Chemical Science | An Interpretable Framework Applying Protein Words to Predict Protein-Small Molecule Complementary Pairing Rules
ABSTRACT: Despite the high accuracy of ‘black box’ deep learning models, drug discovery still relies on protein–ligand interaction principles and heuristics. To improve interp…
BMC Bioinformatics | ICFinder: ion channel identification and ion permeation residue prediction using protein language models
ABSTRACT: Ion channel dysfunction underlies many diseases (e.g., arrhythmias, epilepsy, cystic fibrosis), and uncharacterized channels may also contribute to pathology. Identi…
Angewandte Chemie International Edition | Enhancing Enzyme Activity with Mutation Combinations Guided by Few-shot Learning and Causal Inference
ABSTRACT: Designing enzyme sequences to enhance product yield represents a fundamental challenge in metabolic engineering. Here, we established a workflow that integrates comp…
Chemical Science | Improving the accuracy and generalizability of molecular property regression models with a substructure-substitution-rule-informed framework
ABSTRACT: Artificial Intelligence (AI)-aided drug discovery is an active research field, yet AI models often exhibit poor accuracy in regression tasks for molecular property p…
Digital Discovery | Reaction center prediction by analyzing attention of a chemical language model
ABSTRACT: Pretrained chemical language models are widely used to predict molecular properties and chemical reactions, yet interpreting their internal attention mechanisms rema…
iscience | Predicting Protein-Nucleic Acid Interactions via Protein Language Models with Biophysical and Evolutionary Priors
ABSTRACT: Protein interactions with nucleic acids are fundamental to numerous biological processes. Here, we present PNABPred, a multi-modal framework that integrates biophysi…
Advanced Science | Automatically Defining Protein Words for Diverse Functional Predictions Based on Attention Analysis of a Protein Language Model
ABSTRACT: Understanding the relationship between protein sequence and function remains a longstanding challenge in bioinformatics, and to date the lion's share of related tool…
Journal of Chemical Information and Modeling | GLMCyp: A Deep Learning-Based Method for CYP450-Mediated Reaction Site Prediction
ABSTRACT: Cytochrome P450 enzymes (CYP450s) play crucial roles in metabolizing many drugs, and thus, local chemical structure can profoundly influence drug efficacy and toxici…
