Zhanglab forum

Your issue is caused by the inability of UCSF chimera to recognize the hydrogen atoms in the I-TASSER model. In fact, structure minimization runs without any issue if the hydrogen atoms are removed prior to loading the structure into UCSF chimera. I am not familiar with how to remove hydrogens in UC...

No, BindProfX is single threaded.

The BindProfX tool was last updated in 2017 but its standalone tool should still work fine.

There is actually precompiled binary at the bottom of https://zhanggroup.org/US-align/

No, -se is not implemented for multiple alignment.

Yes, some entries are removed due to correction of van deer Waals radius calculation.
https://github.com/kad-ecoli/mmCIF2BioL ... d9349c02c9

Dear user, To address your request, I have uploaded all BioLiP (version 1) webserver data to https://doi.org/10.5281/zenodo.8407896 and https://zenodo.org/record/8407920 You may concatenate the two files and decompress them by: $ cat BioLiP1aa BioLiP1ab > BioLiP.tar.bz2 $ tar -xvf BioLiP.tar.bz2 You...

Most likely we will not update PDB records that are changed after initial release, as regenerating the full database for every weekly release is a huge undertake. By the way, for the cases you mentioned where the ligand name is changed, it is not entirely true that the ligand is not present in the c...

There is no need to download http://zhanglab.ccmb.med.umich.edu/BioL ... LiP_ax.txt
You can download all current biolip entries from https://zhanggroup.org/BioLiP/download/BioLiP.txt.gz
May I know why you need BioLiP_*.txt?

US-align does not output the guide tree. Sorry.