AIMC Topic: Protein Binding

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Machine learning models for predicting interaction affinity energy between human serum proteins and hemodialysis membrane materials.

Scientific reports
Membrane incompatibility poses significant health risks, including severe complications and potential fatality. Surface modification of membranes has emerged as a pivotal technology in the membrane industry, aiming to improve the hemocompatibility an...

Transformer Decoder Learns from a Pretrained Protein Language Model to Generate Ligands with High Affinity.

Journal of chemical information and modeling
The drug discovery process can be significantly accelerated by using deep learning methods to suggest molecules with druglike features and, more importantly, that are good candidates to bind specific proteins of interest. We present a novel deep lear...

Deep Learning of CYP450 Binding of Small Molecules by Quantum Information.

Journal of chemical information and modeling
Drug-drug interaction can lead to diminished therapeutic effects or increased toxicity, posing significant risks, especially in polypharmacy, and cytochrome P450 plays an indispensable role in this interaction. Cytochrome P450, responsible for the me...

Challenges and compromises: Predicting unbound antibody structures with deep learning.

Current opinion in structural biology
Therapeutic antibodies are manufactured, stored and administered in the free state; this makes understanding the unbound form key to designing and improving development pipelines. Prediction of unbound antibodies is challenging, specifically modellin...

Feature selection enhances peptide binding predictions for TCR-specific interactions.

Frontiers in immunology
INTRODUCTION: T-cell receptors (TCRs) play a critical role in the immune response by recognizing specific ligand peptides presented by major histocompatibility complex (MHC) molecules. Accurate prediction of peptide binding to TCRs is essential for a...

DisDock: A Deep Learning Method for Metal Ion-Protein Redocking.

Proteins
The structures of metalloproteins are essential for comprehending their functions and interactions. The breakthrough of AlphaFold has made it possible to predict protein structures with experimental accuracy. However, the type of metal ion that a met...

Deep learning methods for proteome-scale interaction prediction.

Current opinion in structural biology
Proteome-scale interaction prediction is essential for understanding protein functions and disease mechanisms. Traditional experimental methods are often limited by scale and complexity, driving the need for computational approaches. Deep learning ha...

MVGNN-PPIS: A novel multi-view graph neural network for protein-protein interaction sites prediction based on Alphafold3-predicted structures and transfer learning.

International journal of biological macromolecules
Protein-protein interactions (PPI) are crucial for understanding numerous biological processes and pathogenic mechanisms. Identifying interaction sites is essential for biomedical research and targeted drug development. Compared to experimental metho...

MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction.

Journal of chemical information and modeling
Predicting drug-target binding affinity (DTA) is a crucial task in drug discovery research. Recent studies have demonstrated that pocket features and interactions between targets and drugs significantly improve the understanding of DTA. However, chal...

Artificial intelligence in peptide-based drug design.

Drug discovery today
Protein-protein interactions (PPIs) are fundamental to a variety of biological processes, but targeting them with small molecules is challenging because of their large and complex interaction interfaces. However, peptides have emerged as highly promi...