Interactions between proteins are orchestrated in a precise and time-dependent manner,
underlying cellular function. The binding affinity, defined as the strength of these …

New molecular modeling approaches, driven by rapidly improving computational platforms,
have allowed many success stories for the use of computer-assisted drug design in the …

Despite recent success in computational design of structured cyclic peptides, de novo
design of cyclic peptides that bind to any protein functional site remains difficult. To address …

The value of thoroughly understanding the thermodynamics specific to a drug
discovery/design study is well known. Over the past decade, the crucial roles of water …

Mitochondrial cytochrome c oxidase (C c O) transfers electrons from cytochrome c (Cyt. c) to
O2 to generate H2O, a process coupled to proton pumping. To elucidate the mechanism of …

Abstract Structure-based virtual screening is currently an established tool in drug lead
discovery projects. Although in the last years the field saw an impressive progress in terms …

A MMGBSA variant (here referred to as Nwat-MMGBSA), based on the inclusion of a certain
number of explicit water molecules (Nwat) during the calculations, has been tested on a set …

Deciphering antibody‐protein antigen recognition is of fundamental and practical
significance. We constructed an antibody structural dataset, partitioned it into human and …

Antibodies recognize protein antigens with exquisite specificity in a complex aqueous
environment, where interfacial waters are an integral part of the antibody–protein complex …

Some water molecules in binding sites are important for intermolecular interactions and
stability. The way binding site explicit water molecules are dealt with affects the diversity and …