Clustering protein motif structures.
You can directly use this tool.
This tool requires a Python version >=3.7, as well as some basic libraries biopython 1.78 and numpy.
The structure of this tool is shown below:
├── cluster.py // Cluster based on the similarity of three-dimensional structures
│ ├── Motif // Motif class contains the segment and structure information
│ ├── collect_motifs // Collect motifs (by k-mer method) from the amino acid sequence
│ ├── cluster_motifs // Cluster motif structures based on depth first search as connected components of undirected graphs
│ ├── calculate_concentration // Calculate the structure cluster concentration of a type of motif
├── comparator.py // Comparator of structures
│ ├── align // Rotate candidate structure unto reference structure using Kabsch algorithm based on each position
│ ├── Similarity // Abstract similarity method class
│ ├── GMD // Similarity method class (global maximum distance)
│ ├── GMV // Similarity method class (global maximum vector)
│ ├── RMSD // Similarity method class (root-mean-square deviation)
│ ├── TMScore // Similarity method class (template modeling score; TM-score)
│ ├── GDTScore // Similarity method class (global distance test score; GDT-score)
├── converter.py // Converter between PDB files and structures (with related information)
│ ├── get_peptides // Obtain peptides from a PDB file
│ ├── get_structures // Obtain secondary structure information from a PDB file
│ ├── set_motif_file // Save structure information to a PDB file
├── README.md // Description document of library