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CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems. | LitMetric

CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems.

Nat Commun

Department of Computer Science & Engineering, Lehigh University, Bethlehem, PA, USA.

Published: June 2024

AI Article Synopsis

  • Atomic-scale molecular modeling and simulation are essential in computational biology but pose challenges in assembling complex models involving large molecules and various materials.
  • The study introduces the Multicomponent Assembler in CHARMM-GUI, which streamlines the assembly and simulation preparation process for diverse biomolecular systems under periodic boundary conditions.
  • The tool's effectiveness is demonstrated through the creation of six complex systems, enhancing research capabilities in studying interactions among small molecules, biomacromolecules, polymers, and nanomaterials.

Article Abstract

Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. In this work, we demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to study complex interactions between small molecules, biomacromolecules, polymers, and nanomaterials.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211406PMC
http://dx.doi.org/10.1038/s41467-024-49700-4DOI Listing

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