{"id":19339516,"url":"https://github.com/becksteinlab/sampl6_logp_data","last_synced_at":"2026-05-16T02:35:34.989Z","repository":{"id":137445029,"uuid":"223044465","full_name":"Becksteinlab/SAMPL6_logP_data","owner":"Becksteinlab","description":"Supplementary data for SAMPL6 Part II (logP) calculations.","archived":false,"fork":false,"pushed_at":"2020-04-10T16:49:32.000Z","size":1148,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-01-06T10:48:27.665Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Becksteinlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-11-20T23:09:14.000Z","updated_at":"2020-04-10T16:47:49.000Z","dependencies_parsed_at":"2024-04-19T02:00:41.908Z","dependency_job_id":null,"html_url":"https://github.com/Becksteinlab/SAMPL6_logP_data","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FSAMPL6_logP_data","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FSAMPL6_logP_data/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FSAMPL6_logP_data/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FSAMPL6_logP_data/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Becksteinlab","download_url":"https://codeload.github.com/Becksteinlab/SAMPL6_logP_data/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240442539,"owners_count":19801917,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-10T03:22:36.309Z","updated_at":"2026-05-16T02:35:29.934Z","avatar_url":"https://github.com/Becksteinlab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Data for SAMPL6 Part II paper\n[![DOI](https://zenodo.org/badge/223044465.svg)](https://zenodo.org/badge/latestdoi/223044465)\n[![CC0](https://licensebuttons.net/p/zero/1.0/80x15.png)](http://creativecommons.org/publicdomain/zero/1.0/)\n\n- **data**: The latest archived version of the data can be found on\n  Zenodo by following the DOI on the badge. If you want to refer to\n  the data over all versions use DOI\n  [10.5281/zenodo.3549988](https://doi.org/10.5281/zenodo.3549988).\n  \n  Data are released under\n  [CC0](http://creativecommons.org/publicdomain/zero/1.0/). Code is released\n  under the MIT license.\n- **paper**: (please cite when using these data)\n\n  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)\n\n## Background\n\nThe [SAMPL6 (Part II) logP\nChallenge](https://github.com/MobleyLab/SAMPL6/blob/master/logP_challenge_instructions.md)\nconsists of predicting the octanol-water partition coefficients (log\nP) of 11 small molecules that resemble fragments of small molecule\nprotein kinase inhibitors. Our aim is to evaluate how well current\nmodels can capture the transfer free energy of small molecules between\ndifferent solvent environments through blind predictions.\n\nThis repository contains all data discussed in our paper _Prediction\nof octanol-water partition coefficients for the SAMPL6-logP molecules\nusing molecular dynamics simulations with OPLS-AA, AMBER and CHARMM\nforce fields_ in the SAMPL6 Special Issue of the Journal of\nComputer-Aided Molecular Design. \n\n## Input files\n\nTopology input files for Gromacs 2018 are provided in the `02_top` directory\nand its subdirectories for the different compounds and force fields. \n\nSimulations were set up and managed with\n[mdpow](https://github.com/Becksteinlab/MDPOW) (0.7.0 development\nversion, equivalent to commit\n20152ad9723fa5ad9d039362233da07b5fa7811a).\n\n**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.\n\n## SAMPL6 submission\n\n- Directory `03_prep_submission` contains scripts to generate the\n  submission files from Google Sheets (which we used for aggregating\n  data). They are not strictly necessary as supporting information but\n  might be of interest for anyone who wants to do something similar\n  (although this was more of an experiment than a workflow we would\n  generally recommend).\n- Directory `04_submission` contains the data for our SAMPL6\n  submissions as CSV files.\n  \n  | number \t| ID    \t| force field          \t| octanol \t|\n  |--------\t|-------\t|----------------------\t|---------\t|\n  | 1      \t| sqosi \t| AMBER/GAFF           \t| dry     \t|\n  | 2      \t| 6nmtt \t| AMBER/GAFF           \t| wet     \t|\n  | 3      \t| eufcy \t| OPLSAA/LigParGen     \t| dry     \t|\n  | 4      \t| mwuua \t| OPLSAA/LigParGen     \t| wet     \t|\n  | 5      \t| cp8kv \t| OPLSAA/transferrable \t| dry     \t|\n  | 6      \t| 623c0 \t| OPLSAA/transferrable \t| wet     \t|\n  | 7      \t| 3oqhx \t| CHARMM/CGENFF        \t| dry     \t|\n- Directory `06_data` contains the same data but organized by force\n  field and molecule.\n\n## Improved protocol\n\nThe paper discusses improvements to our protocol. The data for these\ncalculations can be found in directory `07_alchemlyb_results`.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fsampl6_logp_data","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbecksteinlab%2Fsampl6_logp_data","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fsampl6_logp_data/lists"}