Custom Structures in mmCIF Format for Epictope #5
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… compiled successfully with the conda C compilers on Ubuntu; use BiocManager to install Biostrings, which also is not compiled successfully by conda
…newer Macs and novel AlphaFold structures, which are delivered in mmCIF format
…p version 4 and mmCIF support to work on Windows
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Epictopecontinues to be of great use to our lab: thanks for the great software! This pull request addresses a few issues that we have identifed when usingEpictope. Most importantly, it provides an option to supply a user-specified .cif file toEpictope, enabling users to useEpictopeon custom AlphaFold simulations.Fixing installation issues on Linux:
Epictopedoes not install successfully on some versions of Linux. It appears that some of the requiredRpackages are not compiled correctly by the C compiler that comes withconda. To avoid this issue, I suggest installing pre-compiled versions of these troublesomeRpackages withcondainstead of compiling them inRwithin thecondaenvironment. These changes are included in commit 8bd7b64.Full upgrade to
dsspversion 4 with mmCIF support:The latest version of
Epictopesupports PDB files but not mmCIF, which is now the recommended file format used by the Protein Data Bank (https://doi.org/10.1007/s10822-014-9770-y). Complicating matters, new AlphaFold simulations are provided in .cif format only, precluding users from supplying these files toEpictopeunless they first convert them to .pdb format. Finally,dsspversions 2 and 3, which support the legacy PDB format, are not currently available for newer Apple computers using the ARM64 architecture (Apple silicon) withconda, makingEpictopeincompatible with many newer Macs. Commit 396477d addresses these shortcomings by updating the Mac/Linux installer to usedsspversion 4 and updatingEpictopeto retrieve .cif files from AlphaFold and accept .cif files as input. Commit 2cb6206 similarly updates the Windows installer. Consequently,Epictopenow supports ARM64-based Macs and the newer .cif file format.Option to supply a user-defined .cif file:
Epictopeworks very nicely for proteins listed in Uniprot that already have structures predicted by AlphaFold. However, not every Uniprot protein has an associated AlphaFold structure. We are usingEpictopein our lab to tag some of these proteins that do not yet have an AlphaFold structure. Commit 31be6d5 enablesEpictopeto accept a user-specified .cif file as a command-line argument, if desired, along with the corresponding Uniprot ID. Users can submit their sequences to AlphaFold, download a .cif output, and submit it toEpictope.An example is provided in the updated README in commit 5a36696.