DrugBank
View article: From Static Pathways to Dynamic Mechanisms: A Committor-Based Data-Driven Approach to Chemical Reactions
From Static Pathways to Dynamic Mechanisms: A Committor-Based Data-Driven Approach to Chemical Reactions Open
As computational chemistry methods evolve, dynamic effects have been increasingly recognized to govern chemical reaction pathways in both organic and inorganic systems. Here, we introduce a committor-based workflow that integrates a path-c…
View article: Conversational no-code and multi-agentic disease module identification and drug repurposing prediction with ChatDRex
Conversational no-code and multi-agentic disease module identification and drug repurposing prediction with ChatDRex Open
Repurposing approved drugs offers a time-efficient and cost-effective alternative to traditional drug development. However, in silico prediction of repurposing candidates is challenging and requires the effective collaboration of specialis…
View article: From Static Pathways to Dynamic Mechanisms: A Committor-Based Data-Driven Approach to Chemical Reactions
From Static Pathways to Dynamic Mechanisms: A Committor-Based Data-Driven Approach to Chemical Reactions Open
As computational chemistry methods evolve, dynamic effects have been increasingly recognized to govern chemical reaction pathways in both organic and inorganic systems. Here, we introduce a committor-based workflow that integrates a path-c…
View article: Integrating GEO Database and Bioinformatics Analysis to Screen the Key Targets of Tanshinone IIA in Myocardial Infarction
Integrating GEO Database and Bioinformatics Analysis to Screen the Key Targets of Tanshinone IIA in Myocardial Infarction Open
Objective: To systematically screen the core targets of Tanshinone IIA in the treatment of myocardial infarction (MI) and to explore its molecular mechanisms based on the Gene Expression Omnibus (GEO) database and bioinformatics methods. M…
View article: Exploiting FAIR interoperability from the ELIXIR –UK IUPHAR/BPS Guide to Pharmacology to an expanding range of ligands, targets, publications and patents
Exploiting FAIR interoperability from the ELIXIR –UK IUPHAR/BPS Guide to Pharmacology to an expanding range of ligands, targets, publications and patents Open
Poster abstract for ELIXIR UK All Hands meeting, Exeter 23 Oct 2025 The IUPHAR/BPS Guide to Pharmacology (GtoPdb; www.guidetopharmacology.org, PMID: 3789734) is a…
View article: Exploiting FAIR interoperability from the ELIXIR –UK IUPHAR/BPS Guide to Pharmacology to an expanding range of ligands, targets, publications and patents
Exploiting FAIR interoperability from the ELIXIR –UK IUPHAR/BPS Guide to Pharmacology to an expanding range of ligands, targets, publications and patents Open
Poster abstract for ELIXIR UK All Hands meeting, Exeter 23 Oct 2025 The IUPHAR/BPS Guide to Pharmacology (GtoPdb; www.guidetopharmacology.org, PMID: 3789734) is an open-access, expert-curated, FAIR-compliant (Findable, Accessible, Interope…
View article: Application of Data-Centric Supervised Machine Learning to Predict Phenotypic Activity Against Clinically Relevant Stages of Trypanosoma cruzi
Application of Data-Centric Supervised Machine Learning to Predict Phenotypic Activity Against Clinically Relevant Stages of Trypanosoma cruzi Open
Background/Objectives: Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi, which currently affects around 8 million people worldwide. The therapeutic arsenal against T. cruzi is so far limited…
View article: Identifying compounds to treat opiate use disorder by leveraging multi-omic data integration and multiple drug repurposing databases
Identifying compounds to treat opiate use disorder by leveraging multi-omic data integration and multiple drug repurposing databases Open
Genes influencing opioid use disorder (OUD) biology have been identified via genome-wide association studies (GWAS), gene expression, and network analyses. These discoveries provide opportunities to identifying existing compounds targeting…
View article: Exploring the role of febuxostat’s drug target XOR in erectile dysfunction: insights from human genetics and rat models
Exploring the role of febuxostat’s drug target XOR in erectile dysfunction: insights from human genetics and rat models Open
Background The use of the uric acid-lowering drug Febuxostat (FB) has been associated with the risk of erectile dysfunction (ED) in men; however, findings from previous studies remain inconsistent. This study aimed to investigate the assoc…
View article: Benchmarking Sequence-Based Compound–Protein Interaction Prediction through Constructing a Debiased Data Set CDPN
Benchmarking Sequence-Based Compound–Protein Interaction Prediction through Constructing a Debiased Data Set CDPN Open
Accurate prediction of compound-protein interactions (CPIs) is critical for drug discovery, but existing data sets often suffer from biases that hinder model generalization. Here, we first highlighted that over-represented molecular scaffo…
View article: Molecular Docking and Virtual Screening of Boswellia dalzielii Phytochemicals as Potential Inhibitors of Rabies lyssavirus.
Molecular Docking and Virtual Screening of Boswellia dalzielii Phytochemicals as Potential Inhibitors of Rabies lyssavirus. Open
Rabies is a fatal viral encephalitic disease caused by the Rabies lyssavirus that has the highest case fatality rate of any infectious disease. Infection with rabies virus takes either the furious form or paralytic form defined by neurolog…
View article: The Deep Core: Cancer Vulnerability, Drug Resistance, and Evolutionary Plasticity in the Human Proteome
The Deep Core: Cancer Vulnerability, Drug Resistance, and Evolutionary Plasticity in the Human Proteome Open
We present a computational method to identify the minimal regulatory backbone of the human proteome using multi-distance dominating set analysis. Applying our DeepDS algorithm to the human protein-protein interaction network, we identified…
View article: Drugs induced Raynaud's phenomenon and underlying mechanism: a disproportionality analysis from the <scp>WHO</scp> pharmacovigilance database
Drugs induced Raynaud's phenomenon and underlying mechanism: a disproportionality analysis from the <span>WHO</span> pharmacovigilance database Open
Objectives The aim of this study is to generate hypotheses about unknown drugs associated with the onset or worsening of Raynaud's Phenomenon (RP) and to explore their potential pathophysiological mechanisms through a mixed disproportional…
View article: Deep learning-based screening and design of novel therapeutics that reverse disease-associated transcriptional phenotype
Deep learning-based screening and design of novel therapeutics that reverse disease-associated transcriptional phenotype Open
Identifying drugs that reverse expression of disease-associated transcriptomic features has been widely explored as a strategy for discovering drug repurposing candidates, but its potential for novel compound discovery and optimization rem…
View article: Darwin PBPK Platform: AI-Powered Pharmacokinetic Prediction
Darwin PBPK Platform: AI-Powered Pharmacokinetic Prediction Open
State-of-the-art deep learning platform for PBPK parameter prediction (fraction unbound, volume of distribution, clearance) using multi-modal molecular representations. Features ChemBERTa embeddings (768d), molecular graphs (PyTorch Geomet…
View article: Investigating the potential anti-cancer mechanism for thyroid cancer: Role of Herba Epimedii via network pharmacology approach
Investigating the potential anti-cancer mechanism for thyroid cancer: Role of Herba Epimedii via network pharmacology approach Open
View article: Knowledge Graph-Guided Identification of Multiple Sclerosis and Therapeutic Trend Analysis: Real-World Evidence from Two Large Healthcare Systems
Knowledge Graph-Guided Identification of Multiple Sclerosis and Therapeutic Trend Analysis: Real-World Evidence from Two Large Healthcare Systems Open
Background The multiple sclerosis (MS) therapeutic landscape has evolved over time. Objective We conducted a knowledge graph-guided analysis of MS-specific disease-modifying therapy (DMT) prescription trends using longitudinal real-world c…
View article: A computer‐aided drug repurposing: the antibacterial agents targeting GroEL
A computer‐aided drug repurposing: the antibacterial agents targeting GroEL Open
Background and Purpose Drug repurposing (DR) presents a compelling alternative to traditional drug discovery, offering lower risk and cost by applying approved drugs to new indications. Computational methods play a vital role in early‐stag…
View article: PuffyBot: An Untethered Shape Morphing Robot for Multi-environment Locomotion
PuffyBot: An Untethered Shape Morphing Robot for Multi-environment Locomotion Open
Amphibians adapt their morphologies and motions to accommodate movement in both terrestrial and aquatic environments. Inspired by these biological features, we present PuffyBot, an untethered shape morphing robot capable of changing its bo…
View article: PuffyBot: An Untethered Shape Morphing Robot for Multi-environment Locomotion
PuffyBot: An Untethered Shape Morphing Robot for Multi-environment Locomotion Open
Amphibians adapt their morphologies and motions to accommodate movement in both terrestrial and aquatic environments. Inspired by these biological features, we present PuffyBot, an untethered shape morphing robot capable of changing its bo…
View article: Integrating In Silico Techniques in Drug Discovery: ADMET, Network Pharmacology, Docking, Dynamics and Deep Learning
Integrating In Silico Techniques in Drug Discovery: ADMET, Network Pharmacology, Docking, Dynamics and Deep Learning Open
Drug discovery remains a resource-intensive process plagued by high failure rates due to efficacy, pharmacokinetics and safety issues. This review explores key in silico computational approaches that enhance efficiency and precision …
View article: Integrating In Silico Techniques in Drug Discovery: ADMET, Network Pharmacology, Docking, Dynamics and Deep Learning
Integrating In Silico Techniques in Drug Discovery: ADMET, Network Pharmacology, Docking, Dynamics and Deep Learning Open
Drug discovery remains a resource-intensive process plagued by high failure rates due to efficacy, pharmacokinetics and safety issues. This review explores key in silico computational approaches that enhance efficiency and precision in mod…
View article: SLC30A3 as a Zinc Transporter-Related Biomarker and Potential Therapeutic Target in Alzheimer’s Disease
SLC30A3 as a Zinc Transporter-Related Biomarker and Potential Therapeutic Target in Alzheimer’s Disease Open
Background: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder with unclear pathogenic mechanisms. Dysregulated zinc metabolism contributes to AD pathology. This study aimed to identify zinc metabolism-related hub genes t…
View article: Artificial intelligence in drug-drug interaction checking
Artificial intelligence in drug-drug interaction checking Open
Artificial Intelligence (AI) has revolutionized modern medicine by providing computational solutions to manage complex clinical data and improve therapeutic outcomes. In pharmacology, AI particularly machine learning (ML) and deep learning…
View article: Integrative Genomic and Computational Drug Discovery Approach to Unveil Key Pathways and Therapeutic Targets in Coronary Artery Disease
Integrative Genomic and Computational Drug Discovery Approach to Unveil Key Pathways and Therapeutic Targets in Coronary Artery Disease Open
Coronary artery disease (CAD) is the most common cardiovascular disorder and the leading cause of heart-related deaths in world. Increasing molecular targets have been discovered for CAD and CAD-related complications prognosis and therapy.…
View article: Enhancing multi-task in vivo toxicity prediction via integrated knowledge transfer of chemical knowledge and in vitro toxicity information
Enhancing multi-task in vivo toxicity prediction via integrated knowledge transfer of chemical knowledge and in vitro toxicity information Open
View article: RNA sequencing and bioinformatics analysis of tissue biopsy of abdominal fat in obesity associated with cardio-metabolic diseases
RNA sequencing and bioinformatics analysis of tissue biopsy of abdominal fat in obesity associated with cardio-metabolic diseases Open
Obesity associated with cardiometabolic diseases is a major metabolic disorder and a significant global health issue. However, the specific molecular mechanisms of obesity associated with cardiometabolic diseases remain unclear. This study…
View article: Dual-Pathway Fusion of EHRs and Knowledge Graphs for Predicting Unseen Drug-Drug Interactions
Dual-Pathway Fusion of EHRs and Knowledge Graphs for Predicting Unseen Drug-Drug Interactions Open
Drug-drug interactions (DDIs) remain a major source of preventable harm, and many clinically important mechanisms are still unknown. Existing models either rely on pharmacologic knowledge graphs (KGs), which fail on unseen drugs, or on ele…
View article: Network Toxicology and Molecular Docking Reveal the Toxicological Mechanisms of DEHP in Bone Diseases
Network Toxicology and Molecular Docking Reveal the Toxicological Mechanisms of DEHP in Bone Diseases Open
Di(2-ethylhexyl) phthalate (DEHP), a widely employed exogenous plasticizer, has become pervasive in the environment and living organisms due to its extensive use in food packaging, medical devices, and daily consumer products, and is estab…
View article: In-silico transformation analysis for exposomics
In-silico transformation analysis for exposomics Open
These are supporting information for the manuscript - "Expanding the chemical exposome using in-silico transformation analysis – an example using insecticides" We analyze the chemical reaction data available in the PubChe…