TY - JOUR
T1 - PepCARES
T2 - A Comprehensive Advanced Refinement and Evaluation System for Peptide Design and Affinity Screening
AU - Xu, Wen
AU - Wu, Zhipeng
AU - Zhang, Chengyun
AU - Zhu, Cheng
AU - Duan, Hongliang
N1 - Publisher Copyright:
© 2024 The Authors. Published by American Chemical Society.
PY - 2024/11/19
Y1 - 2024/11/19
N2 - Peptides are crucial in vaccine research, and their remarkable specificity and efficacy make them a promising potential drug class. However, designing and screening these peptides computationally is challenging. Here, we present the comprehensive advanced refinement and evaluation system (PepCARES), a program utilizing our novel model called PeptideMPNN and score evaluation for peptide design and affinity screening. PeptideMPNN, built on ProteinMPNN with transfer learning, significantly enhances sequence recovery (by 26.26%) and reduces perplexity (by 0.536) in a sequence generation task. We designed peptides targeting two HLA alleles and, using MHCfovea and PDBePISA, identified candidates with high potential. From 20 designed peptides, 14 and 7 peptides were selected, respectively. Our research provides a method for designing and screening peptides, making an important step toward the development of peptide-based vaccines.
AB - Peptides are crucial in vaccine research, and their remarkable specificity and efficacy make them a promising potential drug class. However, designing and screening these peptides computationally is challenging. Here, we present the comprehensive advanced refinement and evaluation system (PepCARES), a program utilizing our novel model called PeptideMPNN and score evaluation for peptide design and affinity screening. PeptideMPNN, built on ProteinMPNN with transfer learning, significantly enhances sequence recovery (by 26.26%) and reduces perplexity (by 0.536) in a sequence generation task. We designed peptides targeting two HLA alleles and, using MHCfovea and PDBePISA, identified candidates with high potential. From 20 designed peptides, 14 and 7 peptides were selected, respectively. Our research provides a method for designing and screening peptides, making an important step toward the development of peptide-based vaccines.
UR - http://www.scopus.com/inward/record.url?scp=85209687473&partnerID=8YFLogxK
U2 - 10.1021/acsomega.4c07682
DO - 10.1021/acsomega.4c07682
M3 - Article
AN - SCOPUS:85209687473
SN - 2470-1343
VL - 9
SP - 46429
EP - 46438
JO - ACS Omega
JF - ACS Omega
IS - 46
ER -
