AlphaFold2-aware protein–DNA binding site prediction using graph transformer

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Human 8-oxoguanine glycosylase OGG1 binds nucleosome at the dsDNA ends and the super-helical locations

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Mass Spectrometry for Assessing Protein–Nucleic Acid Interactions

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Improving PTM Site Prediction by Coupling of Multi-Granularity Structure and Multi-Scale Sequence Representation

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CrossBind: Collaborative Cross-Modal Identification of Protein Nucleic-Acid-Binding Residues

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Identification of Catechins’ Binding Sites in Monomeric Aβ42 through Ensemble Docking and MD Simulations

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Accurate Identification of Protein Binding Sites for All Drug Modalities Using ALLSites

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CLAPE: Protein–Ligand Binding Site Prediction via Protein Language Models

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Classification of Calcium-Dependent Protein Kinases and Their Transcriptional Response to Abiotic Stresses in Halophyte Nitraria sibirica

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Advance technologies for DNA-protein interactions and future research prospect

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Geometric deep learning assists protein engineering. Opportunities and Challenges

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STNMDA: A Novel Model for Predicting Potential Microbe-Drug Associations with Structure-Aware Transformer

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Protein Sequence Design by Entropy-based Iterative RefinementPreprint

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Human O-linked Glycosylation Site Prediction Using Pretrained Protein Language ModelPreprint

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Cerebra: a computationally efficient framework for accurate protein structure predictionPreprint

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DPAC: Prediction and Design of Protein-DNA Interactions via Sequence-Based Contrastive LearningPreprint

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NNSFMDA: Lightweight Transformer Model with Bounded Nuclear Norm Minimization for Microbe-Drug Association Prediction

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Partner-RBR: Predicting Multitype RNA-Binding Residues Based on Mutual Learning

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Computation empowers CRISPR discovery and technology

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ULDNA: Integrating Unsupervised Multi-Source Language Models with LSTM-Attention Network for Protein-DNA Binding Site PredictionPreprint

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AI ‐Based Protein Structure Predictions and Their Implications in Drug Discovery

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MPBind: Multitask Protein Binding Site Prediction by Protein Language Models and Equivariant Graph Neural NetworksPreprint

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Neutrophil elastase binds at the central domain of extracellular Toll-like receptor 4: AI prediction, docking, and validation in disease model

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An Online Server for Geometry-Aware Protein Function Annotations Through Predicted Structure

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A novel prediction method for protein-DNA binding sites based on protein language model fusion features with SE-connection pyramidal network and ensemble learning

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Protein-DNA Binding Sites Prediction via Integrating Pretrained Large Language Models and Contrastive Learning

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Prediction of Protein-DNA Binding Sites Based on Protein Language Model and Deep Learning

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A sparse and wide neural network model for DNA sequences

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How Deepbics Quantifies Intensities of Transcription Factor-DNA Binding and Facilitates Prediction of Single Nucleotide Variant Pathogenicity With a Deep Learning Model Trained On ChIP-Seq Data Sets

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Identification of Catechins Binding Pockets in Monomeric A β 42 Through Ensemble Docking and MD SimulationsPreprint

Firouzi, R., Sowlati‐Hashjin, S., Chávez-García, C., Ashouri, M., Karimi‐Jafari, M. H., & Karttunen, M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.09.479729 · Cited by 1 · see citing works

Human O -linked Glycosylation Site Prediction Using Pretrained Protein Language ModelPreprint

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USPDB: A novel U-shaped equivariant graph neural network with subgraph sampling for protein-DNA binding site prediction

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Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures

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