2026-10-12 https://api.researchdata.se/oai-pmh

oai:researchdata.se:doi-10-17044-scilifelab-22348714/0 2023-05-31 subject:ssif:3 subject:ssif:10203 subject:ssif:102 subject:ssif:1 principal:slug:uppsala-university

info:eu-repo/semantics/other http://purl.org/dc/dcmitype/Dataset https://doi.org/10.17044/SCILIFELAB.22348714 Can we use molecular dynamics to simulate biomolecular recognition? https://orcid.org/0000-0002-6825-909X David van der Spoel https://orcid.org/0000-0001-5522-1810 Gareth A. Tribello Medical and Health Sciences Medicin och hälsovetenskap Bioinformatics (Computational Biology) Bioinformatik (beräkningsbiologi) This Dataset contains starting structures, inout files and scripts to prepare and run normal and biased simulations on the LacI Transcriptionfactor and DNA (with different sequences). The starting structures (based on the crystal structure with PDB ID 1EFA), input files for GROMACS and PLUMED and scripts for prepartion and analysis are also available on GitHub. In this dataset, one can additionally find the trajetories of the simulations that were run to produce the linked publication. The trajectories include the follwing sets: Unbiased simulations  5 replica of 50 ns each NMR restraint simulations  2 DNA sequences: specific, OSymL and non-specific NOD 3 replica of 250 ns each Metadynamics simulations OSymL (specific DNA sequence) bias on selected contacts between the protein and the DNA bias on selected contacts between the protein and the DNA and between the two hinge helices bias on selected contacts between the protein and the DNA and between the two hinge helices and the hinge helixity NOD (non-specific DNA sequence) bias on selected contacts between the protein and the DNA and between the two hinge helices and the hinge helixity Code contains the scripts used for preparing, running and analysing the simulations. It is also available on GitHub (https://github.com/mallu2/Transcriptionfactor_unbinding) (https://github.com/mallu2/Transcriptionfactor_unbinding) . https://creativecommons.org/licenses/by/4.0/ Uppsala University Uppsala universitet 2023-04-11T00:00:00Z