Align-It input format issues

[JeongSoo Na]

Align-It input format issues

Hi this is JeongSoo Na, in-silico lab in Korean company.

First, I want to set process, Pharmacophore Analysis, screening, alignments, modeling ect.
But I don't know about this input formats.
Is this input format is specific in tool?

[Vadim Kotov]

Hello!

I am not an expert user of Align-It, but I managed to get it to work some time ago in my project.

If I understand correctly, you need to first create a pharmacophore from your reference compound:

$ align-it -d ReferenceLigand.pdb -p Pharmacophore.phar

If you have several references, e.g. different ligands binding in the same pocket, you can create a merged pharmacophore:

$ obabel Ligand1.pdb Ligand2.pdb Ligand3.pdb -O Ligands.sdf

$ align-it -d Ligands.sdf -r Ligands.sdf -p LigandsPharmacophore.phar --merge --noNormal

Btw, align-it is distributed with a PyMOL plugin (see pymol/align-it.py) which can be used to visualize the pharmacophores.

To align a database of compounds to a pharmacophore, run the following command:

align-it -d CompoundsDatabase.sdf -r Pharmacophore.phar --refType phar -o AlignedDatabase.sdf -p DatabasePharmacophores.phar -s scores.tab

The aligned compounds will be in AlignedDatabase.sdf, and some scores and statistics will be saved to file scores.tab

Hope this helps!

[JeongSoo Na]

Thank U for your kindely answer, Kotov!

When I enter the input format sdf and pdb file(in only compounds), I can get this output log.

Can you share your test set, used in align-it or output log in test case?

Many Thanks,
JeongSoo Na

2024년 7월 11일 목요일 오후 4시 30분 29초 UTC+9에 Vadim Kotov님이 작성:

[Vadim Kotov]

Hello!

My commands are for align-it version 1.0.4, whereas you are running v.1.0.3, so there may be differences in the syntax. From what I remember, I had to build it from scratch, which was a true nightmare...

Anyway, I think you just need specify the database format with option:

--dbType pdb

Or use option "sdf" if your input file is SDF

Good luck!

[JeongSoo Na]

Thanks to you Kotov!

When I tried, I installed it with conda (v1.04 in Bioconda) but When I installed it, it was recognized as version 1.03 :(

I will try to install it with github source later.
And I'm going to experience nightmares too..

Kind regards,
JeongSoo Na

2024년 7월 16일 (화) 오전 4:48, Vadim Kotov <vadim....@gmail.com>님이 작성:

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