Protein-protein structures

dataset logo thumbnail

Data DOI: 10.15785/SBGRID/843 | ID: 843

Xue Laboratory, Radboud University Medical Center

Release Date: Oct. 28, 2021

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/843

2. To download this dataset, please run the following command from your Terminal on a Linux or OS X workstation:

'rsync -av rsync://data.sbgrid.org/10.15785/SBGRID/843 .' (Harvard Medical School, USA)

Depending on your location, faster access may be available from a Tier 1 site closer to your location

'rsync -av rsync://sbgrid.icm.uu.se/10.15785/SBGRID/843 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/843 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/843 .' (Shanghai Institutes for Biological Sciences, China)

3. After the transfer is completed, please issue the following command to verify data integrity:

'cd 843 ; shasum -c files.sha'

Biological Sample:

Protein-protein structures

Dataset Type:

Structural Model

Subject Composition:

Protein

Collection Facility:

N/A

Data Creation Date:

July 13, 2021

Related Datasets:

None


Cite this Dataset

Marzella, DF; Ambrosetti, F; Bonvin, AMJJ; Geng, C; Georgievska, S; Renaud, N; Ridder, L; Xue, LC. 2021. "Protein-protein structures.", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/843.

Download Citation

Dataset Description

HADDOCK refined 3D structures from multiple datasets (BM5, MANY, DC, CAPRI), used for experiments in the DeepRank paper. 1.Renaud, N. et al. DeepRank: A deep learning framework for data mining 3D protein-protein interfaces. bioRxiv 2021.01.29.425727 (2021) doi:10.1101/2021.01.29.425727.

Project Members

Name Additional Roles Affiliation While Working on the Project
Dario F MarzellaDepositorCenter for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
Francesco AmbrosettiFaculty of Science - Chemistry, Bijvoet Centre, Utrecht University, Utrecht, The Netherlands
Alexandre MJJ BonvinFaculty of Science - Chemistry, Bijvoet Centre, Utrecht University, Utrecht, The Netherlands
Cunliang GengData CollectorNetherlands eScience Center, Amsterdam, The Netherlands
Sonja GeorgievskaNetherlands eScience Center, Amsterdam, The Netherlands
Nicolas RenaudData CollectorNetherlands eScience Center, Amsterdam, The Netherlands
Lars RidderNetherlands eScience Center, Amsterdam, The Netherlands
Li C XueData CollectorCenter for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
Li XuePIRadboud University Medical Center

Reprocessing Instructions

none


License and Terms of use

License: CC0

Terms: Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation, as generated by the SBGrid Data Bank.