Analysis script for Supervised Molecular Dynamics (SuMD) trajectories
N.B.: the Python code to run SuMD simulations can be found at github.com/molecularmodelingsection/SuMD
Reference publication:
"Investigating RNA-Protein Recognition Mechanisms through Supervised Molecular Dynamics (SuMD) Simulations."
Pavan M., Bassani D., Sturlese M., Moro S. NAR Genomics and Bioinformatics https://doi.org/10.1093/nargab/lqac088
SuMD-analyzer is a Python code that can be utilized to analyze Supervised Molecular Dynamics (SuMD) trajectories and is an evolution of the original tool by V. Salmaso, described in Salmaso, V.; Sturlese, M.; Cuzzolin, A.; Moro, S. Exploring Protein-Peptide Recognition Pathways Using a Supervised Molecular Dynamics Approach. Structure. 2017, 25,655–662.e2. Although the script has been originally developed to analyze trajectories involving RNA-protein complexes, it can be easily repurposed for the scope of analyzing trajectories containing peptide/small molecule ligands with small tweaks to the codebase. Generally speaking, we are actively working on making this script usable to analyze whatever trajectory involves the recognition between a receptor and a ligand, regardless of its origin.
The script allows performing both geometric and energetic analysis and is split into seven different analysis protocol:
-geometry: perform different geometric analyses on trajectory. This pool of analyses exploits the MDAnalysis (essential) and Barbaba Python package (only really required for working with nucleic acids).
-mmgbsa: performs MMGBSA calculation of the receptor-ligand interaction energy and plots the related profiles (AMBER >= 16 required). By default, the script points out to the $AMBERHOME, so if multiple instances of AMBER are installed within your machine you will have to manually edit the script or your environment variables in order to use the intended version.
-intEnergy: performs force field calculation of the receptor-ligand interaction energy and plots the related profiles. This protocol relies on VMD, the NAMD Energy plugin for VMD and NAMD as external dependencies.
-perResRec: performs and plots a receptor-based per-residue decomposition of the receptor-ligand interaction energy. This protocol relies on VMD, the NAMD Energy plugin for VMD and NAMD as external dependencies.
-perResLig: performs and plots a ligand-based per-residue decomposition of the receptor-ligand interaction energy. This protocol relies on VMD, the NAMD Energy plugin for VMD and NAMD as external dependencies (only useful if working with nucleic/peptide ligands, do not use when working with small molecules).
-matrix: performs and plots a 2D (receptor vs ligand) interaction energy matrix. This protocol relies on VMD, the NAMD Energy plugin for VMD and NAMD as external dependencies (only useful if working with nucleic/peptide ligands, do not use when working with small molecules).
-video: collects data from previous analyses and assembles a four-panel video. This script does NOT generate the trajectory snapshots for the movie generation: the user has to generate them separately using VMD (in the .tga format), put them in a folder called "frame" within the working directory.
Editable settings can be set at the beginning of the script. A YAML file is provided in order to reconstitute the right Python environment to make the script work. To run:
- conda activate rna-sumd
- python3 RNASuMDAnalyzer.py [protocol]