Build peptide#

Building peptides.

Peptides are essential building blocks in molecular modeling. MolSysMT offers a convenient tool to construct them from amino acid sequences. The function molsysmt.build.build_peptide() generates an all-atom molecular system with topology and coordinates for a peptide chain, optionally capped and customizable in format.

Added in version 1.0.0.

How this function works#

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function:molsysmt.build.build_peptide().

Given a sequence of residues using standard or extended three-letter or single-letter codes, this function constructs the corresponding peptide. Terminal cappings such as ACE and NME can be included directly in the sequence or added later. The resulting system includes atom coordinates and is returned in a MolSysMT-compatible form, ready for further processing.

Let’s see how to generate a peptide from a sequence, obtaining a molecular system with all-atom topology and coordinates:

import molsysmt as msm

molsys = msm.build.build_peptide('AceAlaNme')

msm.view(molsys)

In the next example, we create a longer peptide using single-letter codes.

These peptides are created in vacuum, but they can be solvated. Let’s show the work flow to create a solvated cationic peptide in the following cells:

molsys = msm.build.build_peptide('GRKFRRKFKK')

By default, peptides are built in vacuum. Let’s now go through the workflow to generate a solvated, capped cationic peptide:

molsys = msm.build.add_missing_terminal_cappings(molsys, N_terminal='ACE', C_terminal='NME')

molsys = msm.structure.center(molsys)

molsys = msm.build.solvate(molsys, box_shape='truncated octahedral', clearance='14.0 angstroms')

The peptide was previously centered and remains near the origin. However, the added water molecules might be distributed beyond the boundaries of the primary box. To ensure a compact representation and properly apply periodic boundary conditions, we rewrap the water molecules around the origin using the minimum image convention.

molsys = msm.pbc.wrap_to_mic(molsys)

Finally, we visualize the system to inspect the solvated peptide in the simulation box.

msm.view(molsys, standard=True, with_water_as='surface')