Simplified free energy calculations based on force field energy estimates of ligand− receptor
interactions and thermal conformational sampling have emerged as a useful tool in structure …

Proteinases perform many beneficial functions that are essential to life, but they are also
dangerous and must be controlled. Here we focus on one of the control mechanisms: the …

The ability of proteins to establish highly selective interactions with a variety of (macro)
molecular partners is a crucial prerequisite to the realization of their biological functions. The …

Motivation: Empirical models for the prediction of how changes in sequence alter protein–
protein binding kinetics and thermodynamics can garner insights into many aspects of …

Serine proteases and their natural protein inhibitors are among the most intensively studied
protein complexes. About 20 structurally diverse inhibitor families have been identified …

Formation of protein–ligand complexes causes various changes in both the receptor and the
ligand. This review focuses on changes in pK and protonation states of ionizable groups that …

To the Editor: Reliable and fast computation of protein free energy is crucial for protein-
structure analysis, structure-based protein design and protein docking. Rigorous treatments …

Publisher Summary This chapter gives an overview of some different methods for calculating
ligand binding free energies that are all based on force fields and conformational sampling …

The pancreatic Kunitz inhibitor, also known as aprotinin, bovine basic pancreatic trypsin
inhibitor (BPTI), and trypsin-kallikrein inhibitor, is one of the most extensively studied …

Kunitz type proteins are an important group of ubiquitous protease inhibitors found spanning
the evolutionary tree from microbes to mammals. These proteins can have single or multiple …