Protein-nucleic acid complexes are important for many cellular processes including the most essential functions such as transcription and translation. For many protein-nucleic acid complexes, flexibility of both macromolecules has been shown to be critical for specificity and/or function. The flexibility-rigidity index (FRI) has been proposed as an accurate and efficient approach for protein fl...

Computational docking of small-molecule ligands into protein receptors is an important tool for modern drug discovery. Although conformational adjustments are frequently observed between the free and ligand-bound states, the conformational flexibility of the protein is typically ignored in protein-small molecule docking programs. We previously described the program RosettaLigand, which leverage...

The “lock-and-key” model emphasizes the importance of shape complementarity between two rigid structures. It can not be used to explain the conformation changes before and after binding. The “induced fit” model considers the conformation change due to non-rigid protein interactions. A geometric fit is ensured only after the structure rearrangement of the base protein. In the preexisting equilib...

Atomic displacement parameters (ADPs) obtained from highresolution refinement of protein structures represent the mean square displacement of protein atoms from their centroid positions. They contain information regarding the flexibility of the polypeptide. Comparative analysis of the ADPs in homologous proteins shows that the local flexibility of the polypeptide is not correlated to the mutabi...

We describe a new method for modeling protein and ligand main-chain flexibility, and show its ability to model flexible molecular recognition. The goal is to sample the full conformational space, including large-scale motions that typically cannot be reached in molecular dynamics simulations due to the computational intensity, as well as conformations that have not been observed yet by crystall...