How to Design Peptides
Document Type
Syllabus
Publication Date
1-1-2023
Abstract
Novel design of proteins to target receptors for treatment or tissue augmentation has come to the fore owing to advancements in computing power, modeling frameworks, and translational successes. Shorter proteins, or peptides, can offer combinatorial synergies with dendrimer, polymer, or other peptide carriers for enhanced local signaling, which larger proteins may sterically hinder. Here, we present a generalized method for designing a novel peptide. We first show how to create a script protocol that can be used to iteratively optimize and screen novel peptide sequences for binding a target protein. We present a step-by-step introduction to utilizing file repositories, data bases, and the Rosetta software suite. RosettaScripts, an.xml interface that allows for sequential functions to be performed, is used to order the functions for repeatable performance. These strategies may lead to more groups venturing into computational design, which may result in synergies from artificial intelligence/machine learning (AI/ML) to phage display and screening. Importantly, the beginner is expected to be able to design their first peptide ligand and begin their journey in peptide drug discovery. Generally, these peptides potentially could be used to interact with any enzyme or receptor, for example, in the study of chemokines and their interactions with glycosoaminoglycans and their receptors.
Identifier
85141936986 (Scopus)
Publication Title
Methods in Molecular Biology
External Full Text Location
https://doi.org/10.1007/978-1-0716-2835-5_15
e-ISSN
19406029
ISSN
10643745
PubMed ID
36374423
First Page
187
Last Page
216
Volume
2597
Recommended Citation
Dodd-o, Joseph; Acevedo-Jake, Amanda M.; Azizogli, Abdul Rahman; Mulligan, Vikram Khipple; and Kumar, Vivek A., "How to Design Peptides" (2023). Faculty Publications. 2130.
https://digitalcommons.njit.edu/fac_pubs/2130