https://github.com/becksteinlab/sampl6_logp_data
Supplementary data for SAMPL6 Part II (logP) calculations.
https://github.com/becksteinlab/sampl6_logp_data
Last synced: 3 months ago
JSON representation
Supplementary data for SAMPL6 Part II (logP) calculations.
- Host: GitHub
- URL: https://github.com/becksteinlab/sampl6_logp_data
- Owner: Becksteinlab
- License: mit
- Created: 2019-11-20T23:09:14.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-04-10T16:49:32.000Z (about 5 years ago)
- Last Synced: 2025-01-06T10:48:27.665Z (5 months ago)
- Language: Jupyter Notebook
- Size: 1.09 MB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Data for SAMPL6 Part II paper
[](https://zenodo.org/badge/latestdoi/223044465)
[](http://creativecommons.org/publicdomain/zero/1.0/)
- **data**: The latest archived version of the data can be found on
Zenodo by following the DOI on the badge. If you want to refer to
the data over all versions use DOI
[10.5281/zenodo.3549988](https://doi.org/10.5281/zenodo.3549988).
Data are released under
[CC0](http://creativecommons.org/publicdomain/zero/1.0/). Code is released
under the MIT license.
- **paper**: (please cite when using these data)
S. Fan, B. I. Iorga, and O. Beckstein. _Prediction of octanol-water partition coefficients for the SAMPL6-log P molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields._ Journal of Computer-Aided Molecular Design, 34:543–560, 2020. DOI: [10.1007/s10822-019-00267-z](https://doi.org/10.1007/s10822-019-00267-z)
## Background
The [SAMPL6 (Part II) logP
Challenge](https://github.com/MobleyLab/SAMPL6/blob/master/logP_challenge_instructions.md)
consists of predicting the octanol-water partition coefficients (log
P) of 11 small molecules that resemble fragments of small molecule
protein kinase inhibitors. Our aim is to evaluate how well current
models can capture the transfer free energy of small molecules between
different solvent environments through blind predictions.
This repository contains all data discussed in our paper _Prediction
of octanol-water partition coefficients for the SAMPL6-logP molecules
using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM
force fields_ in the SAMPL6 Special Issue of the Journal of
Computer-Aided Molecular Design.
## Input files
Topology input files for Gromacs 2018 are provided in the `02_top` directory
and its subdirectories for the different compounds and force fields.
Simulations were set up and managed with
[mdpow](https://github.com/Becksteinlab/MDPOW) (0.7.0 development
version, equivalent to commit
20152ad9723fa5ad9d039362233da07b5fa7811a).
**Note:** _CHARMM simulations_ were performed with the _CHARMM TIP3P water model_ (LJ interactions on hydrogens) whereas AMBER simulations were performed with the standard TIP3P water model. We used the TIP3P input files provided by Gromacs. The paper was not clear on this distinction between the two TIP3P water models.
## SAMPL6 submission
- Directory `03_prep_submission` contains scripts to generate the
submission files from Google Sheets (which we used for aggregating
data). They are not strictly necessary as supporting information but
might be of interest for anyone who wants to do something similar
(although this was more of an experiment than a workflow we would
generally recommend).
- Directory `04_submission` contains the data for our SAMPL6
submissions as CSV files.
| number | ID | force field | octanol |
|-------- |------- |---------------------- |--------- |
| 1 | sqosi | AMBER/GAFF | dry |
| 2 | 6nmtt | AMBER/GAFF | wet |
| 3 | eufcy | OPLSAA/LigParGen | dry |
| 4 | mwuua | OPLSAA/LigParGen | wet |
| 5 | cp8kv | OPLSAA/transferrable | dry |
| 6 | 623c0 | OPLSAA/transferrable | wet |
| 7 | 3oqhx | CHARMM/CGENFF | dry |
- Directory `06_data` contains the same data but organized by force
field and molecule.
## Improved protocol
The paper discusses improvements to our protocol. The data for these
calculations can be found in directory `07_alchemlyb_results`.