Review of predicting protein stability changes upon variations

Y Qiu, T Huang, YD Cai - Proteomics, 2024 - Wiley Online Library
Forecasting alterations in protein stability caused by variations holds immense importance.
Improving the thermal stability of proteins is important for biomedical and industrial …

AlphaMut: a deep reinforcement learning model to suggest helix-disrupting mutations

P Bhargav, A Mukherjee - Journal of Chemical Theory and …, 2024 - ACS Publications
Helices are important secondary structural motifs within proteins and are pivotal in
numerous physiological processes. While amino acids (AA) such as alanine and leucine are …

[HTML][HTML] PepCA: Unveiling protein-peptide interaction sites with a multi-input neural network model

J Huang, W Li, B Xiao, C Zhao, H Zheng, Y Li, J Wang - Iscience, 2024 - cell.com
The protein-peptide interaction plays a pivotal role in fields such as drug development, yet
remains underexplored experimentally and challenging to model computationally. Herein …

Synergistic Attention-Guided Cascaded Graph Diffusion Model for Complementarity Determining Region Synthesis

R Zhang, Y Huang, Y Lou, W Ding… - IEEE Transactions on …, 2024 - ieeexplore.ieee.org
Complementarity determining region (CDR) is a specific region in antibody molecules that
binds to antigens, where a small portion of residues undergoes particularly pronounced …

[HTML][HTML] The Accurate Prediction of Antibody Deamidations by Combining High-Throughput Automated Peptide Mapping and Protein Language Model-Based Deep …

B Niu, B Lee, L Wang, W Chen, J Johnson - Antibodies, 2024 - mdpi.com
Therapeutic antibodies such as monoclonal antibodies (mAbs), bispecific and multispecific
antibodies are pivotal in therapeutic protein development and have transformed disease …

PLMTHP: An Ensemble Framework for Tumor Homing Peptide Prediction based on Protein Language Model

Y Chen, H Qin, X Cui, T Yang, P Sun… - … on Bioinformatics and …, 2023 - ieeexplore.ieee.org
Tumor homing peptides (THPs) play significant role in recognizing and specifically binding
to tumor cells. Traditional experimental methods can accurately identify THPs but often suffer …

An antigen design method based on molecular dynamics and deep learning

H Li, S Zhou - 2024 IEEE International Conference on Medical …, 2024 - ieeexplore.ieee.org
The prediction of the impact of amino acid mutations on the change in binding free energy
(\varDelta\varDeltaG), is critically important for both biomedical and industrial applications …

Advances in Zero‐Shot Prediction‐Guided Enzyme Engineering Using Machine Learning

C Liu, J Wu, Y Chen, Y Liu, Y Zheng, L Liu, J Zhao - ChemCatChem - Wiley Online Library
The advent of machine learning (ML) has significantly advanced enzyme engineering,
particularly through zero‐shot (ZS) predictors that forecast the effects of amino acid …