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  • Identifiers in PDB - RCSB PDB
    Each polymer and non-polymer has a separate chain ID, with the exception of chain IDs for solvents In the "auth" system the solvent (and ligand) is assigned a chain ID to match the chain ID of the polymer close to the groups
  • Chains and Chain IDs - Proteopedia, life in 3D
    Consistent with the chain ID assignment policies of the wwPDB for mmCIF files, every entity is assigned a unique chain ID, including polymer chains, ligands, metal ions, and glycans including oligo- and monosaccharides The following three examples are provided by the Server
  • Tutorial: Ligand Fitting with Coot - MRC Laboratory of . . .
    In this tutorial, we will build a ligand and search the density for this ligand, add the ligand to main protein molecule and refine and validate the ligand This protein is the catalytic domain of poly(ADP-ribose)polymerase 2 crystallised from PEG 3350 (polyethylene glycol), Tris and cryoprotected using glycerol
  • Recognizing and validating ligands with CheckMyBlob - PMC
    Ligand identification can be aided by automatic methods such as CheckMyBlob, a machine learning algorithm that learns to generalize ligand descriptions from sets of moieties deposited in the Protein Data Bank
  • Protein and ligand preparation: parameters, protocols, and . . .
    In this work, we systematically explore each of the steps involved in preparing a system for virtual screening We first explore a large number of parameters using the Glide validation set of 36 crystal structures and 1,000 decoys We then apply a subset of protocols to the DUD database
  • Rosetta Projects: Ligand Dock Application - Rosetta Commons
    Here is a "checklist" for setting up a ligand docking experiment Details for all the steps are given below Protein receptor in PDB format with no waters or cofactors; each metal ion should have a unique chain ID Cofactors, if any, should be in sdf or mol2 format, with coordinates taken from the original PDB file





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