… pose a fundamental barrier to the problem of ligand design. (Developing the understanding
necessary to solve this very difficult problem has not been helped by the erosion of the place …

… consisting of three proteins, cyclin-dependent kinase 2 (CDK2), heat shock protein 90 alpha
(… We prepared 20 binding poses that included one or more ‘correct’ poses for each complex. …

… ligands binding to proteins. The power of structural biology is in translating knowledge of
protein structures into insights about their forces, binding… A pose is one conformation of a ligand …

… the geometrical change of the ligand relative to the protein, dRMS can be used to classify
the binding poses. For each protein–ligand complex, we treated the docking pose as the …

… correct and incorrect ligand poses under MD … ligand is docked back to its cognate protein.
We then evaluate the relative stability of various ligand binding poses (correct/decoy poses) …

… prediction of protein–ligand binding sites and ligand-binding poses. The protein–ligand
binding sites are … The ligands from the users or the templates are then docked into the predicted …

… The 3D structures of the protein–ligand poses employed in the present manuscript were
obtained from the Supporting Information of the publication by Clark et al. (10) All systems were …

… yield accurate binding pose information even when the “predicted” protein chemical shifts …
; diamagnetic protein statistics). The results are shown to improve with more accurate protein …

… Given the protein structure and the ligand on the true ligand position (the position of ligand
as in the crystal structure from the PDB), we at first randomly rotate the whole structure, and …

… correct ligand binding pose … protein–ligand binding poses obtained from crystal structures,
identified using both RSCC value and analysis of the ED maps. It is hypothesized that ligands …