MonteCarbo

MonteCarbo constructs and docks multifunctionalized 5-, 6-, and 7-membered ring molecules, such as monosaccharides and nucleobases, into enzyme active sites to explore their conformations and enzyme interactions.

Key Features:

• Ring generation: Generates multifunctionalized 5-, 6-, and 7-membered ring molecules, explicitly including monosaccharides and nucleobases.
• Z-matrix construction: Uses a core bash script to generate Z-matrix representations of neutral molecules.
• Monte Carlo conformer sampling: Runs a Fortran90 program with a pseudo-random number generator to apply the Monte Carlo method and assign dihedral angles to rotamers.
• Rotamer handling: Assigns dihedral angles to both ring rotamers and rotating functional-group rotamers for comprehensive conformational coverage.
• Generalized internal coordinates: Implements generalized internal coordinates (GIC) incorporating Cremer and Pople puckering coordinates for ring conformation modeling.
• Serial docking: Docks multiple generated conformers into enzyme active sites in serial to evaluate potential interactions.
• Target scope: Focuses on carbohydrate-active enzymes and enzymes involved in glyco- and RNA/DNA-related processes.

Scientific Applications:

• Glycoscience enzymology: Analyzing docking interactions of monosaccharide derivatives with carbohydrate-active enzymes.
• Nucleic acid enzymology: Studying interactions of nucleobase-containing rings with RNA/DNA-related enzymes.
• Conformational analysis: Exploring ring puckering and rotamer distributions using Monte Carlo sampling and Cremer and Pople coordinates.

Methodology:

MonteCarbo generates Z-matrix representations via a bash script, uses a Fortran90 program with a pseudo-random number generator to apply the Monte Carlo method and assign dihedral angles to ring and functional-group rotamers, employs generalized internal coordinates (GIC) with Cremer and Pople puckering coordinates for ring modeling, and docks multiple conformers into enzyme active sites in serial.