Large Language Models (LLMs) in Protein Bioinformatics

A Survey of Pre-Trained Protein Language Models.- Enhancing Structure-Aware Protein Language Models with Efficient Fine-Tuning for Various Protein Prediction Tasks.- Exploring ProtFlash: An Efficient Approach to Protein Data Analysis.- Ranking Protein-Protein Models with Large Language Models and Graph Neural Networks.- Translating a GO Term List to Human Readable Function Description Using GO2Sum.- TransFun: A Tool of Integrating Large Language Models, Transformers, and Equivariant Graph Neural Networks to Predict Protein Function.- Using InterLabelGO+ for Accurate Protein Language Model-Based Function Prediction.- Functional Annotation of Proteomes Using Protein Language Models: A High-Throughput Implementation of the ProtTrans Model.- Advances in Language-Model-Informed Protein-Nucleic Acid Binding Site Prediction.- Practical Applications of Language Models in Protein Sorting Prediction: SignalP 6.0, DeepLoc 2.1, and DeepLocPro 1.0.- CNN-Meth: A Tool to Accurately Predict Lysine Methylation Sites Using Evolutionary Information-Based Protein Modeling.- Predicting the Pathogenicity of Human Protein Variants: Not Only a Matter of Residue Labeling.- A Survey of Biological Function Prediction Methods with Focus on Natural Language Processing (NLP) and Large Language Models (LLM).- PLMSearch and PLMAlign: Protein Language Model-Based Homologous Sequence Search and Alignment.- Large Context, Deeper Insights: Harnessing Large Language Models for Advancing Protein-Protein Interaction Analysis.- Prediction of Protein-Peptide Binding Sites Using PepBCL.- Predicting Peptide Bioactivity Using the Unified Model Architecture UniDL4BioPep.- CLAPE: Protein-Ligand Binding Site Prediction via Protein Language Models.- Large Language Model-Based Advances in Prediction of Post-Translational Modification Sites in Proteins.