Computational Biology
371 items from inoue0426/awesome-computational-biology ★159
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SIGNOR 2.0 signor.uniroma2.it
Database of causal signaling interactions and pathways, with signed and directed relationships between proteins.
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SIDER (Side Effect Resource) sideeffects.embl.de
Database of 1,430 approved drugs with their recorded adverse drug reactions across 27 system-organ classes.
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SeqBench seqbench.com
Web-based molecular biology sequence workbench for primer design, cloning simulation (Gibson, Golden Gate, restriction digest), CRISPR guide RNA design, and sequence analysis, with a public REST API, OpenAPI 3.1 spec, and MCP server.
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scvi-tools scvi-tools.org
Probabilistic models for single-cell omics data analysis.
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Scanpy scanpy.readthedocs.io
Python library for scRNA-seq analysis.
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Seurat satijalab.org
R library for scRNA-seq analysis.
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ROADMAP Epigenomics roadmapepigenomics.org
Reference epigenome maps for 111 primary human cell types and tissues, including histone modifications, chromatin accessibility, and DNA methylation.
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Rhea rhea-db.org
Database of chemical reactions.
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Rfam rfam.org
Database of RNA families with sequence alignments and consensus structures.
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Ensembl REST API rest.ensembl.org
API for genomic annotations, variants, genes, and comparative genomics.
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Drug Repurposing Hub repo-hub.broadinstitute.org
Collections of drug repurposing data (drug, MoA, target, etc).
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RegNetwork regnetworkweb.org
Database of gene regulatory networks covering transcription factor–target gene and miRNA–gene interaction data across multiple species.
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Reactome reactome.org
Expert-curated, peer-reviewed pathway database with detailed reaction mechanisms.
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PROTEIN DATA BANK (PDB) rcsb.org
3D structures of proteins, nucleic acids, complexes.
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PubChem pubchem.ncbi.nlm.nih.gov
One of the largest chemical databases (compounds, genes, and proteins).
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CPTAC (Clinical Proteomic Tumor Analysis Consortium) proteomics.cancer.gov
Multi-omic proteogenomic datasets for multiple cancer types linking proteomics with genomics.
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THE HUMAN PROTEIN ATLAS proteinatlas.org
Comprehensive human protein database (cells, tissues, organs).
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Critical Assessment of Structure Prediction (CASP) predictioncenter.org
Assessing methods for protein structure prediction.
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Cancer Therapeutics Response Portal (CTRP) portals.broadinstitute.org
Drug sensitivity profiles across ~900 cancer cell lines for >400 compounds.
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Replogle et al. 2022 K562 Genome-wide Perturb-seq plus.figshare.com
Genome-scale CRISPRi Perturb-seq targeting nearly all expressed genes in K562 cells.
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Open Targets Platform API platform.opentargets.org
API for target–disease associations integrating genetics, genomics, and drug data.
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Open Targets Platform platform.opentargets.org
Systematic target identification and prioritization platform integrating genetics, genomics, and drug data for drug discovery.
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PK-DB pk-db.com
Open database of experimental pharmacokinetics (PK) and ADME data from clinical and preclinical studies.
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PharmGKB pharmgkb.org
Curated pharmacogenomics dataset linking genetic variants to drug response phenotypes across thousands of drugs.
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PDBBind pdbbind-plus.org.cn
Binding affinity data for biomolecular complexes.
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PathwayCommons pathwaycommons.org
Database of pathways and interactions.
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kallisto pachterlab.github.io
Near-optimal RNA-seq quantification using pseudoalignment for fast transcript abundance estimation.
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SAbDab opig.stats.ox.ac.uk
Structural Antibody Database containing all antibody structures in the PDB.
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OADB (Observed Antibody Space Database) opig.stats.ox.ac.uk
Database of antibody sequences from immune repertoire sequencing.
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OncoKB oncokb.org
Precision oncology knowledge base of cancer genes, variants, and therapeutic implications.
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OmniPath omnipathdb.org
Comprehensive resource integrating protein interactions, signaling pathways, gene regulatory networks, and miRNA targets from over 100 databases.
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OMIM (Online Mendelian Inheritance in Man) omim.org
Comprehensive database of human genes and genetic disorders.
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OGB (Open Graph Benchmark) ogb.stanford.edu
Large-scale graph ML benchmark suite including biological datasets such as ogbl-ppa (protein-protein associations) and ogbg-molhiv.
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PubMed E-utilities (esearch/efetch) nlm.nih.gov
APIs for searching and retrieving biomedical literature from PubMed.
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NeXtProt nextprot.org
Expert knowledge base on human proteins with deep functional annotation, complementary to UniProt.
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Human Genome Resources at NCBI ncbi.nlm.nih.gov
Database for genomics, proteomics, transcriptomics, and systems biology.
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Datlinger et al. 2017 CROP-seq ncbi.nlm.nih.gov
Pooled CRISPR knockout screen with single-cell transcriptomic readout in Jurkat cells under T-cell receptor stimulation.
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Adamson et al. 2016 Perturb-seq ncbi.nlm.nih.gov
CRISPRi Perturb-seq in K562 cells for systematic dissection of the unfolded protein response.
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Dixit et al. 2016 Perturb-seq ncbi.nlm.nih.gov
Pooled CRISPR knockout with single-cell RNA-seq across K562 and dendritic-cell screens, including stimulated conditions and combinatorial perturbations.
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GSE191127 Breast Cancer Pre/Post Chemotherapy ncbi.nlm.nih.gov
Bulk RNA-seq and genomics from matched pre- and post-neoadjuvant chemotherapy breast tumors with treatment outcomes.
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sci-Plex ncbi.nlm.nih.gov
Single-cell chemical perturbation screen of ~650,000 transcriptomes across three cancer cell lines, 188 compounds, and four doses.
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Gasperini et al. 2019 CRISPRi enhancer screen ncbi.nlm.nih.gov
High-MOI single-cell CRISPRi screen in K562 cells targeting thousands of candidate enhancers to map enhancer-gene regulation.
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Gene Expression Omnibus ncbi.nlm.nih.gov
Public functional genomics database.
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NCBI E-utilities ncbi.nlm.nih.gov
Unified APIs for accessing NCBI databases (Gene, GEO, SRA, PubChem, etc).
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MIX-Seq nature.com
Multiplexed single-cell transcriptional profiling of chemical and genetic perturbation responses across pools of cancer cell lines.
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PDX-Atlas muralportal.pdxatlas.org
Portal integrating clinical, genomic, transcriptomic, and drug-response data from patient-derived xenograft models.
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MoNA MassBank of North America mona.fiehnlab.ucdavis.edu
Meta-database of metabolite mass spectra, metadata, and associated compounds.
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MoleculeNet moleculenet.ai
Benchmark datasets for molecular machine learning.
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miRBase mirbase.org
Reference repository for microRNA gene annotations, sequences, and experimentally validated targets.
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MIMIC-IV mimic.mit.edu
Freely accessible critical care database.
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