| Running ColabFold notebook on a HPC |
Covers basics of ssh and jupyter notebooks on a HPC
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| ColabFold tutorial |
Three short tutorials for running ColabFold
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| BLAST tutorial |
Short how-to guide on using BLAST from the command line
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| Amber tutorial |
Molecular Dynamics simulation tutorials
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| LAMMPS tutorials |
Molecular Dynamics simulation tutorials
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| GROMACS tutorials |
Molecular Dynamics simulation tutorials
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| GROMACS tutorials |
Molecular Dynamics simulation tutorials
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| ColabDesign notebooks |
Google Colab notebooks for running protein design
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| Pyrosetta tutorials |
Collection of how-to guides for protein design
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| Rosetta tutorial |
User guide on protein design with Rosetta
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| RFDiffusion |
Walkthrough guide on running RFDiffusion
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| HMMER tutorial |
User guide for running HMMER on the command line
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| HH-suite tutorial |
User guide for running Hiden Markov Models of protein sequences on the command line
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| MMseqs2 tutorial |
User guide for running MMseqs from the command line
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| Biomolecular Structure Prediction Tools |
Lists state-of-the-art and emerging tools for Biomolecular Structure Prediction.
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| AlphaFold3 explainer |
A visual walkthrough of the AlphaFold3 architecture, with more details and diagrams than you were probably looking for.
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| EMBL-EBI AlphaFold Guide |
The best way to get up to competency with using an interpreting AlphaFold. Should be done by all grad students using AF
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