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MonteCarbo: A software to generate and dock multifunctionalized ring molecules.

Santiago Alonso-Gil1

  • 1Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.

Journal of Computational Chemistry
|May 13, 2021
PubMed
Summary

MonteCarbo is open-source software for creating multifunctional monosaccharides and nucleobases. It models their structures and docks them into carbohydrate-active enzymes using computational methods.

Keywords:
Monte Carlocarbohydratesconformationsdockingdrug design

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Area of Science:

  • Computational chemistry
  • Structural biology
  • Biochemistry

Background:

  • Carbohydrate-active enzymes are crucial in biological processes.
  • Understanding enzyme-substrate interactions requires accurate molecular modeling.
  • Existing tools may lack comprehensive features for monosaccharide and nucleobase modeling.

Purpose of the Study:

  • To introduce MonteCarbo, an open-source software for computational modeling.
  • To enable the construction and conformational analysis of multifunctional monosaccharides and nucleobases.
  • To facilitate the docking of generated molecules into carbohydrate-active enzyme active sites.

Main Methods:

  • Utilizes a bash script for Z-matrix generation.
  • Employs a Fortran90 code with Monte Carlo methods for dihedral angle assignment.
  • Incorporates Generalized Internal Coordinates (GIC) for ring puckering analysis.
  • Performs serial docking of generated conformers into enzyme active sites.

Main Results:

  • Successfully generates Z-matrices for diverse molecular structures.
  • Assigns dihedral angles to model rotamers and ring conformations.
  • Optimizes generated structures for accurate representation.
  • Enables docking of multiple conformers into various enzyme active sites.

Conclusions:

  • MonteCarbo provides a robust platform for in silico studies of carbohydrate-enzyme interactions.
  • The software aids in exploring the conformational space of monosaccharides and nucleobases.
  • Facilitates the investigation of ligand binding within enzyme active sites.