Ranjee

Hi, I am new to machine-learning scoring functions, and I want to use RFScore to re-train your model on PDBbind_v2016. I have read the csv of v1 descriptors: ``` pdbid,2016_general,2016_refined,2016_core,2015_general,2015_refined,2015_core,2014_general,2014_refined,2014_core,2013_general,2013_refined,2013_core,2012_general,2012_refined,2012_core,2007_general,2007_refined,2007_core,act,0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35...

Please help me checking my script to predict on my ./coreset: ``` import os import pandas as pd import csv import oddt from oddt.scoring.functions import RFScore oddt.toolkit = oddt.toolkits.rdk #...

### Issue summary gnina/gnina ``` root@5c5f8f785b7b:~/data/1a4k# apt-get update The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 871920D1991BC93C Get:5 http://archive.ubuntu.com/ubuntu jammy-backports InRelease [109 kB] Err:5...

Scores are almost the same for RF-Score-VS on PDBbind

2

Dear developer, When I use your binary RF-Score-VS to dock multiple complexes in PDBbind2019, they just get almost the same score (near 6), which is unbelievable terrible! ``` pdb_id,prot_name,rf_score_vs_v2,ref_affinity 1a1e,1a1e_pocket,6.00580229596,6.00...

Question about only train CNN_affinity for crossdock_default2018.

4

Hello developers! I saw the format of types for training both CNN_score and CNN_affinity needs rmsd and affinity label, but I don't wanna train or use CNN_score in my work,...

Trouble install when in ubuntu without nvidia GPU

1

### Issue summary $ cmake .. -- The C compiler identification is GNU 9.4.0 -- The CXX compiler identification is GNU 9.4.0 CMake Error at /usr/local/share/cmake-3.25/Modules/CMakeDetermineCUDACompiler.cmake:180 (message): Failed to find...

Dear Wang, I noticed that you updated the script that generate the complex's features. As I remember, the script before is called prepare.sh, and I am going to use it...

How to evaluate the binding affinity of Covalent bond?

1

I have used gnina to do covalent docking and the result was output as the same format with non-covalent docking. But I want to evaluate whether this covalent binding is...

can we use openbabel instead of meeko to prepare PDBQT files?

1

we had trouble with meeko to prepare receptor pdbqt file: ``` mk_prepare_receptor.py -i 5tmn_protein.pdb -o 5tmn -p mk_prepare_receptor.py: error: unrecognized arguments: -i 5tmn_protein.pdb -p ``` and we find it convenient...