tlitfin-unsw
tlitfin-unsw
Running --alphafold2_mode split_msa_prediction on our H200 nodes leads to: - Falling back to the CUDA driver for PTX compilation; ptxas does not support CC 9.0 - failed to get PTX...
### Description of the bug When running multiple pipelines, the comparison report displays sequence coverage plots to vizualize the MSA for each of the methods. ESMfold does not produce an...
### Description of the bug One of the options for --colabfold_model_preset is 'auto' which will detect whether the system is a monomer or multimer and run the appropriate model (alphafold2_ptm...
Several issues here and on the slack are related to VRAM limitations: #71, #83, #106, #167, #169, #197, #214 By tweaking the chunking parameters, you can significantly reduce the VRAM...
### Description of feature The stockholm format MSAs are extremely bulky files which leave a large disk footprint - particularly the uniprot.sto files generated for pairing sequences in AlphaFold2 multimer....
- Added mode-specific usage documentation. - Added table to README to demonstrate mode capabilities. TODO: - [ ] Add new metro-map - [ ] Complete RF2NA docs when mode is...
### Description of feature AlphaFold3, RoseTTAFold-All-Atom, Boltz and HelixFold3 all have the ability to model non-protein entities. AlphaFold3 currently only supports protein monomers. Boltz, RoseTTAFold-All-Atom and HelixFold3 support non-protein entities...
### Description of feature AlphaFold2 and ESMFold modules have different behaviour for monomer and multimer mode. Currently this is controlled by a CLI flag that the user must provide at...
### Description of the bug AlphaFold2 multimer pads MSAs to a minimum depth by filling with 0s. In MSA parsing, 0 is interpreted as Alanine such that plots with shallows...
### Description of feature #303 involves adding a PAE plot to the HTML report to support interpretation of outputs. This is particularly relevant for multimers (and multi-domain proteins) which will...