ParallelFold
ParallelFold copied to clipboard
Zuricho
Modified version of Alphafold to divide CPU part (MSA and template searching) and GPU part. This can accelerate Alphafold when predicting multiple structures
Last day, I make some experiments in a Server to run the `./run_alphafold.sh -d /dataset/ -o result -p monomer -m model_2 -i input/T1061.fasta` and I read the log, confused, the...
When I use the code to compute T1050.fasta, which is composed of 700 residuses， the command line output the problem。 The Environment is GPU： A100， Ubuntu，but I use higher version...
Hello, When i use this code to generate features, this problem occurred. But i am sure that this path `/mnt/VMSTORE/protein/pdb70/` exists. 
Hi, First of all, thanks for developing this tool, I'm looking forward to playing with it! I installed the ParallelFold into a Ubuntu 18 machine, and the full alphafold database...
Here is the paper: 4.2.1 CPU acceleration. To accelerate the CPU stage, three independent sequential MSA searches can be arranged in parallel (Fig 4). Due to the limited CPU cores...
I have a fundamental doubt about the difference between Alphafold2 and Parafold running procedure, how to determine whether Parafold is doing Parallel task unlike sequential tasks performed by Alphafold2 for...
Hi, When I used your new version to make fearure.pkl, this error occurred, could you give any advice on how to solve it? FATAL Flags parsing error: Unknown command line...
Same multimer sequence,two chains,in total 646AA. Use ParallelFold,CPU phase use 1h33min,GPU phase use 5h30min,generate five models.command: -p multimer -m model_1_multimer,model_2_multimer,model_3_multimer,model_4_multimer,model_5_multimer. Use ParallelFold,CPU phase use 1h27min,GPU phase use 1h25min,generate one models.command:...
Hello, Thank you very much for this effort. I just wonder why is the following script now missing in your current `master` branch. https://github.com/Zuricho/ParallelFold/blob/0b2b66b0d11fd717eb10809cba2424822a46374f/run_figure.py
Hi! I have been using ParaFold for a couple of months without any major errors to generate thousands of structures, however, today I saw what seems like a kalign glitch...
