PENSA

PENSA enables comprehensive analysis of biomolecular conformational ensembles through feature transformations, comparison of conformational distributions, and identification of allosteric pathways.

Key Features:

• Featurization and Feature Transformations: PENSA provides complete representation of biomolecules including proteins, nucleic acids, water and ion binding sites, avoiding bias from manual feature selection.
• Ensemble Comparison: PENSA implements methods to systematically compare distributions of molecular features across ensembles to find significant differences and identify regions of interest.
• State-Specific Information Quantification: PENSA includes a novel approach to quantify state-specific information between two regions of a biomolecule to trace information flow and identify allosteric pathways.

Scientific Applications:

• Comparison of Molecular Simulations: PENSA compares simulations of a molecular system under several conditions, such as with various mutations or bound ligands, to identify differences between adopted molecular conformations.
• Allosteric Pathway Identification: PENSA traces information flow between regions of a biomolecule to identify allosteric pathways and determine molecular mechanisms.
• Structural Feature Analysis: PENSA identifies structural features relevant to particular biochemical phenomena from large simulation datasets of complex systems.

Methodology:

PENSA uses featurization and feature transformations for biomolecular representation, systematically compares distributions of molecular features across ensembles, and quantifies state-specific information between two regions of a biomolecule.