An ultrafast and accurate scoring function for protein–protein docking is presented. It
includes (1) a molecular mechanics (MM) part based on a 12–6 Lennard-Jones potential;(2) …

Deciphering the structural determinants of protein–protein interactions (PPIs) is essential to
gain a deep understanding of many important biological functions in the living cells …

To aid the evaluation of protein-protein complex model structures generated by protein
docking prediction (decoys), we previously developed a method to calculate the binding free …

A method for evaluating binding free energy differences of protein-protein complex
structures generated by protein docking was recently developed by some of us. The method …

Understanding protein–protein interactions (PPIs) is quite important to elucidate crucial
biological processes and even design compounds that interfere with PPIs with …

The accurate prediction of protein–protein complex geometries is of major importance to
ultimately model the complete interactome of interacting proteins in a cell. A major …

Protein–protein interactions are fundamental for the majority of biological processes, so their
structural, functional, and energetic characterization is of enormous biotechnological and …

Crystallization of protein–protein complexes can often be problematic and therefore
computational structural models are often relied on. Such models are often generated using …

A detailed error analysis is presented for the computation of protein− ligand interaction
energies. In particular, we show that it is probable that even highly accurate computed …

In a previous paper, we described a novel empirical free energy function that was used to
accurately predict experimental binding free energies for a diverse test set of 31 protein …