MonteCarbo: A software to generate and dock multifunctionalized ring molecules

Abstract

MonteCarbo is an open-source software to construct simple 5-, 6-, and 7-membered ring multifunctionalized monosaccharides and nucleobases and dock them into the active site of carbohydrate-active enzymes. The core bash script executes simple orders to generate the Z-matrix of the neutral molecule of interest. After that, a Fortran90 code based on a pseudo-random number generator (Monte Carlo method) is executed to assign dihedral angles to the different rotamers present in the structure (ring and rotating functional groups). The program also has a generalized internal coordinates (GIC) implementation of the Cremer and Pople puckering coordinates ring. Once the structures are generated and optimized, a second code is ready to execute in serial the docking of multiple conformers in the active site of a wide family of enzymes.