Search found 69 matches

by zcx@umich.edu
Wed Oct 25, 2023 12:51 am
Forum: Main Forum
Topic: BioLiP Has Fewer Entries Than Before
Replies: 2
Views: 31106

Re: BioLiP Has Fewer Entries Than Before

Yes, some entries are removed due to correction of van deer Waals radius calculation.
https://github.com/kad-ecoli/mmCIF2BioL ... d9349c02c9
by zcx@umich.edu
Mon Oct 09, 2023 8:37 pm
Forum: Main Forum
Topic: Deprecated Biolip File Downloads
Replies: 7
Views: 58632

Re: Deprecated Biolip File Downloads

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...
by zcx@umich.edu
Tue Oct 03, 2023 1:03 am
Forum: Main Forum
Topic: BioLiP mismatch with updated PDB atom records (ligand residue name & identifier)
Replies: 2
Views: 31697

Re: BioLiP mismatch with updated PDB atom records (ligand residue name & identifier)

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...
by zcx@umich.edu
Mon Sep 25, 2023 5:52 pm
Forum: Main Forum
Topic: Deprecated Biolip File Downloads
Replies: 7
Views: 58632

Re: Deprecated Biolip File Downloads

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?
by zcx@umich.edu
Tue Sep 12, 2023 8:33 pm
Forum: Main Forum
Topic: US align phylogenetic tree availability
Replies: 1
Views: 18214

Re: US align phylogenetic tree availability

US-align does not output the guide tree. Sorry.
by zcx@umich.edu
Wed Sep 06, 2023 3:01 pm
Forum: Main Forum
Topic: Deprecated Biolip File Downloads
Replies: 7
Views: 58632

Re: Deprecated Biolip File Downloads

I have uploaded that file now. Please retry download.
by zcx@umich.edu
Thu Aug 31, 2023 9:51 pm
Forum: Main Forum
Topic: Deprecated Biolip File Downloads
Replies: 7
Views: 58632

Re: Deprecated Biolip File Downloads

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.
by zcx@umich.edu
Tue Jul 18, 2023 1:58 am
Forum: Main Forum
Topic: EDock
Replies: 12
Views: 88732

Re: EDock

x-score (http://websites.umich.edu/~shaomengwang ... are/xtool/) is a scoring function used by EDock to rank different poses.
by zcx@umich.edu
Wed Jun 28, 2023 1:15 pm
Forum: Main Forum
Topic: Questions about 3DRobot
Replies: 2
Views: 3126

Re: Questions about 3DRobot

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.
by zcx@umich.edu
Mon Jun 26, 2023 11:44 am
Forum: Main Forum
Topic: EDock
Replies: 12
Views: 88732

Re: EDock

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