CYCLOPEp Builder

CYCLOPEp Builder generates molecular topologies for cyclic peptides and self-assembling cyclic peptide nanotubes to enable Molecular Dynamics simulations across All-Atom to Coarse-Grain resolutions.

Key Features:

• Molecular topology generation: Creates molecular topologies essential for conducting Molecular Dynamics simulations.
• Multi-resolution simulation support: Supports Molecular Dynamics simulations spanning All-Atom to Coarse-Grain resolutions.
• Force field versatility: Equipped with various force fields for simulation flexibility.
• Nanotube orientation options: Produces self-assembling cyclic peptide nanotubes with parallel and antiparallel orientations.
• Sequence diversity: Capable of generating structures with different sequences ranging from individual cyclic peptides to complex nanotubes.
• Molecular assembly visualization: Enhances understanding of cyclic peptide and nanotube molecular interactions through detailed visualization of molecular assemblies.

Scientific Applications:

• Biomedicine: Advances applications in biomedical research through cyclic peptide and nanotube design and simulation.
• Nanoelectronics: Supports research in nanoelectronic applications involving self-assembling cyclic peptide nanotubes.
• Catalysis: Facilitates study of catalytic applications using cyclic peptide-based supramolecular structures.
• Supramolecular structure exploration: Enables scientific community engagement in exploration of supramolecular structures through accessible simulation capabilities.

Methodology:

The tool generates molecular topologies for cyclic peptides and self-assembling cyclic peptide nanotubes, enabling Molecular Dynamics simulations across All-Atom to Coarse-Grain resolutions with various force fields.