User Guide

This section explains the basics of using MolCube-API Client, and shows some examples of common operations. For an in-depth description of the available modules, functions, classes, etc., see API Reference.

Contents:

• PDB Reader
  • Background
  • Overview
  • Create PDB Reader project
  • Check available info about PDB
  • Check default settings
  • Chain selection
  • Usage example
  • Confirm chain selection (required)
  • Model manipulation (required)
  • Terminal patching
  • Mutations
  • Phosphorylation and Protonation
  • Disulfide bonds
  • Stapling
• Glycosylation
  • Check default GLYC Chains
  • Understanding Glycosylation Structure
  • Building a Glycosylation Structure
  • Managing Glycosylations in PDBReader
  • Common Errors and Constraints
• Solution Builder
  • Create Solution Builder project
• Membrane Builder
  • Create Membrane Builder Project
• Ligand Modeler
  • Create Ligand Modeler project
  • Modify SDF file (optional)
• Free Energy
  • Creating a Alchemical Free Energy Simulator Project
  • AMBER-TI Relative Binding