filipsPL / annapurna-additional

AnnapuRNA scoring function - additional materials

AnnapuRNA scoring function - additional materials.

• Data from manuscript
• Training and testing datasets
• Correlation plots for described scoring functions
• How to cite
• Contact

Data from manuscript

📁 directory: data_from_manuscript/

Here is deposited data described in the manuscript:

• 1-selected_examples - selected examples from the test set

docking.rmsd        -- RMSD values
docking.score       -- score values from the docking program
annapurna.score     -- score values from AnnapuRNA
pymol-session.pse   -- PyMOL session with structures

• 2-case_study - the files used in the study: RNA structures, best docking poses from rDock and selected by AnnapuRNA, the reference ligand coordinates; the PyMOL session with all results visualized.

Training and testing datasets

📁 directory: docking/

Please note, that some of the files are compressed with the xz. To uncompress the file, just type xz -d file.xz or use 7-zip archiver.

• datasets.csv - definitions of 2013, 2016, and testing datasets

For each pdb the directory tree is as follows:

.
├── docking
│   └── dockprep                -- docking results
├── ligand                      -- ligand structures
│   ├── 3D-babel
│   ├── 3D-balloon
│   ├── 3D-PDB-idealized
│   ├── ligand.smi
│   └── native_conformation
└── rna
    └── dockprep                -- RNA structures

docking/dockprep/ contains data for the native conformer and conformers generated with two different methods (OpenBabel and Balloon). Each "conformer" directory contains four subdirectories containing docking results for four docking programs:

.
├── 3D-babel
│   ├── AutodockVina
│   ├── iDock
│   ├── rdock-dock
│   └── rdock-dock_solv
├── 3D-balloon
│   ├── AutodockVina
│   ├── iDock
│   ├── rdock-dock
│   └── rdock-dock_solv
└── native_conformation
    ├── AutodockVina
    ├── iDock
    ├── rdock-dock
    └── rdock-dock_solv

each docking dir contains results of docking (in the main dir) and rescoring:

.
├── docking.rmsd
├── docking.score
├── docking.sdf.xz
├── docking.titles.sdf.xz
└── rescoring
    ├── annapurna_AD_1_2A.score
    ├── annapurna.score
    ├── ligandrna_basic.score
    ├── ligandrna_modern.score
    ├── rdock-dock.score
    ├── rdock-docksolv.score
    └── rfscore_vs_v2.score

Correlation plots for described scoring functions

📁 directory: correlations/

Correlation plots for described scoring functions are available in the correlations/ directory.

Please look at the md file or clone the repository and open html file in your browser.

How to cite

Stefaniak F, Bujnicki JM (2021) AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses. PLoS Comput Biol 17(2): e1008309. https://doi.org/10.1371/journal.pcbi.1008309

Filip Stefaniak, Janusz M. Bujnicki, AnnapuRNA: a scoring function for predicting RNA-small molecule interactions, bioRxiv 2020.09.08.287136;

Contact

Laboratory of Bioinformatics and Protein Engineering International Institute of Molecular and Cell Biology in Warsaw ul. Ks. Trojdena 4, 02-109 .Warsaw, Poland

Head of the Laboratory: Janusz M. Bujnicki [e-mail]