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

Journal of Chemical Information and Modeling, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 20, 2025

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 drugs significantly improve the understanding of DTA. However, challenges remain, particularly detailed consideration both global local information further modeling features. In this paper, we propose novel multimodal deep learning model named MMPD-DTA for predicting to address these challenges. The integrates graph sequence modalities targets, pockets, capture target information. introduces pocket-drug (PD graph) simultaneously models atomic within target, drug, drug. We employ GraphSAGE representation from PD graph, complemented by via transformers isomorphism network molecular graph. These representations are then concatenated, multilayer perceptron generates final predictions. Experimental results on three real-world test sets demonstrate outperforms baseline methods. Ablation confirm effectiveness each module model. Our code available at https://github.com/zhc-moushang/MMPD-DTA.

Language: Английский

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Integrating transcriptomic and polygenic risk scores to enhance predictive accuracy for ischemic stroke subtypes

Human Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 18, 2024

Language: Английский

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The 2025 Nucleic Acids Research database issue and the online molecular biology database collection

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D1 - D9

Published: Dec. 10, 2024

The 2025 Nucleic Acids Research database issue contains 185 papers spanning biology and related areas. Seventy three new databases are covered, while resources previously described in the account for 101 update articles. Databases most recently published elsewhere a further 11 papers. acid include EXPRESSO multi-omics of 3D genome structure (this issue's chosen Breakthrough Resource Article) NAIRDB Fourier transform infrared data. New protein predictions human isoforms at ASpdb viral proteins BFVD. UniProt, Pfam InterPro have all provided updates: metabolism signalling covered by descriptions STRING, KEGG CAZy, updated microbe-oriented Enterobase, VFDB PHI-base. Biomedical research is supported, among others, ClinVar, PubChem DrugMAP. Genomics-related Ensembl, UCSC Genome Browser dbSNP. plant cover Solanaceae (SolR) Asteraceae (AMIR) families an from NCBI Taxonomy also features. Database Issue freely available on website (https://academic.oup.com/nar). At NAR online Molecular Biology Collection (http://www.oxfordjournals.org/nar/database/c/), 932 entries been reviewed last year, 74 added 226 discontinued URLs eliminated bringing current total to 2236 databases.

Language: Английский

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Shared genetic architecture and bidirectional clinical risks within the psycho-metabolic nexus

EBioMedicine, Journal Year: 2024, Volume and Issue: 111, P. 105530 - 105530

Published: Dec. 27, 2024

Language: Английский

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