LocalMove

LocalMove fits protein and RNA three-dimensional structures from Protein Data Bank (PDB) files onto cubic and face-centered cubic lattice models to generate on-lattice representations for structural and conformational analysis.

Key Features:

• Input format: Accepts Protein Data Bank (PDB) files representing protein and RNA three-dimensional structures.
• Algorithmic Approach: Employs a Markov Chain Monte Carlo (MCMC) algorithm integrated with simulated annealing to explore conformational space and optimize the fit to lattice models.
• Lattice Models: Supports coarse-grain and backbone models on cubic and face-centered cubic lattices.
• Local Moves: Applies sequences of local moves, including backbone modifications, to iteratively adjust the biomolecule's configuration within the lattice framework.
• Output Generation: Produces an output PDB file of the best-fitting lattice model and 3D movies depicting intermediate conformations encountered during computation.

Scientific Applications:

• Structural biology: Approximates biomolecular structures on lattices to analyze spatial configuration and conformational properties.
• Conformational and stability analysis: Provides insights into conformational properties, stability, and potential functional mechanisms of proteins and RNA.
• Model simplification: Simplifies complex molecular structures for downstream computational analysis or experimental validation.

Methodology:

LocalMove applies sequences of local moves (e.g., backbone modifications) within an MCMC framework enhanced by simulated annealing to iteratively improve the fit to the input 3D model until a user-defined stopping condition is met, after which the best-fitting model is selected.