Advancing antibody engineering through synthetic evolution and machine learning

EB Irvine, ST Reddy - The Journal of Immunology, 2024 - journals.aai.org
Abs are versatile molecules with the potential to achieve exceptional binding to target Ags,
while also possessing biophysical properties suitable for therapeutic drug development …

Addressing epistasis in the design of protein function

R Lipsh-Sokolik, SJ Fleishman - Proceedings of the National Academy of …, 2024 - pnas.org
Mutations in protein active sites can dramatically improve function. The active site, however,
is densely packed and extremely sensitive to mutations. Therefore, some mutations may …

[HTML][HTML] Best practices for machine learning in antibody discovery and development

L Wossnig, N Furtmann, A Buchanan, S Kumar… - Drug Discovery …, 2024 - Elsevier
In the past 40 years, therapeutic antibody discovery and development have advanced
considerably, with machine learning (ML) offering a promising way to speed up the process …

Assessing the functional roles of coevolving PHD finger residues

S Basu, U Subedi, M Tonelli, M Afshinpour… - Protein …, 2024 - Wiley Online Library
Although in silico folding based on coevolving residue constraints in the deep‐learning era
has transformed protein structure prediction, the contributions of coevolving residues to …

[HTML][HTML] Reactive Oxygen Species Mechanisms that Regulate Protein–Protein Interactions in Cancer

S Iliadis, NA Papanikolaou - International Journal of Molecular Sciences, 2024 - mdpi.com
Reactive oxygen species (ROS) are produced during cellular metabolism and in response to
environmental stress. While low levels of ROS play essential physiological roles, excess …

Computational tools for plant genomics and breeding

H Wang, M Chen, X Wei, R Xia, D Pei, X Huang… - Science China Life …, 2024 - Springer
Plant genomics and crop breeding are at the intersection of biotechnology and information
technology. Driven by a combination of high-throughput sequencing, molecular biology and …

Protein Language Model Supervised Precise and Efficient Protein Backbone Design Method

B Zhang, K Liu, Z Zheng, Y Liu, J Mu, T Wei, H Chen - bioRxiv, 2023 - biorxiv.org
Proteins are essential macromolecules that play crucial roles in nearly every type of
biological function. Most of the protein functions are determined by their position topologies …

Employing Active Learning in Medium Optimization for Selective Bacterial Growth

S Zhang, H Aida, BW Ying - Applied Microbiology, 2023 - mdpi.com
Medium optimization and development for selective bacterial cultures are essential for
isolating and functionalizing individual bacteria in microbial communities; nevertheless, it …

Leveraging Deep Generative Model For Computational Protein Design And Optimization

B Lai - arXiv preprint arXiv:2408.17241, 2024 - arxiv.org
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living
matter and have tremendous implications in healthcare, manufacturing, and biotechnology …

A library-on-library screen reveals the breadth expansion landscape of a broadly neutralizing betacoronavirus antibody

MY Ornelas, WO Ouyang, NC Wu - bioRxiv, 2024 - biorxiv.org
Broadly neutralizing antibodies (bnAbs) typically evolve cross-reactivity breadth through
acquiring somatic hypermutations. While evolution of breadth requires improvement of …