Qgrid

Qgrid identifies and clusters charged and hydrophobic regions in protein structures to characterize electrostatic and hydrophobic organization.

Key Features:

• Charge Assignment: Each atom is assigned a charge based on standard force fields.
• Spatial Grid Division: A three-dimensional bounding box of atomic coordinates is subdivided into cubic grids of user-defined size, each containing one or more charged atoms.
• Charge-Based Clustering: Cubic grids whose net charge exceeds a predefined threshold are grouped by hierarchical clustering using Euclidean distance.
• Tree Diagram Visualization: Clustered regions are represented as a tree diagram showing hierarchical relationships among charged and hydrophobic regions.
• Hydrophobic Cluster Analysis: Hydrophobic clusters are identified by grouping positions of C(alpha) atoms from hydrophobic residues.

Scientific Applications:

• Protein-Protein Interface Detection: Highlighting charged and hydrophobic clusters to predict potential protein-protein interaction sites.
• Structure Similarity Analysis: Comparing distributions of charged and hydrophobic clusters across proteins to assess structural similarity.
• Motif Detection: Detecting recurring charged or hydrophobic structural motifs that may relate to function or interaction.

Methodology:

Assign atomic charges using standard force fields; construct a 3D bounding box from atomic coordinates and subdivide it into cubic grids of user-defined size; compute net charge per grid and select grids exceeding a predefined threshold; group selected grids by hierarchical clustering using Euclidean distance; represent clustering as a tree diagram; identify hydrophobic clusters by grouping C(alpha) atom positions of hydrophobic residues.