superpositions of ligand-bound and unbound states that commonly occur in crystallographic data sets is emphasized and demonstrated. The generation of an ensemble that models not only the state of interest is important for the high-quality refinement of low-occupancy ligands, as well as to explain the observed density more completely.

The XChemExplorer graphical workflow tool for routine or large-scale protein–ligand structure determination

XChemExplorer is a graphical workflow and data-management tool for the parallel determination of protein–ligand complexes. Its implementation, usage and application are described here.

WONKA and OOMMPPAA: analysis of protein–ligand interaction data to direct structure-based drug design

The background to and development of WONKA and OOMMPPAA, tools for structure-based drug design, are described.