EnsembleLab
Google Colaboratory-based notebooks to study conformational ensembles of proteins.
IDRLab
MD simulations of IDPs and IDRs with the CALVADOS2 coarse-grained model, including calculation of sequence features and structural parameters.
Run the notebook on Google Colab.
If you use IDRLab, we ask you to cite Tesei, Trolle et al. [1]. In addition, you may consider citing Tesei & Lindorff-Larsen [2] for CALVADOS 2 and Eastman et al. [3] for OpenMM.
[1] G. Tesei, A. I. Trolle, N. Jonsson, J. Betz, F. Pesce, K. E. Johansson, K. Lindorff-Larsen Conformational ensembles of the human intrinsically disordered proteome: Bridging chain compaction with function and sequence conservation bioRxiv 2023 2023.05.08.539815 DOI: https://doi.org/10.1101/2023.05.08.539815
[2] G. Tesei and K. Lindorff-Larsen Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range [version 2; peer review: 2 approved] Open Research Europe 2023 2(94) DOI: https://doi.org/10.12688/openreseurope.14967.2
[3] P. Eastman, J. Swails, J. D. Chodera et al. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics PLoS Computational Biology 2017 13(7):e1005659 DOI: https://doi.org/10.1371/journal.pcbi.1005659