# Query

alphafold vs standard structure

# Start Alphafold-Multitimer

## Start Fold!

our alphafold2 is installed in /smb/jiangyd/alphafold

or you can make a script(such as run_alphafold_yida.sh) in your love directory

## Model

1. You can control which AlphaFold model to run by adding the -model_preset= flag. We provide the following models:
• monomer: This is the original model used at CASP14 with no ensembling.
• monomer_casp14: This is the original model used at CASP14 with num_ensemble=8, matching our CASP14 configuration. This is largely provided for reproducibility as it is 8x more computationally expensive for limited accuracy gain (+0.1 average GDT gain on CASP14 domains).
• monomer_ptm: This is the original CASP14 model fine tuned with the pTM head, providing a pairwise confidence measure. It is slightly less accurate than the normal monomer model.
• multimer: This is the AlphaFold-Multimer model. To use this model, provide a multi-sequence FASTA file. In addition, the UniProt database should have been downloaded.

## run_alphafold.sh的具体参数

• optionally set the -is_prokaryote_list flag with booleans that determine whether all input sequences in the given fasta file are prokaryotic. If that is not the case or the origin is unknown, set to false for that fasta.

## Scripts

How to run a number of fasta files at once?

# Reference

GitHub - deepmind/alphafold: Open source code for AlphaFold.

https://github.com/kalininalab/alphafold_non_docker

CASP14：谷歌DeepMind的AlphaFold 2到底取得了什么成就? 它对蛋白质折叠, 生物学和生物信息学意味着什么?

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