February 23, 2024

Bioinformatics Databases

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Bioinformatics Databases

Bioinformatics databases play a crucial role in pharmaceutical research and drug discovery by providing access to a vast amount of biological and chemical data. These databases contain information on genes, proteins, small molecules, interactions, pathways, and various other biological entities. Here are some notable bioinformatics databases used in the pharmaceutical industry:


PubChem is a comprehensive database maintained by the National Center for Biotechnology Information (NCBI). It provides information on the biological activities of small molecules, including drugs and drug-like compounds. PubChem includes chemical structures, biological assays, compound properties, and associated references.


DrugBank is a widely used database that combines comprehensive drug information with bioinformatics and cheminformatics data. It provides data on drug targets, drug metabolism, pharmacokinetics, drug-drug interactions, and drug-like properties. DrugBank is valuable for studying drug mechanisms of action and identifying potential drug targets.


ChEMBL is a database maintained by the European Molecular Biology Laboratory (EMBL). It focuses on the bioactivity and chemical properties of small molecules, primarily drugs. ChEMBL includes data on binding affinities, target annotations, compound structures, and bioactivity assays. It is particularly useful for exploring drug-target interactions and compound optimization.

Protein Data Bank (PDB):

PDB is a worldwide repository of three-dimensional (3D) structures of biological macromolecules, including proteins and nucleic acids. It provides information on the 3D structures of protein targets, allowing researchers to study protein-ligand interactions, perform structure-based drug design, and understand protein function.


UniProt is a comprehensive protein database that provides information on protein sequences, functions, structures, and interactions. It integrates data from various resources, including PDB and scientific literature. UniProt is valuable for identifying potential drug targets, studying protein families, and retrieving protein-related information.

Kyoto Encyclopedia of Genes and Genomes (KEGG):

KEGG is a database that focuses on biological pathways and their associated genes, proteins, and small molecules. It provides information on metabolic pathways, signaling pathways, and diseases. KEGG helps researchers understand the molecular mechanisms underlying diseases and identify potential drug targets.


ClinicalTrials.gov is a registry and database of clinical trials conducted worldwide. It provides information on ongoing and completed clinical trials, including details about study design, interventions, outcomes, and participating organizations. ClinicalTrials.gov is useful for tracking the progress of drug development and exploring potential collaborations.


The Cancer Genome Atlas (TCGA) is a resource that provides genomic and clinical data on various cancer types. It offers access to multi-omics data, including DNA sequencing, gene expression, and epigenetic profiles of tumors. TCGA aids in identifying potential biomarkers and therapeutic targets for cancer drug discovery.

These databases, among many others, offer valuable resources and tools for pharmaceutical researchers. They enable data integration, analysis, and visualization, helping to accelerate drug discovery, target identification, lead optimization, and personalized medicine research.

Suggested readings:

First Year B Pharm Notes, Syllabus, Books, PDF Subjectwise/Topicwise

F Y B Pharm Sem-IF Y B Pharm Sem-II
BP101T Human Anatomy and Physiology I TheoryBP201T Human Anatomy and Physiology II – Theory
BP102T Pharmaceutical Analysis I TheoryBP202T Pharmaceutical Organic Chemistry I Theory
BP103T Pharmaceutics I TheoryBP203T Biochemistry – Theory
BP104T Pharmaceutical Inorganic Chemistry TheoryBP204T Pathophysiology – Theory
BP105T Communication skills TheoryBP205T Computer Applications in Pharmacy Theory
BP106RBT Remedial BiologyBP206T Environmental sciences – Theory
BP106RMT Remedial Mathematics TheoryBP207P Human Anatomy and Physiology II Practical
BP107P Human Anatomy and Physiology PracticalBP208P Pharmaceutical Organic Chemistry I Practical
BP108P Pharmaceutical Analysis I PracticalBP209P Biochemistry Practical
BP109P Pharmaceutics I PracticalBP210P Computer Applications in Pharmacy Practical
BP110P Pharmaceutical Inorganic Chemistry Practical
BP111P Communication skills Practical
BP112RBP Remedial Biology Practical