MoViES

MoViES analyzes vibrational and thermal fluctuational dynamics of biomolecules, including proteins and nucleic acids, to evaluate vibrational normal modes and thermal bond-disruption probabilities.

Key Features:

• Input Format: Accepts structural input in PDB (Protein Data Bank) format.
• Normal mode calculation: Computes vibrational normal modes using modified AMBER molecular mechanics force fields.
• Thermal fluctuation analysis: Calculates thermal fluctuational properties using a self-consistent harmonic approximation.
• Bond disruption probabilities: Produces thermal fluctuational bond disruption probabilities derived from the fluctuation calculations.
• Validation: Methods have been tested on selected proteins and shown to agree with experimental findings and established normal mode computations.

Scientific Applications:

• Biomolecular dynamics analysis: Characterizes structural and dynamic behavior of proteins and nucleic acids via vibrational and thermal fluctuation data.
• Functional inference: Assesses how vibrational motions and thermal fluctuations influence macromolecular function.
• Mechanistic and drug-design support: Informs elucidation of biological mechanisms and evaluation of molecular interactions relevant to drug design.

Methodology:

Vibrational normal modes are computed using modified AMBER molecular mechanics force fields, thermal fluctuational properties are calculated via a self-consistent harmonic approximation, and thermal fluctuational bond disruption probabilities are derived from these calculations.