RASMOT-3D PRO

RASMOT-3D PRO identifies structural motifs in 3D protein structures by detecting residue sets with specified topology to support protein engineering and scaffold selection.

Key Features:

• Systematic 3D Search: Performs systematic searches across 3D protein structures to identify residue sets with a specified topology by analyzing spatial arrangements and distances between alpha carbon (Cα) and beta carbon (Cβ) atoms.
• Input: Accepts PDB files containing the 3D coordinates of the motif of interest.
• Output: Produces a list of protein structures that contain residues with topology similar to the input motif.
• Comparative Metrics: Compares candidates using inter-atomic distance metrics and root-mean-square deviation (RMSD) between the motif and candidate residue sets.
• Database Sources: Can search user-supplied PDB files or entries from the Protein Data Bank (PDB).
• Scaffold Compatibility Assessment: Filters out protein scaffolds that are sterically incompatible with the target motif.

Scientific Applications:

• Protein Engineering: Enables selection of protein scaffolds suitable for motif transplantation in protein engineering projects.
• Motif Identification: Detects structural motifs and uncovers structural or functional similarities between proteins by topology matching.
• Design of Novel Proteins: Supports design of novel proteins with desired functions by locating compatible structural frameworks for motif insertion.
• Structure–Function Studies: Facilitates systematic mapping of motifs across structures to investigate protein structure–function relationships.

Methodology:

Performs systematic 3D searches comparing spatial arrangement and inter-atomic distances of Cα and Cβ atoms, computes RMSD for candidate matches, uses PDB files as input (user-supplied or from the Protein Data Bank), and rejects scaffolds with steric incompatibilities.