Zhanglab forum

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 ...

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.

I have uploaded that file now. Please retry download.

The tar files you mentioned are indeed available through the links. You probably were not able to download them due to University-wide Internet outage. Please try to download them again.

x-score (http://websites.umich.edu/~shaomengwang ... are/xtool/) is a scoring function used by EDock to rank different poses.

3DRobot may sometimes generate less decoys than that specified by the user. This is why you receive the warning on missing decoys. Otherwise, your run looks fine.

You can compress your file by zip and attach the zip archive.

FASPR aims to achieve the global minimum energy configuration (GMEC) by fully deterministic algorithms, such as dead end elimination. Therefore, it is not possible to force it to generate multiple conformation. The temp variable in Search.cpp is not related to temperature annealing.

From: <l*@opnbnch.com> Date: Friday, June 2, 2023 at 14:25 Subject: On FASPR and rotamer sampling Hi Prof. Zhang, I've been really impressed with using your FASPR tool - it's very fast and generates plausible coordinates. It's been a great addition to the suite of protein structure modeling tools ...