A dynamical view of protein-protein complexes: studies by molecular dynamics simulations
Authors/Creators
- 1. Univ Lyon, CNRS, UMR 5086 MMSB, 7 passage du Vercors F-69367, Lyon, France
- 2. CiTCoM, CNRS, Université Paris Cité, Paris, France
Description
All-atom MD simulations generated for the manuscript "A dynamical view of protein-protein complexes: studies by molecular dynamics simulations". Eight binary protein-protein complexes from the Docking benchmark and the Affinity benchmark are studied in this work: 2OOB (an ubiquitin/ubiquitin ligase complex), 1AY7 (a ribonuclease Sa/barstar complex), 1BRS (a barnase/barstar complex), 3SGB (a proteinase B/inhibitor), 1EMV (a colicin/immunity protein complex), 1PVH (complex between Interleukine 6 receptor and leukemia inhibitory factor), 1GCQ (Vav/GRB2 SH3 domains complex) and 1AK4 (cyclophilin/HIV capsid complex)
Each folder for a binary complex is organised as followed:
- in A and B there are the dry MD simulations for the unbound proteins
- in complex there are two folders (without_water and water) where the dry simulation and the simulation with water molecules are provided
Files
Files
(21.2 GB)
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md5:7d3ec73e3da0ba58050c2b47ac657bfb
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md5:2ba2ae5d53801a3362144311a67ef9ee
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3.4 GB | Download |
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md5:5ad9163c5c8e9093040f4baa0d84edc7
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2.4 GB | Download |
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1.4 GB | Download |
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md5:bccf1ae9e04fd0e47264faeae15f3783
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6.8 GB | Download |
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md5:16c2848a02aa5d844650a8f67c673810
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1.4 GB | Download |
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md5:3b7607acad9834aad00631155b879f0b
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2.3 GB | Download |
Additional details
Related works
- Is cited by
- Journal article: 10.3389/fmolb.2022.970109 (DOI)