Water is a key actor of various processes of nature and, therefore, molecular engineering
has to take the structural and energetic consequences of hydration into account. While the …

Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately
determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere …

Coot is a molecular-graphics program primarily aimed at model building using X-ray data.
Recently, tools for the manipulation and representation of ligands have been introduced …

Remarkable success in engineering novel efficient biomarkers based on fluorescent and
photoactive proteins provokes a question of whether computational modeling of their …

The anticancer activity of platinum-containing drugs such as cisplatin and carboplatin is
considered to primarily arise from their interactions with nucleic acids; nevertheless, these …

Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-
density maps often inhibit the building of complete structural models during X-ray structure …

Schistosomiasis is caused by parasites of the genus Schistosoma, which infect more than
200 million people. Praziquantel (PZQ) has been the main drug for controlling …

In this review, we address a fundamental question: What is the range of conformational
energies seen in ligands in protein‐ligand crystal structures? This value is important …

Membrane-bound pyrophosphatases (M-PPases) are homodimeric primary ion pumps that
couple the transport of Na+-and/or H+ across membranes to the hydrolysis of …

Different methods for tunnel identification, geometry-based and small-molecule tracking
approaches, were compared to provide their benefits and pitfalls. Results obtained for both …