Bioinformatics in translational drug discovery

Bioinformatics approaches are becoming ever more essential in translational drug discovery both in academia and within the pharmaceutical industry. Computational exploitation of the increasing volumes of data generated during all phases of drug discovery is enabling key challenges of the process to be addressed. Here, we highlight some of the areas in which bioinformatics resources and methods are being developed to support the drug discovery pipeline. These include the creation of large data warehouses, bioinformatics algorithms to analyse ‘big data’ that identify novel drug targets and/or biomarkers, programs to assess the tractability of targets, and prediction of repositioning opportunities that use licensed drugs to treat additional indications.

• Publication year

  2017

• Venue

  Bioscience Reports

• Publication date

  2017-05-09

• Fields of study

  Medicine, Computer Science

• Identifiers
  DOI 10.1042/BSR20160180PMID 28487472PMCID 6448364
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Metabolomics study of cancer targeting small molecule kinase inhibitors in cell culture

  2017cited by this paper
• Fragment Profiling Approach to Inhibitors of the Orphan M. tuberculosis P450 CYP144A1.

  2017cited by this paper
• Identification and analysis of mutational hotspots in oncogenes and tumour suppressors

  2017cited by this paper
• Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction

  2017cited by this paper
• PARP inhibitors: the race is on

  2016cited by this paper
• ClinicalTrials.gov and Drugs@FDA: A Comparison of Results Reporting for New Drug Approval Trials

  2016cited by this paper
• Toward a Shared Vision for Cancer Genomic Data.

  2016cited by this paper
• Expanding the antimalarial toolkit: Targeting host–parasite interactions

  2016cited by this paper
• Mutational patterns in oncogenes and tumour suppressors.

  2016cited by this paper
• Drug-repositioning opportunities for cancer therapy: novel molecular targets for known compounds.

  2016cited by this paper
• Molecular Pharmacology of Malignant Pleural Mesothelioma: Challenges and Perspectives From Preclinical and Clinical Studies.

  2016cited by this paper
• Molecular signatures associated with ZIKV exposure in human cortical neural progenitors

  2016cited by this paper
• A Landscape of Pharmacogenomic Interactions in Cancer

  2016cited by this paper
• Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer

  2016cited by this paper
• DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

  2016cited by this paper
• A survey of current trends in computational drug repositioning

  2016cited by this paper
• Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond

  2016cited by this paper
• Pharos: Collating protein information to shed light on the druggable genome

  2016cited by this paper
• ADA-SCID Gene Therapy Endorsed By European Medicines Agency For Marketing Authorization.

  2016cited by this paper
• canSAR: an updated cancer research and drug discovery knowledgebase

  2015cited by this paper
• A novel locus of resistance to severe malaria in a region of ancient balancing selection

  2015cited by this paper
• Pocketome of Human Kinases: Prioritizing the ATP Binding Sites of (Yet) Untapped Protein Kinases for Drug Discovery

  2015cited by this paper
• In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities.

  2015cited by this paper
• Computational and experimental advances in drug repositioning for accelerated therapeutic stratification.

  2015cited by this paper
• Therapeutic opportunities within the DNA damage response

  2015cited by this paper
• The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

  2015cited by this paper
• PubChem Substance and Compound databases

  2015cited by this paper
• Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery

  2015cited by this paper
• Impact of IL28B gene polymorphisms rs8099917 and rs12980275 on response to pegylated interferon-α/ribavirin therapy in chronic hepatitis C genotype 4 patients

  2015cited by this paper
• FDA Approval Summary: Olaparib Monotherapy in Patients with Deleterious Germline BRCA-Mutated Advanced Ovarian Cancer Treated with Three or More Lines of Chemotherapy

  2015cited by this paper
• Distinctive Behaviors of Druggable Proteins in Cellular Networks

  2015cited by this paper
• DMAP: a connectivity map database to enable identification of novel drug repositioning candidates

  2015cited by this paper
• Genomic risk prediction of complex human disease and its clinical application.

  2015cited by this paper
• SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets

  2015cited by this paper
• Breast cancer patient stratification using a molecular regularized consensus clustering method.

  2014cited by this paper
• Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples.

  2014cited by this paper
• Drugging the p53 pathway: understanding the route to clinical efficacy

  2014cited by this paper
• Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin.

  2014cited by this paper
• Computational and Experimental Prediction of Human C-Type Lectin Receptor Druggability

  2014cited by this paper
• TuberQ: a Mycobacterium tuberculosis protein druggability database

  2014cited by this paper
• GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database

  2014cited by this paper
• Role of the host genetic variability in the influenza A virus susceptibility.

  2014cited by this paper
• STRING v10: protein–protein interaction networks, integrated over the tree of life

  2014cited by this paper
• Guidelines for investigating causality of sequence variants in human disease

  2014cited by this paper
• GWAS and drug targets

  2014cited by this paper
• The BioGRID interaction database: 2015 update

  2014cited by this paper
• Gene Ontology Consortium: going forward

  2014cited by this paper
• Mutational heterogeneity in cancer and the search for new cancer genes

  2014cited by this paper
• Molecular testing guideline for selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors: guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology.

  2013cited by this paper
• Cancer Genome Landscapes

  2013cited by this paper
• Comprehensive identification of mutational cancer driver genes across 12 tumor types

  2013cited by this paper
• Syn-Lethality: An Integrative Knowledge Base of Synthetic Lethality towards Discovery of Selective Anticancer Therapies

  2013cited by this paper
• Drug repositioning: a machine-learning approach through data integration

  2013cited by this paper
• Molecular testing guideline for selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors: guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology.

  2013cited by this paper
• DrugBank 4.0: shedding new light on drug metabolism

  2013cited by this paper
• PharmGKB: the Pharmacogenomics Knowledge Base.

  2013cited by this paper
• The Open Access Malaria Box: A Drug Discovery Catalyst for Neglected Diseases

  2013cited by this paper
• Network-based stratification of tumor mutations

  2013cited by this paper
• Gene therapy clinical trials worldwide to 2012 – an update

  2013cited by this paper
• Molecular Testing Guideline for Selection of Lung Cancer Patients for EGFR and ALK Tyrosine Kinase Inhibitors: Guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology

  2013cited by this paper
• canSAR: updated cancer research and drug discovery knowledgebase

  2013cited by this paper
• Open source drug discovery for malaria

  2013cited by this paper
• Mutational heterogeneity in cancer and the search for new cancer genes

  2013cited by this paper
• Five years of GWAS discovery.

  2012cited by this paper
• SIFT web server: predicting effects of amino acid substitutions on proteins

  2012cited by this paper
• Introduction to the genetics and biology of interleukin‐28B

  2012cited by this paper
• Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation

  2012cited by this paper
• Machine Learning Prediction of Cancer Cell Sensitivity to Drugs Based on Genomic and Chemical Properties

  2012cited by this paper
• Open access

  2012cited by this paper
• Translational research in infectious disease: current paradigms and challenges ahead

  2012cited by this paper
• Combining Global and Local Measures for Structure-Based Druggability Predictions

  2012cited by this paper
• Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

  2012cited by this paper
• Druggability Analysis and Structural Classification of Bromodomain Acetyl-lysine Binding Sites

  2012cited by this paper
• Structural Chemistry of the Histone Methyltransferases Cofactor Binding Site

  2011cited by this paper
• BioStar: An Online Question & Answer Resource for the Bioinformatics Community

  2011cited by this paper
• The role of translational bioinformatics in drug discovery.

  2011cited by this paper
• Predicting the functional impact of protein mutations: application to cancer genomics

  2011cited by this paper
• CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

  2011cited by this paper
• A Genome-Wide Meta-Analysis of Six Type 1 Diabetes Cohorts Identifies Multiple Associated Loci

  2011cited by this paper
• ChEMBL: a large-scale bioactivity database for drug discovery

  2011cited by this paper
• Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel.

  2011cited by this paper
• Fragment screening to predict druggability (ligandability) and lead discovery success.

  2011cited by this paper
• Principles and strategies for developing network models in cancer.

  2011cited by this paper
• What makes a good drug target?

  2011cited by this paper
• Exploiting drug-disease relationships for computational drug repositioning

  2011cited by this paper
• Structure-based druggability assessment--identifying suitable targets for small molecule therapeutics.

  2011cited by this paper
• International Cancer Genome Consortium Data Portal—a one-stop shop for cancer genomics data

  2011cited by this paper
• Phase 2a Study of the CCR5 Monoclonal Antibody PRO 140 Administered Intravenously to HIV-Infected Adults

  2010cited by this paper
• Multiple common variants for celiac disease influencing immune gene expression

  2010cited by this paper
• Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery.

  2010cited by this paper
• Binding-Site Assessment by Virtual Fragment Screening

  2010cited by this paper
• Understanding and predicting druggability. A high-throughput method for detection of drug binding sites.

  2010cited by this paper
• Drug-like Density: A Method of Quantifying the "Bindability" of a Protein Target Based on a Very Large Set of Pockets and Drug-like Ligands from the Protein Data Bank

  2010cited by this paper
• Gene Expression Signature-Based Screening Identifies New Broadly Effective Influenza A Antivirals

  2010cited by this paper
• A method and server for predicting damaging missense mutations

  2010cited by this paper
• How to improve R&D productivity: the pharmaceutical industry's grand challenge

  2010cited by this paper
• Prioritizing GWAS results: A review of statistical methods and recommendations for their application.

  2010cited by this paper
• An integrated approach to uncover drivers of cancer.

  2010cited by this paper
• Infectious diseases not immune to genome-wide association

  2010cited by this paper
• Genetic studies reveal the role of the endocrine and metabolic systems in aging.

  2010cited by this paper

• Didymin Inhibits Proliferation and Induces Apoptosis in Gastric Cancer Cells by Modulating the PI3K/Akt Pathway

  2025cites this paper
• A Computational Biophysical Approach to Inhibit the Oncogenic Activity of CRIPTO Protein in Human Cancers

  2025cites this paper
• LAX1 as a core biomarker in Alzheimer’s disease and periodontitis via the STAT signaling pathway

  2025cites this paper
• Current Status on the Convergence of Artificial Intelligence and Formulation Development in Industry: A Review

  2025cites this paper
• Bu Yang Huan Wu Decoction controls synovitis via HIF-1/VEGF signaling for osteoarthritis therapy

  2025cites this paper
• Identification of HK3 as a Potential Key Biomarker in the Progression of Temporomandibular Joint Osteoarthritis via RNA Sequencing

  2025cites this paper
• Interactions of Linalool and Linalyl Acetate with Selected Dog Cytochrome P450 (CYP) Proteins Identified by In Silico Drug Discovery Followed by Molecular Docking Analysis

  2025cites this paper
• Potential mechanisms of acupuncture treatment for rheumatoid arthritis: a study based on network topology and machine learning

  2025cites this paper
• Uncovering Overlapping Gene Networks and Potential Therapeutic Targets in Osteoporosis and COVID-19 Through Bioinformatics Analysis

  2025cites this paper
• In-Silico Pharmacology, Methods and Applications for Drug Design and Discovery: A Review

  2025cites this paper
• The role of ELK4 up-regulation in macrophage polarization and its mechanism in connective tissue disease-associated interstitial lung disease.

  2025cites this paper
• Exploring research trends and hotspots in PI3K/Akt signaling pathway in ischemic stroke: a bibliometric analysis

  2025cites this paper
• AI-Based Drug Discovery and Design for Different Genetic Designs.

  2025cites this paper
• Value of Bioinformatics Models for Predicting Translational Control of Angiogenesis

  2025cites this paper
• A Comprehensive Review of Harnessing Bioinformatics in Biochemistry: A New Era of Data-Driven Discoveries and Applications

  2025cites this paper
• Meta-analysis and review of in silico methods in drug discovery – part 1: technological evolution and trends from big data to chemical space

  2025cites this paper
• Functional characterization of key protein biomarkers in spontaneous intracerebral hemorrhage pathogenesis: Structure and function of NUAK1 protein and ERO1L protein macromolecules.

  2025cites this paper
• Advances in bioinformatic methods for the acceleration of the drug discovery from nature.

  2025cites this paper
• Integrated Bioinformatics Analysis Identified ASNS and DDIT3 as the Therapeutic Target in Castrate-Resistant Prostate Cancer

  2024cites this paper
• Advancements in Contemporary Pharmacological Innovation: Mechanistic Insights and Emerging Trends in Drug Discovery and Development

  2024cites this paper
• Bioinformatics and network pharmacology discover the molecular mechanism of Liuwei Dihuang pills in treating cerebral palsy

  2024cites this paper
• Strategic Tasks and Prospects for the Development of the Resource Base of Healthcare and Health Saving through the Prism of Personalized and Precision Medicine

  2024cites this paper
• Tribuloside: Mechanisms and Efficacy in Treating Acute Lung Injury Revealed by Network Pharmacology and Experimental Validation

  2024cites this paper
• Bioinformatics-based discovery of biomarkers and immunoinflammatory targets in children with cerebral palsy: An observational study

  2024cites this paper
• Prognostic Model Construction of Disulfidptosis-Related Genes and Targeted Anticancer Drug Research in Pancreatic Cancer

  2024cites this paper
• Skeletal Transformations of Terpenoid Forskolin Employing an Oxidative Rearrangement Strategy.

  2024cites this paper
• Synthesis, spectroscopic analysis, and computational-based investigations on ‘azo-coumarin-Co(II)-galangin’ hybrids exhibit multipotential activities

  2024cites this paper
• STUDI BIOINFORMATIKA KONSTITUEN MAYOR Centella asiatica DALAM MEMODULASI KECEMASAN DAN DEPRESI

  2024cites this paper
• Characterization of prevalent tyrosine kinase inhibitors and their challenges in glioblastoma treatment

  2024cites this paper
• An AI Approach to Identifying Novel Therapeutics for Rheumatoid Arthritis

  2023cites this paper
• An integrated strategy to explore the wine-processed mechanism of Corni Fructus on chronic renal failure based on metabolomics, network analysis and bioinformatics approaches.

  2023cites this paper
• Computer-aided identification of bioactive compounds from Gongronema latifolium leaf with therapeutic potential against GSK3β, PTB1B and SGLT2

  2023cites this paper
• Prediction of resveratrol target proteins: a bioinformatics analysis

  2023cites this paper
• Exploring the role of differentially expressed metabolic genes and their mechanisms in bone metastatic prostate cancer

  2023cites this paper
• Integrative analysis of tertiary lymphoid structures and immune microenvironment in patients with esophageal carcinoma

  2023cites this paper
• Advancements in portable instruments based on affinity-capture-migration and affinity-capture-separation for use in clinical testing and life science applications.

  2023cites this paper
• Bibliometric Analysis of Artificial Intelligence in Drug Development

  2023cites this paper
• Design and Diversity Analysis of Chemical Libraries in Drug Discovery.

  2023cites this paper
• Introducing JMIR Bioinformatics and Biotechnology: A Platform for Interdisciplinary Collaboration and Cutting-Edge Research

  2023cites this paper
• Identification of key genes in spontaneous cerebral hemorrhage and prevention of disease damage: LASSO and SVM regression.

  2023cites this paper
• A review of SARS-CoV-2 drug repurposing: databases and machine learning models

  2023cites this paper
• Identification of Hub Genes in the Pathogenesis of Bronchiolitis Obliterans via Bioinformatic Analysis and Experimental Verification

  2023cites this paper
• Transcriptome analysis constructed the necroptosis associated prognostic signature in endometrial cancer and identified EZH2 as a potential biomarker

  2023cites this paper
• OTTM: an automated classification tool for translational drug discovery from omics data

  2023cites this paper
• Precision drug design against Acidovorax oryzae: leveraging bioinformatics to combat rice brown stripe disease

  2023cites this paper
• Danggui Shaoyao San ameliorates the lipid metabolism via the PPAR signaling pathway in a Danio rerio (zebrafish) model of hyperlipidemia.

  2023cites this paper
• Using CADD tools to inhibit the overexpressed genes FAP, FN1, and MMP1 by repurposing ginsenoside C and Rg1 as a treatment for oral cancer

  2023cites this paper
• Identification of hub genes and their correlation with immune infiltrating cells in membranous nephropathy: an integrated bioinformatics analysis

  2023cites this paper
• Computational Approaches: A New Frontier in Cancer Research.

  2023cites this paper
• Investigating trial design variability in trials of disease-modifying therapies in Parkinson’s disease: a scoping review protocol

  2023cites this paper
• Role of prognostic gene DKK1 in oral squamous cell carcinoma

  2023cites this paper
• Identifying the natural products in the treatment of atherosclerosis by increasing HDL-C level based on bioinformatics analysis, molecular docking, and in vitro experiment

  2023cites this paper
• The Potential Mechanisms of Acupuncture in Cardiac Arrhythmias by Bioinformatics

  2023cites this paper
• Bioinfo-pharmacology: the example of therapeutic hypothermia

  2022cites this paper
• Elucidation of the Key Therapeutic Targets and Potential Mechanisms of Marmesine against Knee Osteoarthritis via Network Pharmacological Analysis and Molecular Docking

  2022cites this paper
• A bioinformatics-based approach to study the mechanism of acupuncture for primary dysmenorrhea

  2022cites this paper
• In Silico Methods for Identification of Potential Active Sites of Therapeutic Targets

  2022cites this paper
• Identifying a Three-Gene Signature and Associated Drugs for Hepatitis B Virus-Related Hepatocellular Carcinoma Using Comprehensive Bioinformatics Analysis.

  2022cites this paper
• Shedding Light on the Drug–Target Prediction of the Anti-Inflammatory Peptide TnP with Bioinformatics Tools

  2022cites this paper
• Molecular docking and molecular dynamic simulation approaches for drug development and repurposing of drugs for severe acute respiratory syndrome-Coronavirus-2

  2022cites this paper
• Artificial intelligence and machine-learning approaches in structure and ligand-based discovery of drugs affecting central nervous system

  2022cites this paper
• Bioinformatics and System Biology Approach to Reveal the Interaction Network and the Therapeutic Implications for Non-Small Cell Lung Cancer Patients With COVID-19

  2022cites this paper
• The Brain Research Hotspot Database (BRHD): A Panoramic Database of the Latest Hotspots in Brain Research

  2022cites this paper
• Development and expansion of the CRISPR/Cas9 toolboxes for powerful genome engineering in yeast.

  2022cites this paper
• Application of computational screening tools and nanotechnology for enhanced drug synergism in cancer therapy.

  2022cites this paper
• Inhibiting effect of miR-29 on proliferation and migration of uterine leiomyoma via the STAT3 signaling pathway

  2022cites this paper
• Anticolon Cancer Targets and Molecular Mechanisms of Tao-He-Cheng-Qi Formula

  2022cites this paper
• A Pharmacoinformatics Analysis of Artemisinin Targets and de novo Design of Hits for Treating Ulcerative Colitis

  2022cites this paper
• Construction of ceRNA network to identify the lncRNA and mRNA related to non-small cell lung cancer

  2021cites this paper
• In silico Methods for Identification of Potential Therapeutic Targets

  2021cites this paper
• Chemical constituents isolated from the aerial parts of Swertia pseudochinensis and their potential neuroprotective effects

  2021cites this paper
• Prioritization of Diagnostic and Prognostic Biomarkers for Lupus Nephritis Based on Integrated Bioinformatics Analyses

  2021cites this paper
• Identification of the similarly expressed genes in patients with polycystic ovary syndrome and transsexuals

  2021cites this paper
• An efficient bioinformatics algorithm for healthcare: Detection and counting of leukocytes, blasts, and erythrocytes

  2021cites this paper
• Bioinformatics prediction of differential miRNAs in non-small cell lung cancer

  2021cites this paper
• Specific Targeting of the Nrf2 Transcription Factor to Prevent Diabetic Kidney Disease Progression by Stimulating the Oxidative Stress Response: A Next-Generation Strategy

  2021cites this paper
• Systems Pharmacology: Enabling Multidimensional Therapeutics

  2021cites this paper
• Is acupuncture effective in the treatment of COVID-19 related symptoms? Based on bioinformatics/network topology strategy

  2021cites this paper
• High Throughput Bioinformatics-based Prediction of the targets for BushenjieduDecoction in preventing relapse of acute leukemia

  2020cites this paper
• Is It Possible to Conduct a Multi-Arm Multi-Stage Platform Trial in Parkinson’s Disease: Lessons Learned from Other Neurodegenerative Disorders and Cancer

  2020cites this paper
• Bioinformatics-based Prediction of the mechanism and targets for BushenjieduDecoction in preventing relapse of acute leukemia

  2020cites this paper
• Metformin coordinates osteoblast/osteoclast differentiation associated with ischemic osteonecrosis

  2020cites this paper
• High-dimensionality Data Analysis of Pharmacological Systems Associated with Complex Diseases

  2019cites this paper
• Computational Drug Repurposing: Current Trends.

  2019cites this paper
• The protective effects of citrullus colocynthis on inhibiting oxidative damage and autophagy-associated cell death in Parkinson's disease

  2019cites this paper
• Bioinformatics approaches for anti-cancer drug discovery.

  2019cites this paper
• TDR Targets 6: driving drug discovery for human pathogens through intensive chemogenomic data integration

  2019cites this paper
• EXPLORING THE EFFECT OF CHRONIC INFLAMMATION ON RESPONSE TO IMMUNE CHECKPOINT INHIBITORS IN CANCER

  2018cites this paper
• Microsecond MD simulations of human CYP2D6 wild-type and five allelic variants reveal mechanistic insights on the function

  2018cites this paper
• System Biology to Access Target Relevance in the Research and Development of Molecular Inhibitors

  2018cites this paper
• A systems biology approach to antimalarial drug discovery

  2018cites this paper
• Advancing Pharmacy Service using Big Data - Are We Fully Utilising the Big Data's Potential Yet?

  2018cites this paper
• Computational Identification and Screening of Natural Compounds as Drug Targets against the Fish Pathogen, Pseudomonas fluorescens

  2017cites this paper
• CURRENT RESEARCH TOPICS IN PHARMACY: In silico Approaches for Drug Design and Discovery

  year unknowncites this paper
• Identification of Potential Biomarkers and Small Molecule Drugs for Bisphosphonate-Related Osteonecrosis of the Jaw (BRONJ): An Integrated Bioinformatics Study Using Big Data

  year unknowncites this paper