MonteGrappa: An iterative Monte Carlo program to optimize biomolecular potentials in simplified models

摘要

Simplified models, including implicit-solvent and coarse-grained models, are useful tools to investigate the physical properties of biological macromolecules of large size, like protein complexes, large DNA/RNA strands and chromatin fibres. While advanced Monte Carlo techniques are quite efficient in sampling the conformational space of such models, the availability of realistic potentials is still a limitation to their general applicability. The recent development of a computational scheme capable of designing potentials to reproduce any kind of experimental data that can be expressed as thermal averages of conformational properties of the system has partially alleviated the problem. Here we present a program that implements the optimization of the potential with respect to the experimental data through an iterative Monte Carlo algorithm and a rescaling of the probability of the sampled conformations. The Monte Carlo sampling includes several types of moves, suitable for different kinds of system, and various sampling schemes, such as fixed-temperature, replica-exchange and adaptive simulated tempering. The conformational properties whose thermal averages are used as inputs currently include contact functions, distances and functions of distances, but can be easily extended to any function of the coordinates of the system.