A review of deep learning methods for antibodies

J Graves, J Byerly, E Priego, N Makkapati, SV Parish… - Antibodies, 2020 - mdpi.com
Driven by its successes across domains such as computer vision and natural language
processing, deep learning has recently entered the field of biology by aiding in cellular …

Antibody variable region engineering for improving cancer immunotherapy

H Lou, X Cao - Cancer Communications, 2022 - Wiley Online Library
The efficacy and specificity of conventional monoclonal antibody (mAb) drugs in the clinic
require further improvement. Currently, the development and application of novel antibody …

Evaluating protein binding interfaces with transformer networks

V Stebliankin, A Shirali, P Baral, J Shi… - Nature Machine …, 2023 - nature.com
Computational protein-binding studies are widely used to investigate fundamental biological
processes and facilitate the development of modern drugs, vaccines and therapeutics …

[HTML][HTML] Artificial intelligence approaches to human-microbiome protein–protein interactions

H Lim, F Cankara, CJ Tsai, O Keskin… - Current Opinion in …, 2022 - Elsevier
Host-microbiome interactions play significant roles in human health and disease. Artificial
intelligence approaches have been developed to better understand and predict the …

Leveraging Artificial Intelligence to Expedite Antibody Design and Enhance Antibody–Antigen Interactions

DN Kim, AD McNaughton, N Kumar - Bioengineering, 2024 - mdpi.com
This perspective sheds light on the transformative impact of recent computational
advancements in the field of protein therapeutics, with a particular focus on the design and …

ProInterVal: Validation of Protein–Protein Interfaces through Learned Interface Representations

D Ovek, O Keskin, A Gursoy - Journal of Chemical Information and …, 2024 - ACS Publications
Proteins are vital components of the biological world and serve a multitude of functions.
They interact with other molecules through their interfaces and participate in crucial cellular …

Improving classification of correct and incorrect protein–protein docking models by augmenting the training set

D Barradas-Bautista, A Almajed, R Oliva… - Bioinformatics …, 2023 - academic.oup.com
Motivation Protein–protein interactions drive many relevant biological events, such as
infection, replication and recognition. To control or engineer such events, we need to access …

Artificial Intelligence for Microbiology and Microbiome Research

XW Wang, T Wang, YY Liu - arxiv preprint arxiv:2411.01098, 2024 - arxiv.org
Advancements in artificial intelligence (AI) have transformed many scientific fields, with
microbiology and microbiome research now experiencing significant breakthroughs through …

PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks

V Stebliankin, A Shirali, P Baral, P Chapagain… - bioRxiv, 2023 - biorxiv.org
The computational studies of protein binding are widely used to investigate fundamental
biological processes and facilitate the development of modern drugs, vaccines, and …