3DFI-v1.0.1a

Minor bug fix:

• Added RoseTTAFold support to run_MICAN_on_homology_results.pl # %Folds();

3DFI-v1.0.1

Minor update:

• Added support for keyboard interrupts (SIGINT + SIGTERM) where possible with checksig(); subroutine
• Added distinct defaults cutoffs for GESAMT and Foldseek
• Fixed the --align cmd line parsing; --align not --aligner
• Removed obsolete descriptive_matches.pl option (-a) from the corresponding cmd line in run_3DFI.pl

AlphaFold:

• Added protobuf==3.20.1 to the AlphaFold Dockerfile; newer versions present the docker image from running

3DFI-v1.0.0

• Added support for MICAN-SQ
• Added support for Foldseek structural homology searches (now set as default instead of GESAMT in run_3DFI.pl)
• Mican and Foldseek are installed automatically with setup_3DFI.pl
• Foldseek RCSB database can be created automatically with create_3DFI_db.pl
• Fixed a bug where ChimeraX alignments for visualization were not generated if # of matches == 1
• Switched to ChimeraX 1.3+ ## APIs 1.2.5 and 1.3 are not compatible
• Added -3dh command line option to run_3DFI.pl [3D folding + homology; no (pre)-visualization step with ChimeraX]
• Updated AlphaFold fork to version 2.2 + added new NVIDIA signing keys (2022) to its Dockerfile
• Minor cosmetic changes for readability

3DFI-v0.9.0

• Updated 3DFI to work with AlphaFold 2.1.0 and homogenized the command line switches to facilitate further updates.
  (if using a previous version of 3DFI, the alphafold_3dfi docker image should be rebuilt to match the new command lines in 0.9.0+)
• Fixed an issue wherein the alphafold database preset was not properly parsed with GetOptions();
• Replaced the hard-coded docker image names by variables.
• Fixed an issue with the jax version in the AlphaFold Dockerfile by replacing ==1.69 with >=1.69

3DFI-v0.8.7a

• Fixed an issue with command -v $program on Ubuntu 20.04+ that would prevent the shell from returning the expected values. Changed to echo \$(command -v $program) as a workaround.

3DFI-v0.8.7

Minor release:

• Fixed an issue in which some of the databases downloaded with create_3DFI_db.pl were only readable by the owner.
• The nvidia-docker2 package used by Alphafold2 is becoming obsolete. It is being replaced by nvidia-container-runtime. Added notes in Installation_notes.sh on how to use nvidia-container-runtime instead of nvidia-docker2 on Fedora 35.
• Added the 'How to cite' section to the README referring to the 3DFI publication in Bioinformatics advances.

3DFI-v0.8.6

• run_visualizations.pl can now iterate through predicted structures without structural homologs.
• made minor cosmetic changes to run_visualizations.pl for increased readability
• fixed run_3DFI.pl typo
• added missing predicted_structures.log to Example/Visualizations
• fixed alignment selection issue

3DFI-v0.8.5

Major changes:

• setup_3DFI.pl => can now install AlphaFold, RaptorX and/or RoseTTAFold automatically
• create_3DFI_db.pl => can now download all databases automatically
• PDB_headers.pl => now updates the RCSB_PDB_titles.tsv list rather than recreating it every time; much faster
• README => updated/simplified for increased readability

3DFI-v0.8a

Alpha version of major update 0.8:

• Added a run_3DFI.pl master script
• Added a create_3DFI_db.pl script to create the 3DFI databases ## initial version, to be improved
• Added a setup_3DFI.pl script ## initial version, to be improved
• Added GZIP compression to GESAMT results to save on storage
• Improved the visualization script and renamed it: run_visualizations.pl (plDDT scores are now colored automatically if present in PDB)
• Made modifications to several scripts for better integration with run_3DFI.pl
• Restructured README for readability
• Added case examples and replaced one example that didn't fit within 8 GB of VRAM with ROSETTAFOLD by a smaller one.
• Removed support for trRosetta/trRosetta2 and moved them to alternate predictors

3DFI-v0.7a

• Fixed issue with multiple models in homology searches and visualizations
• Added setup_3DFI.pl to help set environment variables
• Added examples of ChimeraX .cxs alignments with prepare_visualizations.pl
• Sent harmless ChimeraX WebEngine message to /dev/null