Citations ========= If **SIRAH** was beneficial to your work, please cite one or more of these SIRAH references: .. |Review| image:: https://img.shields.io/badge/DOI-10.1016%2Fj.jsb.2023.107985-blue :alt: Access the paper :target: https://doi.org/10.1016/j.jsb.2023.107985 .. |Review-cit| image:: https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1016%2Fj.jsb.2023.107985 :alt: Citation :target: https://scholar.google.com/scholar?cites=11014340861876399425 - Klein, F.; Soñora, M.; Santos, L. H.; Frigini, E. N.; Ballesteros-Casallas, A.; Machado, M. R.; Pantano, S. The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels. Journal of Structural Biology 2023, 107985. |Review| |Review-cit| .. |SIRAH1.0| image:: https://img.shields.io/badge/DOI-10.1021%2Fct5007746-blue :alt: Access the paper :target: https://doi.org/10.1021/ct5007746 .. |SIRAH1.0-cit| image:: https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1021%2Fct5007746 :alt: Citation :target: https://scholar.google.com/scholar?oi=bibs&hl=es&cites=6310976936290764166 - Darré, L.; Machado, M. R.; Brandner, A. F.; González, H. C.; Ferreira, S.; Pantano, S. SIRAH: A Structurally Unbiased Coarse-Grained Force Field for Proteins with Aqueous Solvation and Long-Range Electrostatics. Journal of Chemical Theory and Computation 2015, 11, 723–739. |SIRAH1.0| |SIRAH1.0-cit| .. |SIRAH2.0| image:: https://img.shields.io/badge/DOI-10.1021%2Facs.jctc.9b00006-blue :alt: Access the paper :target: https://doi.org/10.1021/acs.jctc.9b00006 .. |SIRAH2.0-cit| image:: https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1021%2Facs.jctc.9b00006 :alt: Citation :target: https://scholar.google.com/scholar?oi=bibs&hl=es&cites=5136612330374064800 - Machado, M. R.; Barrera, E. E.; Klein, F.; Soñora, M.; Silva, S.; Pantano, S. The SIRAH 2.0 Force Field: Altius, Fortius, Citius. Journal of Chemical Theory and Computation 2019, 15, 2719–2733. |SIRAH2.0| |SIRAH2.0-cit| In addition, please include the following citations if the following parameters were used: .. |PostTrans| image:: https://img.shields.io/badge/DOI-10.1021%2Facs.jcim.9b00900-blue :alt: Access the paper :target: https://doi.org/10.1021/acs.jcim.9b00900 .. |PostTrans-cit| image:: https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1021%2Facs.jcim.9b00900 :alt: Citation :target: https://scholar.google.com/scholar?oi=bibs&hl=es&cites=4741245244387638059 * **Post-translational modifications**: * Garay, P. G.; Barrera, E. E.; Pantano, S. Post-Translational Modifications at the Coarse-Grained Level with the SIRAH Force Field. Journal of Chemical Information and Modeling 2020, 60, 964–973. |PostTrans| |PostTrans-cit| .. |Metal| image:: https://img.shields.io/badge/DOI-10.1021%2Facs.jcim.0c00160-blue :alt: Access the paper :target: https://doi.org/10.1021/acs.jcim.0c00160 .. |Metal-cit| image:: https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1021%2Facs.jcim.0c00160 :alt: Citation :target: https://scholar.google.com/scholar?oi=bibs&hl=es&cites=2583810250614166915 * **Metal ions**: * Klein, F.; Cáceres, D.; Carrasco, M. A.; Tapia, J. C.; Caballero, J.; Alzate-Morales, J.; Pantano, S. Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field. Journal of Chemical Information and Modeling 2020, 60, 3935–3943. |Metal| |Metal-cit| .. |DNA| image:: https://img.shields.io/badge/DOI-10.1021%2Fct900653p-blue :alt: Access the paper :target: https://doi.org/10.1021/ct900653p .. |DNA-cit| image:: https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1021%2Fct900653p :alt: Citation :target: https://scholar.google.com/scholar?oi=bibs&hl=es&cites=12499613729973955498 * **DNA**: * Dans, P. D.; Zeida, A.; Machado, M. R.; Pantano, S. A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics. Journal of Chemical Theory and Computation 2010, 6, 1711–1725. |DNA| |DNA-cit| .. |FatSirah| image:: https://img.shields.io/badge/DOI-10.1021%2Facs.jctc.9b00435-blue :alt: Access the paper :target: https://doi.org/10.1021/acs.jctc.9b00435 .. |FatSirah-cit| image:: https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1021%2Facs.jctc.9b00435 :alt: Citation :target: https://scholar.google.com/scholar?oi=bibs&hl=es&cites=13191972720970339574 * **Lipids**: * Barrera, E. E.; Machado, M. R.; Pantano, S. Fat SIRAH: Coarse-Grained Phospholipids To Explore Membrane–Protein Dynamics. Journal of Chemical Theory and Computation 2019, 15, 5674–5688. |FatSirah| |FatSirah-cit| .. |Solvent| image:: https://img.shields.io/badge/DOI-10.1021%2Fct100379f-blue :alt: Access the paper :target: https://doi.org/10.1021/ct100379f .. |Solvent-cit| image:: https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1021%2Fct100379f :alt: Citation :target: https://scholar.google.com/scholar?oi=bibs&hl=es&cites=11533073503238221292 * **Solvent with simple electrolytes**: * Darré, L.; Machado, M. R.; Dans, P. D.; Herrera, F. E.; Pantano, S. Another Coarse Grain Model for Aqueous Solvation: WAT FOUR? Journal of Chemical Theory and Computation 2010, 6, 3793–3807. |Solvent| |Solvent-cit| .. |MC1| image:: https://img.shields.io/badge/DOI-10.1021%2Facs.jctc.7b00659-blue :alt: Access the paper :target: https://doi.org/10.1021/acs.jctc.7b00659 .. |MC1-cit| image:: https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1021%2Facs.jctc.7b00659 :alt: Citation :target: https://scholar.google.com/scholar?cites=16637391138490147245 .. |MC2| image:: https://img.shields.io/badge/DOI-10.1098%2Frsfs.2018.0085-blue?label=DOI :alt: Access the paper :target: https://doi.org/10.1098/rsfs.2018.0085 .. |MC2-cit| image:: https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1098%2Frsfs.2018.0085 :alt: Citation :target: https://scholar.google.com/scholar?cites=5473055142318037579 * **Multiscale Simulations**: * Machado, M. R.; Zeida, A.; Darré, L.; Pantano, S. From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field. Interface Focus 2019, 9, 20180085. |MC2| |MC2-cit| * Machado, M. R.; González, H. C.; Pantano, S. MD Simulations of Virus like Particles with Supra CG Solvation Affordable to Desktop Computers. Journal of Chemical Theory and Computation 2017, 13, 5106–5116. |MC1| |MC1-cit| If **SIRAH Tools** were used please cite: .. |Tools| image:: https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtw020-blue :alt: Access the paper :target: https://doi.org/10.1093/bioinformatics/btw020 .. |Tools-cit| image:: https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1093%2Fbioinformatics%2Fbtw020 :alt: Citation :target: https://scholar.google.com/scholar?oi=bibs&hl=es&cites=8075862653806269057 - Machado, M. R.; Pantano, S. SIRAH tools: mapping, backmapping and visualization of coarse-grained models. Bioinformatics 2016, 32, 1568–1570. |Tools| |Tools-cit| .. seealso:: If you wish to view some SIRAH applications, please visit the :doc:`Further reading ` page.