DynOmics EMN

DynOmics EMN analyzes the intrinsic and environment-dependent collective dynamics of structurally resolved biomolecular systems to characterize functional sites, allosteric communication, and interaction conformers.

Key Features:

• Elastic Network Models (ENM 1.0): Integrates the Gaussian Network Model (GNM) and the Anisotropic Network Model (ANM) to model biomolecular dynamics.
• Environment-aware modeling: Considers molecular environment factors such as lipid bilayers, crystal contacts, substrates or ligands, and surrounding subunits in multimeric structures or assemblies.
• PDB-format structure support: Generates analyses from structural coordinates provided in PDB format, including user-uploaded files or structures retrieved from databases.
• Collective dynamics generation: Produces detailed information on collective motions and accessible conformational variability of structures.
• Functional site and mechanism analysis: Identifies potentially functional sites and supports interpretation of mechanisms such as signal transduction and allosteric communication.
• Interaction pose assessment and ensemble reconstruction: Assesses protein-protein and protein-DNA interaction poses and delivers ensembles of accessible conformers reconstructed at atomic detail based on ANM-predicted global modes.
• Structural proteomics dataset focus: Targets analysis of structurally resolved data from structural proteomics datasets to evaluate dynamics across molecules and assemblies.

Scientific Applications:

• Dynamics characterization: Evaluating intrinsic and environment-modulated dynamics of individual molecules to complex assemblies in physiological contexts.
• Allostery and signaling: Mapping allosteric communication and signal transduction pathways via collective motion analysis.
• Interaction modeling: Assessing protein-protein and protein-DNA interaction poses and generating conformational ensembles for interaction interpretation.
• Environmental effect studies: Investigating how lipid bilayers, crystal contacts, ligands/substrates, and multimeric context alter intrinsic biomolecular dynamics.
• Structural proteomics interpretation: Interpreting large-scale structurally resolved datasets to extract dynamic and functional insights.

Methodology:

ENM 1.0 integrates Gaussian Network Model (GNM) and Anisotropic Network Model (ANM); ANM predicts global modes of motion that are used to reconstruct ensembles of accessible conformers at atomic detail, with models parameterized to include specified environmental contexts for input structures in PDB format.