Learning, Societies & Courses
7 entriesWhere to learn the field and meet its community.
01ISCB: International Society for Computational BiologyProfessional society behind the ISMB conference, with training, careers and community resources.
02MIT 6.047: Computational Biology (Fall 2015)Open course on genomes, networks and evolution, covering sequence analysis, hidden Markov models and gene expression, with a student-compiled open textbook.
03RosalindLearn computational biology by solving programming problems.
04EMBL-EBI TrainingFree online courses and webinars on biological data resources and analysis.
05Galaxy Training NetworkCommunity-written tutorials for analysis with Galaxy.
06The CarpentriesWorkshops on the programming and data skills researchers need.
07BiostarsQuestion-and-answer community for bioinformatics and computational biology.
Protein Structure & Biomolecular AI
11 entriesPrediction, design and visualisation of proteins and other biomolecules.
08AlphaFold Protein Structure DatabasePredicted protein structures from DeepMind and EMBL-EBI. The 2024 Nobel Prize in Chemistry recognised protein structure prediction (Demis Hassabis and John Jumper) and computational protein design (David Baker).
09AlphaFold ServerWeb tool for predicting biomolecular complexes with AlphaFold 3, offered for non-commercial use.
10AlphaFold 3 codeGoogle DeepMind's AlphaFold 3 inference code on GitHub.
11RCSB Protein Data BankArchive of experimentally determined 3D structures of proteins, nucleic acids and complexes.
12Rosetta CommonsCommunity behind the Rosetta software suite for modelling and designing macromolecules.
13OpenFoldTrainable, open-source reproduction of AlphaFold 2.
14ColabFoldFaster protein structure prediction with AlphaFold 2 and fast homology search, usable from a notebook.
15BoltzOpen-source model for biomolecular structure prediction.
16ESM (EvolutionaryScale)Protein language models and code from EvolutionaryScale.
17PyMOLMolecular visualisation system.
18UCSF ChimeraXVisualisation and analysis of molecular structures and related data.
Molecular Simulation
4 entriesPhysics-based simulation of how biomolecules move and interact.
19GROMACSOpen-source molecular dynamics package for biomolecular systems.
20OpenMMToolkit for molecular simulation with GPU support, scriptable from Python.
21NAMDParallel molecular dynamics code from the University of Illinois for large biomolecular systems.
22AmberSuite of biomolecular simulation programs and force fields.
Systems Biology & Cell Modelling
9 entriesMathematical and agent-based models of pathways, metabolism and cells.
23SBMLSystems Biology Markup Language, a standard format for exchanging computational models.
24BioModelsEMBL-EBI repository of curated mathematical models of biological processes.
25CellMLOpen standard for storing and exchanging computer-based mathematical models.
26COPASISoftware for simulating and analysing biochemical networks.
27COBRApyPython package for constraint-based reconstruction and analysis of metabolic networks.
28Virtual Cell (VCell)Modelling and simulation platform for cell biology from UConn Health.
29TelluriumPython environment for building and simulating systems biology models.
30PhysiCellOpen-source physics-based simulator of multicellular systems.
31CompuCell3DModelling environment for multicellular, cell-based simulations.
Single-Cell, Genomics & Cell Atlases
10 entriesAnalysis of cells and genomes at scale, including AI models of DNA.
32ScanpyPython toolkit for single-cell gene expression analysis.
33SeuratR toolkit for single-cell genomics.
34scverseCommunity and ecosystem of Python tools for single-cell omics.
35CZ CELLxGENEPlatform for exploring and sharing single-cell datasets.
36AlphaGenomeGoogle DeepMind's model for predicting how DNA variants affect gene regulation, with a peer-reviewed paper in Nature.
37Evo (Arc Institute)Genomic foundation models from the Arc Institute.
38nf-coreCommunity-curated Nextflow pipelines for bioinformatics.
39NCBIUS National Center for Biotechnology Information: GenBank, PubMed and many analysis resources.
40EnsemblGenome browser and annotation for vertebrate and other genomes.
41UniProtComprehensive protein sequence and functional annotation resource.
Computational Drug Discovery
4 entriesCheminformatics, docking and machine learning for molecules.
42RDKitOpen-source cheminformatics toolkit.
43DeepChemPython library for deep learning in drug discovery, materials science and biology.
44AutoDock VinaMolecular docking program for predicting how small molecules bind to proteins.
45ChEMBLCurated database of bioactive molecules with drug-like properties.
Journals, Conferences & Preprints
7 entriesWhere computational biology research is published.
46PLOS Computational BiologyOpen-access journal for research on the computational analysis of biological systems.
47Nature Computational ScienceNature journal covering computational science across disciplines, including biology.
48Cell SystemsJournal on systems-level and quantitative biology.
49Bioinformatics (OUP)Journal of the International Society for Computational Biology.
50RECOMBAnnual conference on research in computational molecular biology.
51bioRxiv: BioinformaticsPreprints in bioinformatics.
52arXiv: Quantitative BiologyRecent preprints in quantitative biology.
Books
3 entriesTexts that teach the methods behind the field.
53Bioinformatics Algorithms: An Active Learning ApproachTextbook and online course by Phillip Compeau and Pavel Pevzner on the algorithms behind genomics.
54Biological Sequence AnalysisDurbin, Eddy, Krogh and Mitchison (Cambridge, 1998): probabilistic models, including hidden Markov models, for proteins and nucleic acids.
55An Introduction to Systems BiologyUri Alon's book on design principles of biological circuits.
Research Institutes
6 entriesInstitutions with strong computational biology programmes.
56EMBL-EBIEuropean Bioinformatics Institute, home of many of the databases and tools above.
57Broad InstituteGenomics and biomedical research institute of MIT and Harvard.
58Arc InstituteNon-profit research institute developing tools such as the Evo models.
59NCBS BengaluruNational Centre for Biological Sciences, Tata Institute of Fundamental Research.
60Institute of Bioinformatics and Applied Biotechnology (IBAB)Bengaluru institute for bioinformatics education and research.
61CSIR-IGIBCSIR Institute of Genomics and Integrative Biology, New Delhi.
Related Pages
10 entriesRelated directories on this site.
62BioinformaticsTools, tutorials, journals and workflows for biological data.
63Biological DatabasesDatabases of sequences, structures and pathways.
64Research ResourcesHub of research directories.
65Medical InformaticsInformatics in medicine and health.
66Agentic AI Platforms for Life SciencesAI agent platforms for biology and drug discovery.
67Graph Neural NetworksGNNs, widely used for molecules and biological networks.
68Deep LearningDeep learning algorithms and resources.
69StatisticsFree textbooks, courses and software.
70Python Libraries for Data ScientistsPython data science libraries.
71Workflow EnginesEngines for orchestrating pipelines.
Frequently Asked Questions
What is computational biology?
Computational biology uses mathematical models, simulation, algorithms and data analysis to understand biological systems, from molecules and cells to populations.
How is computational biology different from bioinformatics?
The two overlap heavily and the boundary is not sharp. Bioinformatics is usually described as focusing on tools, databases and methods for managing and analysing biological data such as sequences, while computational biology is usually described as building models and simulations to explain how biological systems work. The Bioinformatics page on this site covers the data-and-tools side.
How do I start learning computational biology?
Learn Python or R and some statistics, then work through Rosalind problems, the free EMBL-EBI courses and the open MIT 6.047 course listed in the learning section.
Which tools predict protein structure?
AlphaFold 2 and 3, OpenFold, ColabFold, Boltz and ESM are covered here, alongside the AlphaFold Protein Structure Database and the RCSB Protein Data Bank for known structures.
Where is computational biology research published?
Journals such as PLOS Computational Biology, Nature Computational Science, Cell Systems and Bioinformatics, conferences such as ISMB and RECOMB, and preprints on bioRxiv and arXiv.