I have a collection (around 500) of peptide 3D structures (PDB file each 10 residues long and for a given sequence). I need to cluster it based on RMSD values among them. Is there any Python module or any other software which could do that and identify the distinct structural clusters among those 500 files?
Yes, and if I were you I would check out these:
MDAnalysis - a Python library that specializes in analyzing molecular dynamics simulations, including RMSD-based clustering. You can use its clustering module to perform hierarchical clustering or k-means clustering based on RMSD values.
MDTraj - another Python library for analyzing molecular dynamics simulations. It provides functions for RMSD-based clustering and analysis.
PyMOL - a popular molecular visualization tool that also provides some clustering capabilities. You can script PyMOL to calculate RMSD and perform clustering.
VMD (Visual Molecular Dynamics) - a molecular visualization and analysis program that can be used for clustering 3D structures based on RMSD. It offers various analysis tools and scripting capabilities.
If you're familiar with GROMACS, a widely used molecular dynamics simulation software, it also offers tools for clustering based on RMSD. You can use the gmx cluster command for this purpose.
RDKit - while primarily focused on cheminformatics, it can be used to calculate RMSD between molecular structures and perform clustering.
Scikit-learn - if you're comfortable with machine learning, you can use Scikit-learn to perform clustering. You would need to calculate RMSD values separately and then use Scikit-learn's clustering algorithms.
Vladan Nedelkovski thanks for the reply. However, MDAnalysis takes in only PSF files and not PDF files. I have already computed the distance matrix and based on which I wanted to do the clustering. I have computed an RMSD-based distance matrix between every pair of structures. Still, I couldn't cluster it properly.
- Badges
- Science topic