#10 · Structural bio & protein design

Docking workflows are coupling pose validation and MD setup into end-to-end pipelines

The common thread is automation of structural modeling workflows, in which individual steps are packaged into reproducible, scriptable, or web-accessible pipelines. The docking-specific item, CHARMM-GUI Ligand Docker, unifies AutoDock Vina, Smina, RxDock, and DiffDock on one platform, applies PoseBuster filtering to generated poses, and hands the resulting systems to MD system setup, coupling pose validation directly to simulation preparation. MartiniSurf similarly automates GROMACS-ready Martini coarse-grained builds for surface-immobilized protein and DNA systems, and GYDE provides bench-accessible web access to structure prediction and design tools. MXtalTools, GlycoDiveR, and the GPCR activation analysis address different problems (machine learning on molecular crystals, glycopeptide data visualization, and experimental structure mining) and do not involve docking directly. What is new here is the integration of docking with validation and simulation setup rather than docking methods themselves.