Zhuoran Qiao

icon indicating a website link https://zrqiao.github.io/

icon company Caltech icon location A chemical physicist working with AI

Results 6 comments of Zhuoran Qiao

Chemical description retrieval / new RCSB API

Thank you @williamgilpin for the information! I'll start to make some modifications and create a PR when it's in a good shape.

Chemical description retrieval / new RCSB API

@williamgilpin I think so, thank you for pinging me! Sorry I have eventually moved to another project and abandoned works on this...

Error: createbintaxonomy failed with malloc error

> Does this happen with the `databases` download of the uniprot or only if you call `createtaxdb` manually? > > `databases` goes through a separate branch to extract taxonomic information...

Error: createbintaxonomy failed with malloc error

> ``` > mmseqs databases UniProtKB uniprot tmp > ``` > > should download the latest uniprot and set it up correctly for use with MMseqs2 including taxonomy information. Thanks...

Issue with Cb atoms of threonines, perhaps other amino-acids?

Thanks for catching the issue. I confirm this observation in the attached `.pdb` files, while in the prediction results we generated in March 2023 (which are deposited to zenodo) as...

torch.cuda.OutOfMemoryError even for a small protein

5.8Gb total capacity is certainly below the GPU RAM we have tested on. As a minimum we recommend testing on a system with at least 16GB CPU and GPU memory.