VPLG

VPLG constructs protein-ligand graphs from atomic coordinates in PDB files to represent secondary structure elements and ligands and analyze their contacts and spatial relationships for studies of protein–ligand interactions and structural motifs.

Key Features:

• Graph computation: Computes protein-ligand graphs derived from atomic coordinates in PDB files.
• DSSP integration: Integrates secondary structure assignments provided by the DSSP algorithm to identify secondary structure elements (SSEs).
• Vertex representation: Represents vertices as SSEs such as alpha helices and beta sheets or as ligand molecules.
• Edge representation: Depicts edges that encode contacts and spatial relationships between SSEs and ligands.
• Super-secondary level: Operates at the super-secondary structure level to capture higher-order topology.
• Motif search: Enables search for specific protein structural motifs within topology graphs.
• API support: Provides an application programming interface (API) to support automated analysis of protein topology.

Scientific Applications:

• Protein–ligand interaction analysis: Analysis of interactions between ligands and secondary structure elements to inform binding studies.
• Structural motif identification: Identification and comparison of conserved structural motifs within proteins.
• Functional inference: Elucidation of functional implications of protein topology and super-secondary arrangements.
• Drug discovery and molecular biology: Support for investigations relevant to drug discovery and molecular biology research.

Methodology:

Computes graphs from atomic coordinates in PDB files, uses DSSP for secondary structure assignment, constructs vertices for SSEs and ligands, and defines edges based on contacts and spatial relationships.