af2complex

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run_alphafold.py kill when running big complex

1

Hi, The process is automatically killed when I predicted a complex with 3000 or longer aa. But there was no problem when I use alphafold2-multimer. Could you please give me...

dantekey

error on installing AF2complex on colab notebook

6

When I try to run AF2complex on colab, I come across the following error. I will very much appreciate if you can solve this error for me. 

herman-einstein

[Question] GPU not utilized

6

First thanks for this great resource! I encountered a problem that my GPU is not utilized. I configured af2complex in the same conda env as the AlphaFold. I run examples...

ww2283

'scipy' has no attribute 'spatial'

8

From af2complex/src/alphafold/common/confidence.py pairwise_dist = scipy.spatial.distance.cdist(a, b, metric='euclidean') AttributeError: module 'scipy' has no attribute 'spatial' when running example1.sh. There does not appear to be an import statement for scipy.spatial.

james-vincent

Getting low interaction scores with existing complexes

1

Hello there, We are currently running different experiments with somewhat confusing results. We selected two proteins, STING (homodimer) and NPC1, to test the af2complex model. According to this paper ->...

outlierd29

Error when generating features with `feature_mode='multimer'`

2

I want to generate features for a protein complex with a modified version of the `example/run_fea_gen.sh` script: ``` #!/bin/bash # An example script of feature generation. This heavily depenedent on...

guzmanfj

reduced_dbs

1

Hi, In example/run_fea_gen.sh, the db_preset uses reduced_db. Is there any performance difference between "reduced_dbs", "full_dbs", and "uniProt"? Which one is suggested?

px172

help setting the env for alphafold

1

I want to run the script to create my features from alphafold (https://github.com/FreshAirTonight/af2complex/blob/main/example/run_fea_gen.sh), but i am not sure how to set up my environment for this. Should downloading all the...

outlierd29

Enhanced interface score assessment

1

Hello, I would like to know whether the interface score calculation between v1.2 and v.1.3 is totally different and if I can keep using the code of v.1.2. Thank you...

IlyesAbdelhamid

how can I create the input features for my own dataset by running the py. file? Is it possible to simply the input to only sequence of the protein?

10

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