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IntroductionUnderstanding the role of water molecules in protein-ligand interactions is critical for rational drug design. Water molecules can mediate binding, stabilize conformations, or even act as bridges between ligands and their targets. In this workflow, we will compare the positions of water molecules across multiple protein-ligand complexes to identify those that are conserved and potentia

BIOVIA DRUG DISCOVERY & DEVELOPMENT

PURPOSE: Converts molecules in the Molecule Window that have the same number of atoms into a single molecule with multiple conformations. This is a modified version of the script found in Scripts > Structure Editing > Molecules to ConformationsIn this version all Molecular properties and copied to the Conformations properties. In addition, if only one molecule is displayed or selected then the scr

BIOVIA DRUG DISCOVERY & DEVELOPMENT

Below are modified versions of the Calculate Mutation Energy (Stability) and Calculate Mutation Energy (Binding) protocols. These protocols take as input a protein structure file and a trajectory file (.dcd). The mutation energy is calculated for each frame in the trajectory and the average mutation energy and Standard Deviation are reported for each unique mutation. The output csv files contain a

BIOVIA DRUG DISCOVERY & DEVELOPMENT