Wagner, Jeffrey R.; Churas, Christopher P.; Liu, Shuai; Swift, Robert V.; Chiu, Michael; Shao, Chenghua; Crawl, Daniel; Feher, Victoria A.; Burley, Stephen K.; Gilson, Michael K.; Amaro, Rommie E. (2019). Data from: Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0610XPS

All structures and RMSDs used in Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking are provided here. Note that:

- Predicted structures and calculated RMSD values are available from 2017 week 5 to 2018 week 28, however several weeks in this interval were excluded from the analysis, as less than three predictions were submitted for any target.
- 2017 week 11 is excluded from the analysis as it had ~300 nearly-identical complexes released.
- The files contained in this repository are grouped by submitter, but have had comment fields scrubbed of information to preserve the anonymity of external participants.
- The settings and software environment of the GLIDE participant were changed during the "live" data collection period, so all GLIDE predictions were regenerated for this paper using Schrodinger suite version 2015-3 and the code at https://github.com/drugdata/d3r_in_house_glide as of commit fb38a3a.
- Sporadic automation and infrastructure issues prevented predictions from being generated or evaluation from being run for some targets. Notably, GLIDE predictions in 2018 between weeks 1-9 had a configuration error and did not generate RMSDs.
- External participants enrolled in CELPP at different times, were not required to submit predictions each week, and were not required to use the same method throughout the data collection period.

• 2017 to 2018

• 2019

• Burley, Stephen K.
• Chiu, Michael
• Churas, Christopher P.
• Feher, Victoria A.
• Liu, Shuai
• Shao, Chenghua
• Swift, Robert V.
• Wagner, Jeffrey R.

• Amaro, Rommie E.
• Gilson, Michael K.

• Crawl, Daniel

The zipped workflows all require installation of the "d3r" python package via pip. Several further require installation of UCSF Chimera, babel, MGLTools, Schrodinger Suite, or the OpenEye Toolkits. Test files and a test run script are provided within each workflow's test_data directory.

Software versions: Chimera 1.10.1, RDKit 2016.3.3, MGLTools 1.5.7, AutoDock Vina 1.1.2, Schrodinger 2015-3 release, Omega 2.5.1.4, FRED 3.0.1, RBDock 2013.1/901

D3R is supported by NIH grant U01 GM111528 to REA and MKG.

• Computational chemistry
• Docking
• Drug design
• Pose prediction
• Structural biology

• data
• text

• English

Doi: https://doi.org/10.6075/J0610XPS

Primary associated publication

• Jeffrey R. Wagner, Christopher P. Churas, Shuai Liu, Robert V. Swift, Michael Chiu, Chenghua Shao, Victoria A. Feher, Stephen K. Burley, Michael K. Gilson, Rommie E. Amaro (2018) Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. bioRxiv. https://doi.org/10.1101/469940
• Jeffrey R. Wagner, Christopher P. Churas, Shuai Liu, Robert V. Swift, Michael Chiu, Chenghua Shao, Victoria A. Feher, Stephen K. Burley, Michael K. Gilson, Rommie E. Amaro (2019) Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. Structure. https://doi.org/10.1016/j.str.2019.05.012

Software

• Scoring code: https://zenodo.org/record/2578191#.XLkHQqZlDOQ

Other resource

• Drug Design Data Resource website: https://drugdesigndata.org/

Creative Commons Attribution 4.0 International Public License

• UC Regents

Under copyright (US)

Use: This work is available from the UC San Diego Library. This digital copy of the work is intended to support research, teaching, and private study.

Constraint(s) on Use: This work is protected by the U.S. Copyright Law (Title 17, U.S.C.). Use of this work beyond that allowed by "fair use" or any license applied to this work requires written permission of the copyright holder(s). Responsibility for obtaining permissions and any use and distribution of this work rests exclusively with the user and not the UC San Diego Library. Inquiries can be made to the UC San Diego Library program having custody of the work.

Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)

2023-06-06