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Examples for Molecular Structure Generation
The general strategy for setting up the molecular
structure for a combination of proteins, water,
substrates, ligands, and/or nucleic acids is:
- Split the original coordinate file into several files containing the segments. A segment is defined as a protein with one continuous polypeptide chain, a continuous protein chain, a substrate, a cofactor, a ligand, all water molecules combined, or a single nucleic acid strand.
- Generate each segment separately.
- If necessary, apply appropriate patches to establish covalent links between segments or within segments, such as disulfide bridges.
Subsections
- What to Do about Unknown Atoms
- A Standard Protein Structure
- How to Set Up Unusual Geometries
- A Protein Structure with Water or Ligands
- A Protein Structure with a Cofactor or Substrate
- A Protein Structure with a Metal Cluster
- A Nucleic Acid Structure
- Virus Structures or Structures with Many Identical Units
Xplor-NIH 2025-03-21