P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.

The interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, ...

One is a protein cutout model, whereby a set of protein atoms in and around the binding site are carved out, dangling bonds are capped with hydrogens, and only atoms directly in the protein binding ...

revealing that overlapping lipid contacts can partially compensate for the effects of binding site mutations. Extending our insights to naturally occurring proteins, we identify a stabilizing CDL site ...

“One often overlooked parameter is the exact binding site of your antibody on the protein of interest, also known as the epitope,” says Danielle Callahan, director of global product management ...

In this paper, the authors present an interesting strategy to interfere with the HBV life cycle: the preparation of geranyl and peptides' dimers that could impede the correct assembly of hepatitis B ...

P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.

These calculations are force-field-based and sample the whole complex (protein and ligand) in solvent. As an alternative, we used a DFT-based approach in which only a minimal model was considered for ...

Most of these antibiotics are produced outside the ribosome, the cellular structure responsible for protein synthesis ... a novel structure, a new binding site, and a distinct mechanism of ...

Based on these results combined with previous research, the authors suggest that MDGA2 and BDNF maintain a natural balance by competing with each other for TrkB protein binding sites, and disruption ...