Zhanglab forum

There were some new structure of protein have been delivered to pdb which contain homologous protein I want. How to add this structural information to the predicted dataset? Could you please provide some suggestions?

Best regards,
Shijie Dong

Dear Wei Zheng, I found the DMFold used AlphaFoldv2.0. Have you considered using the latest AlphaFoldv2.3.0? I can run the AlphaFoldv2.3.0 locally. Maybe this will help us run sucessfully with RTX4090. I have another question. Does the online version of DMFold use the model_multimer_v2? I check the ...

Dear Wei Zheng, Thanks for your suggestions. I downgraded the version with jax==0.2.14 jaxlib==0.1.69+cuda111 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html. It's work, but a new error when running Run_DMFold.py, as follow: I0117 07:23:01.527364 22723190105920 run_alphafold ...

I created alphafold2nondocker env with following code: conda install -y -c conda-forge openmm==7.5.1 cudnn==8.2.1.32 cudatoolkit==11.3.1 cudatoolkit-dev==11.3.1 pdbfixer==1.7 conda install -y -c bioconda hmmer==3.3.2 hhsuite==3.3.0 kalign2==2.04 pip install absl-py==0.13.0 biopython==1.79 chex==0.0 ...