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5. Datasets
This dataset is the default dataset which is supplied with the application and is automatically loaded upon start. It is a small dataset of 500 frames and consists of a single chain of 15 Alanine residues.
This dataset consists of an aspirin ligand being pulled out of its specific binding to Phospholipase A2. The dynamic was performed from the crystal structure (1OXR) of the complex.[1] In this dynamic a biased potential was applied to pull the molecule out of pocket. This trajectory has been obtain with GROMACS[2] using the Amber force-field[3]. This trajectory was produced for pedagogical purpose. It is available to download from the provided link. A edr file is also provided.
This non-biased molecular dynamic simulation illustrates the binding of a pentameric oligothiophene used for the detection of amyloid-β(1–42), responsible for Alzheimer’s disease.[4] It is available to download from the provided link.
This simulation shows sodium ions passing though a membrane under an electric field. The dataset is available following the link. This dataset has been provided by Koushik Choudhury and Lucie Delemotte and is extracted from their work "Modulation of Pore Opening of Eukaryotic Sodium Channels by π‑Helices in S6".[5]
[1] Singh, R. K.; Ethayathulla, A.; Jabeen, T.; Sharma, S.; Kaur, P.; Singh, T. P. "Aspirin induces its anti-inflammatory effects through its specific binding to phospholipase A2: Crystal structure of the complex formed between phospholipase A2 and aspirin at 1.9 Å resolution." Journal of Drug Targeting 2005, 13, 113–119, PMID: 15823962.
[2] M.J. Abraham, T. Murtola, R. Schulz, S. Páll, J.C. Smith, B. Hess, and E. Lindahl, “GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers,” SoftwareX, 1–2 19–25 (2015
[3] C.Tian, K. Kasavajhala, K. A. A. Belfon, L. Raguette, H. Huang, A. N. Migues J. Bickel, Y. Wang, J. Pincay, Q. Wu and C. Simmerling. (2019) "ff19SB: Amino-Acid-Specific Protein Backbone Paramters Trained against Quantum Mechanics Energy Surfaces in Solution." J. Chem. Theory Comput.16, 528-552.
[4] König, C.; Skånberg, R.; Hotz, I.; Ynnerman, A.; Norman, P.; Linares, "M. Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations." Chem. Commun. 2018, 54, 3030–3033.
[5] K. Choudhury and L. Delemotte, "Modulation of Pore Opening of Eukaryotic Sodium Channels by π‑Helices in S6". J. Phys. Chem. Lett. 2023, 14, 5876−5881.
