Geo-Measures

Geo-Measures performs geometric and trajectory analyses of protein structures from molecular dynamics (MD) simulations to quantify structural dynamics and extract geometric and statistical descriptors.

Key Features:

• Comprehensive Analysis Tools: Supports 14 distinct types of analyses, including Probability Density Function (PDF), Root Mean Square Deviation (RMSD), Radius of Gyration (RG), Free Energy Landscape (FEL), Principal Component Analysis (PCA), Ramachandran map, Root Mean Square Fluctuation (RMSF), Define Secondary Structure of Proteins (DSSP), and Modevectors.
• Integration with PyMOL: Integrates with PyMOL to enable visualization and interpretation of protein structures and MD trajectories.
• MDTraj-based Trajectory Analysis: Leverages the MDTraj library for parsing and analyzing molecular dynamics trajectory files.

Scientific Applications:

• MD trajectory analysis of biomolecular systems: Extracts structural and dynamical information from MD simulation trajectory files for biomolecular studies.
• Hemoglobin analysis: Applied to an MD trajectory from the MoDEL MD bank to compute RMSD, RG, FEL, and PCA for hemoglobin structural dynamics.
• Ecto-5'-nucleotidase study: Applied to a LiGRO-generated trajectory to analyze carbon alpha pincer angles, secondary structure via DSSP, and Modevectors for ecto-5'-nucleotidase.

Methodology:

Uses MDTraj for MD trajectory parsing and analysis and performs analyses such as PDF, RMSD, RG, FEL, PCA, Ramachandran maps, RMSF, DSSP, and Modevectors; demonstrated on trajectories from the MoDEL MD bank and LiGRO.