Many research groups and institutions have created a variety of databases curating
experimental and predicted data related to protein-ligand binding. The landscape of …

Motivation The discovery of protein–ligand-binding sites is a major step for elucidating
protein function and for investigating new functional roles. Detecting protein–ligand-binding …

The protein databank now contains the structures of over 11,000 ligands bound to proteins.
These structures are invaluable in applied areas such as structure-based drug design, but …

Protein binding sites undergo ligand specific conformational changes upon ligand binding.
However, most docking protocols rely on a fixed conformation of the receptor, or on the prior …

Predicting conformational changes of both the protein and the ligand is a major challenge
when a protein–ligand complex structure is predicted from the unbound protein and ligand …

We have investigated the efficacy of generating multiple sidechain conformations using a
rotamer library in order to find the experimentally observed ligand binding site conformation …

Computational design of binding sites in proteins remains difficult, in part due to limitations
in our current ability to sample backbone conformations that enable precise and accurate …

Abstract EvoDesign (https://zhanglab. ccmb. med. umich. edu/EvoDesign) is an online
server system for protein design. The method uses evolutionary profiles to guide the …

Proteins perform their functions mainly via active sites, whereas other parts of the proteins
comprise the scaffolds, which support the active sites. One strategy for protein functional …

Interactions between proteins and small molecules are critical for biological functions. These
interactions often occur in small cavities within protein structures, known as ligand-binding …