MVsim

MVsim simulates and quantitatively analyzes multivalent ligand–receptor interactions to enable mechanistic evaluation, design of monospecific and multispecific binding behaviors, and extraction of conformational switching rate constants.

Key Features:

• Quantification and Design: Quantifies multivalent binding phenomena for monospecific and multispecific ligand–receptor interactions, including noncanonical binding kinetics.
• Simulation Capabilities: Simulates multivalent interactions to provide dynamic insights into how multiple binding elements influence interaction properties.
• Mechanistic Evaluation: Enables mechanistic dissection of multivalent binding processes to identify underlying principles governing interaction behavior.
• Protein Logic Gates Analysis: Quantitatively predicts ultrasensitivity and performance metrics for multivalent-encoded protein logic gates.
• Selective Receptor Targeting: Evaluates the programmability of multispecificity for designing selective receptor-targeting strategies.
• Conformational Switching Rate Constants: Extracts rate constants associated with conformational switching events, demonstrated on the SARS-CoV-2 spike protein interaction with ACE2 and multivalent inhibitors.

Scientific Applications:

• Virology: Analyzes binding dynamics of viral proteins such as the SARS-CoV-2 spike protein with host receptor ACE2.
• Therapeutics Development: Supports design and evaluation of multivalent inhibitors and selective receptor-targeting therapeutics.
• Synthetic Biology: Informs engineering of protein logic gates and synthetic constructs that rely on multivalent interactions for function.

Methodology:

Implements a configurational network model to simulate multivalent interactions and to extract conformational switching rate constants.