Date of Award
May 2019
Degree Type
Thesis
Degree Name
Master of Science (MS)
Department
Biomedical and Chemical Engineering
Advisor(s)
Shikha Nangia
Subject Categories
Engineering
Abstract
Peptidoglycan (PG), also known as murein, is an essential component in both Gram-positive and Gram-negative bacteria. However, even if the chemical structure has been well-known for long, the great tertiary structure remains not clear due to its variability and complicated cross-link mechanism. And it inevitably raises the huge challenge for computational simulations. Against the background, here we present a method for building a solvated peptidoglycan system at coarse-grained level as required. The method is named PEPpy, which represents a Peptidoglycan python code. It reads in the user’s parameters in sequence and automatically generates a topological file and a structure file in the meantime. With these files generated, molecular dynamics simulations and a series of analyses can be easily performed afterwards.
Access
Open Access
Recommended Citation
Xu, Xichen, "PEPpy: A tool to generate bacterial peptidoglycan scaffolds for coarse-grained simulations" (2019). Theses - ALL. 293.
https://surface.syr.edu/thesis/293
