{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T13:01:00Z","timestamp":1779886860524,"version":"3.53.1"},"reference-count":68,"publisher":"AIP Publishing","issue":"20","license":[{"start":{"date-parts":[[2024,5,30]],"date-time":"2024-05-30T00:00:00Z","timestamp":1717027200000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,5,30]],"date-time":"2024-05-30T00:00:00Z","timestamp":1717027200000},"content-version":"tdm","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/E022197\/1"],"award-info":[{"award-number":["EP\/E022197\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/F010516\/1"],"award-info":[{"award-number":["EP\/F010516\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/G042853\/1"],"award-info":[{"award-number":["EP\/G042853\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/I030395"],"award-info":[{"award-number":["EP\/I030395"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/P011330\/1"],"award-info":[{"award-number":["EP\/P011330\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/P022138\/1"],"award-info":[{"award-number":["EP\/P022138\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/V011421"],"award-info":[{"award-number":["EP\/V011421"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/K016601"],"award-info":[{"award-number":["BB\/K016601"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006041","name":"Innovate UK","doi-asserted-by":"publisher","award":["011120"],"award-info":[{"award-number":["011120"]}],"id":[{"id":"10.13039\/501100006041","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000288","name":"Royal Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000288","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011199","name":"FP7 Ideas: European Research Council","doi-asserted-by":"publisher","award":["336289"],"award-info":[{"award-number":["336289"]}],"id":[{"id":"10.13039\/100011199","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["pubs.aip.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2024,5,28]]},"abstract":"<jats:p>Sire is a Python\/C++ library that is used both to prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of many other programs and libraries. This empowers researchers to use sire to write a single script that can, for example, load a molecule from a PDBx\/mmCIF file via Gemmi, perform SMARTS searches via RDKit, parameterize molecules using BioSimSpace, run GPU-accelerated molecular dynamics via OpenMM, and then display the resulting dynamics trajectory in a NGLView Jupyter notebook 3D molecular viewer. This functionality is built on by BioSimSpace, which uses sire\u2019s molecular information engine to interconvert with programs such as GROMACS, NAMD, Amber, and AmberTools for automated molecular parameterization and the running of molecular dynamics, metadynamics, and alchemical free energy workflows. Sire comes complete with a powerful molecular information search engine, plus trajectory loading and editing, analysis, and energy evaluation engines. This, when combined with an in-built computer algebra system, gives substantial flexibility to researchers to load, search for, edit, and combine molecular information from multiple sources and use that to drive novel algorithms by combining functionality from other programs. Sire is open source (GPL3) and is available via conda and at a free Jupyter notebook server at https:\/\/try.openbiosim.org. Sire is supported by the not-for-profit OpenBioSim community interest company.<\/jats:p>","DOI":"10.1063\/5.0200458","type":"journal-article","created":{"date-parts":[[2024,5,30]],"date-time":"2024-05-30T11:28:53Z","timestamp":1717068533000},"update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":13,"title":["Sire: An interoperability engine for prototyping algorithms and exchanging information between molecular simulation programs"],"prefix":"10.1063","volume":"160","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6563-9903","authenticated-orcid":false,"given":"Christopher J.","family":"Woods","sequence":"first","affiliation":[{"name":"Advanced Computing Research Centre, University of Bristol 1 , Bristol, United Kingdom"},{"name":"Centre for Computational Chemistry, School of Chemistry, University of Bristol 2 , Bristol, United Kingdom"},{"name":"OpenBioSim Community Interest Company 3 , Edinburgh, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lester O.","family":"Hedges","sequence":"additional","affiliation":[{"name":"Advanced Computing Research Centre, University of Bristol 1 , Bristol, United Kingdom"},{"name":"OpenBioSim Community Interest Company 3 , Edinburgh, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1015-4567","authenticated-orcid":false,"given":"Adrian J.","family":"Mulholland","sequence":"additional","affiliation":[{"name":"Centre for Computational Chemistry, School of Chemistry, University of Bristol 2 , Bristol, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maturos","family":"Malaisree","sequence":"additional","affiliation":[{"name":"Centre for Computational Chemistry, School of Chemistry, University of Bristol 2 , Bristol, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paolo","family":"Tosco","sequence":"additional","affiliation":[{"name":"Cresset 4 , Cambridgeshire, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannes H.","family":"Loeffler","sequence":"additional","affiliation":[{"name":"Cresset 4 , Cambridgeshire, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miroslav","family":"Suruzhon","sequence":"additional","affiliation":[{"name":"Exscientia Plc. 5 , Oxford, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Burman","sequence":"additional","affiliation":[{"name":"OpenBioSim Community Interest Company 3 , Edinburgh, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sofia","family":"Bariami","sequence":"additional","affiliation":[{"name":"EaStCHEM School of Chemistry, University of Edinburgh 6 , Edinburgh, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefano","family":"Bosisio","sequence":"additional","affiliation":[{"name":"EaStCHEM School of Chemistry, University of Edinburgh 6 , Edinburgh, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gaetano","family":"Calabro","sequence":"additional","affiliation":[{"name":"EaStCHEM School of Chemistry, University of Edinburgh 6 , Edinburgh, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Finlay","family":"Clark","sequence":"additional","affiliation":[{"name":"EaStCHEM School of Chemistry, University of Edinburgh 6 , Edinburgh, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7512-5252","authenticated-orcid":false,"given":"Antonia S. J. S.","family":"Mey","sequence":"additional","affiliation":[{"name":"EaStCHEM School of Chemistry, University of Edinburgh 6 , Edinburgh, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0360-1760","authenticated-orcid":false,"given":"Julien","family":"Michel","sequence":"additional","affiliation":[{"name":"OpenBioSim Community Interest Company 3 , Edinburgh, United Kingdom"},{"name":"EaStCHEM School of Chemistry, University of Edinburgh 6 , Edinburgh, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"317","published-online":{"date-parts":[[2024,5,30]]},"reference":[{"key":"2024072213203798700_c1","doi-asserted-by":"publisher","first-page":"054114","DOI":"10.1063\/1.3519057","article-title":"A water-swap reaction coordinate for the calculation of absolute protein\u2013ligand binding free energies","volume":"134","year":"2011","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024072213203798700_c2","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1039\/c3fd00125c","article-title":"Rapid decomposition and visualisation of protein\u2013ligand binding free energies by residue and by water","volume":"169","year":"2014","journal-title":"Faraday Discuss."},{"key":"2024072213203798700_c3","doi-asserted-by":"publisher","first-page":"717","DOI":"10.4155\/fmc-2021-0348","article-title":"Discovery of novel and potent InhA inhibitors by an in silico screening and pharmacokinetic prediction","volume":"14","year":"2022","journal-title":"Future Med. Chem."},{"key":"2024072213203798700_c4","doi-asserted-by":"publisher","first-page":"014109","DOI":"10.1063\/1.2805379","article-title":"An efficient method for the calculation of quantum mechanics\/molecular mechanics free energies","volume":"128","year":"2008","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024072213203798700_c5","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1021\/ct400783h","article-title":"Prediction of small molecule hydration thermodynamics with grid cell theory","volume":"10","year":"2014","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024072213203798700_c6","doi-asserted-by":"publisher","first-page":"5340","DOI":"10.1021\/acs.jpcb.6b03296","article-title":"Elucidation of nonadditive effects in protein\u2013ligand binding energies: Thrombin as a case study","volume":"120","year":"2016","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024072213203798700_c7","doi-asserted-by":"publisher","first-page":"2485","DOI":"10.1021\/acs.jcim.5b00368","article-title":"FESetup: Automating setup for alchemical free energy simulations","volume":"55","year":"2015","journal-title":"J.\u00a0Chem. Inf. Model."},{"key":"2024072213203798700_c8","doi-asserted-by":"publisher","first-page":"1831","DOI":"10.21105\/joss.01831","article-title":"BioSimSpace: An interoperable Python framework for biomolecular simulation","volume":"4","year":"2019","journal-title":"J.\u00a0Open Source Softw."},{"key":"2024072213203798700_c9","doi-asserted-by":"publisher","first-page":"2375","DOI":"10.33011\/livecoms.5.1.2375","article-title":"A suite of tutorials for the BioSimSpace framework for interoperable biomolecular simulation [article v1.0]","volume":"5","year":"2023","journal-title":"Living J. Comput. Mol. Sci."},{"key":"2024072213203798700_c10","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1021\/ci050357s","article-title":"Molecular field extrema as descriptors of biological activity: Definition and validation","volume":"46","year":"2006","journal-title":"J.\u00a0Chem. Inf. Model."},{"key":"2024072213203798700_c11","doi-asserted-by":"publisher","first-page":"3036","DOI":"10.1021\/acs.jmedchem.8b01925","article-title":"Electrostatic complementarity as a fast and effective tool to optimize binding and selectivity of protein\u2013ligand complexes","volume":"62","year":"2019","journal-title":"J.\u00a0Med. Chem."},{"key":"2024072213203798700_c12","doi-asserted-by":"publisher","first-page":"3120","DOI":"10.1021\/acs.jcim.0c00165","article-title":"Assessment of binding affinity via alchemical free-energy calculations","volume":"60","year":"2020","journal-title":"J.\u00a0Chem. Inf. Model."},{"key":"2024072213203798700_c13","year":"2024"},{"key":"2024072213203798700_c14","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1021\/acs.jpcb.3c06662","article-title":"OpenMM 8: Molecular dynamics simulation with machine learning potentials","volume":"128","year":"2024","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024072213203798700_c15","doi-asserted-by":"publisher","first-page":"4200","DOI":"10.21105\/joss.04200","article-title":"GEMMI: A library for structural biology","volume":"7","year":"2022","journal-title":"J.\u00a0Open Source Softw."},{"key":"2024072213203798700_c16","doi-asserted-by":"publisher","first-page":"1241","DOI":"10.1093\/bioinformatics\/btx789","article-title":"NGLview\u2013interactive molecular graphics for Jupyter notebooks","volume":"34","year":"2018","journal-title":"Bioinformatics"},{"key":"2024072213203798700_c17","doi-asserted-by":"publisher","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding principles for scientific data management and stewardship","volume":"3","year":"2016","journal-title":"Sci. Data"},{"key":"2024072213203798700_c18","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1-2","year":"2015","journal-title":"SoftwareX"},{"key":"2024072213203798700_c19","doi-asserted-by":"publisher","first-page":"1781","DOI":"10.1002\/jcc.20289","article-title":"Scalable molecular dynamics with NAMD","volume":"26","year":"2005","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024072213203798700_c20","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1002\/wcms.1121","article-title":"An overview of the Amber biomolecular simulation package","volume":"3","year":"2013","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2024072213203798700_c21","doi-asserted-by":"publisher","first-page":"6183","DOI":"10.1021\/acs.jcim.3c01153","article-title":"AmberTools","volume":"63","year":"2023","journal-title":"J.\u00a0Chem. Inf. Model."},{"key":"2024072213203798700_c22","doi-asserted-by":"publisher","DOI":"10.26434\/ChemRxiv\/chemrxiv-2023-6rng3","article-title":"emle-engine: a flexible electrostatic machine learning embedding package for multiscale molecular dynamics simulations","year":"2023","journal-title":"chemRxiv:10.26434"},{"key":"2024072213203798700_c23","first-page":"8024","article-title":"PyTorch: An imperative style, high-performance deep learning library","volume-title":"Advances in Neural Information Processing Systems","year":"2019"},{"key":"2024072213203798700_c24","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1002\/jcc.21287","article-title":"CHARMM: The biomolecular simulation program","volume":"30","year":"2009","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024072213203798700_c25","year":"2007"},{"key":"2024072213203798700_c26","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/1758-2946-3-33","article-title":"Open Babel: An open chemical toolbox","volume":"3","year":"2011","journal-title":"J.\u00a0Cheminf."},{"key":"2024072213203798700_c27","article-title":"The PyMOL molecular graphics system","author":"LLC Schr\u00f6dinger","year":"2015"},{"key":"2024072213203798700_c28","doi-asserted-by":"publisher","first-page":"2319","DOI":"10.1002\/jcc.21787","article-title":"MDAnalysis: A toolkit for the analysis of molecular dynamics simulations","volume":"32","year":"2011","journal-title":"J.\u00a0Comput. Chem."},{"key":"2024072213203798700_c29","doi-asserted-by":"publisher","first-page":"1528","DOI":"10.1016\/j.bpj.2015.08.015","article-title":"MDTraj: A modern open library for the analysis of molecular dynamics trajectories","volume":"109","year":"2015","journal-title":"Biophys. J."},{"key":"2024072213203798700_c30","doi-asserted-by":"publisher","first-page":"184108","DOI":"10.1063\/5.0006002","article-title":"PSI4 1.4: Open-source software for high-throughput quantum chemistry","volume":"152","year":"2020","journal-title":"J.\u00a0Chem. Phys."},{"key":"2024072213203798700_c31","year":"2024"},{"key":"2024072213203798700_c32","year":"2020"},{"key":"2024072213203798700_c33","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1007\/s10822-016-9977-1","article-title":"Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset","volume":"31","year":"2017","journal-title":"J.\u00a0Comput.-Aided Mol. Des."},{"key":"2024072213203798700_c34","unstructured":"R.\n            Yakovenko\n          , Y.Yakovenko, J.Pallister, M.Baas, A.Bierbaum, L.Wecker, G.Dernovoy, G.Ganssauge, A.Miller, M.Preisler, M.Haridev, J.Scheid, O.Schweitzer, H.Ordiales, B.Fritzke, A.Vermel, P.Kellom\u00e4ki, B.Leveau, N.Rath, A.Birtles, M.-T.Pham, A.Xu, and M.Moll, Py++; https:\/\/github.com\/ompl\/pyplusplus."},{"key":"2024072213203798700_c35","unstructured":"D.\n            Abrahams\n           and S.Seefeld, Boost.Python; https:\/\/www.boost.org\/doc\/libs\/1_76_0\/libs\/python."},{"key":"2024072213203798700_c36","unstructured":"Qt, Implicit Sharing; https:\/\/doc.qt.io\/qt-5\/implicit-sharing.html, 2023."},{"key":"2024072213203798700_c37","unstructured":"J.\n            de Guzman\n           and Kaiser, Boost.Spirit; https:\/\/www.boost.org\/doc\/libs\/1_78_0\/libs\/spirit."},{"key":"2024072213203798700_c38","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1021\/ci00057a005","article-title":"SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules","volume":"28","year":"1988","journal-title":"J.\u00a0Chem. Inf. Comput. Sci."},{"key":"2024072213203798700_c39","unstructured":"C. J.\n            Woods\n          , Sire: Detailed search guide; https:\/\/sire.openbiosim.org\/cheatsheet\/search, 2024."},{"key":"2024072213203798700_c40","doi-asserted-by":"publisher","first-page":"3686","DOI":"10.1021\/acs.jctc.3c00139","article-title":"Comparison of receptor\u2013ligand restraint schemes for alchemical absolute binding free energy calculations","volume":"19","year":"2023","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024072213203798700_c41","doi-asserted-by":"publisher","first-page":"4055","DOI":"10.1021\/ct500368p","article-title":"Evaluation of host\u2013guest binding thermodynamics of model cavities with grid cell theory","volume":"10","year":"2014","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024072213203798700_c42","doi-asserted-by":"publisher","first-page":"8416","DOI":"10.1039\/c4cp05572a","article-title":"Evaluation of water displacement energetics in protein binding sites with grid cell theory","volume":"17","year":"2015","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2024072213203798700_c43","doi-asserted-by":"publisher","first-page":"10442","DOI":"10.1021\/acs.jpcb.6b07993","article-title":"Assessment of hydration thermodynamics at protein interfaces with grid cell theory","volume":"120","year":"2016","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"2024072213203798700_c44","doi-asserted-by":"publisher","first-page":"3023","DOI":"10.1039\/c8sc00299a","article-title":"Metabolism and hydrophilicity of the polarised \u2018Janus face\u2019 all-cis tetrafluorocyclohexyl ring, a candidate motif for drug discovery","volume":"9","year":"2018","journal-title":"Chem. Sci."},{"key":"2024072213203798700_c45","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1038\/s42004-022-00754-9","article-title":"An open-source molecular builder and free energy preparation workflow","volume":"5","year":"2022","journal-title":"Commun. Chem."},{"key":"2024072213203798700_c46","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1039\/d2dd00083k","article-title":"Data-driven generation of perturbation networks for relative binding free energy calculations","volume":"1","year":"2022","journal-title":"Digital Discovery"},{"key":"2024072213203798700_c47","doi-asserted-by":"publisher","first-page":"5220","DOI":"10.1039\/d2sc00028h","article-title":"Energetics of a protein disorder\u2013order transition in small molecule recognition","volume":"13","year":"2022","journal-title":"Chem. Sci."},{"key":"2024072213203798700_c48","doi-asserted-by":"publisher","first-page":"2124","DOI":"10.1021\/acs.jcim.1c00328","article-title":"Implementation of the QUBE force field in SOMD for high-throughput alchemical free-energy calculations","volume":"61","year":"2021","journal-title":"J.\u00a0Chem. Inf. Model."},{"key":"2024072213203798700_c49","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1007\/s10822-020-00290-5","article-title":"The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations","volume":"34","year":"2020","journal-title":"J.\u00a0Comput.-Aided Mol. Des."},{"key":"2024072213203798700_c50","doi-asserted-by":"publisher","first-page":"e0213217","DOI":"10.1371\/journal.pone.0213217","article-title":"Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors","volume":"14","year":"2019","journal-title":"PLoS One"},{"key":"2024072213203798700_c51","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1039\/c8sc03831g","article-title":"A computationally designed binding mode flip leads to a novel class of potent tri-vector cyclophilin inhibitors","volume":"10","year":"2019","journal-title":"Chem. Sci."},{"key":"2024072213203798700_c52","doi-asserted-by":"publisher","first-page":"5567","DOI":"10.1021\/acs.jctc.8b00544","article-title":"Reproducibility of free energy calculations across different molecular simulation software packages","volume":"14","year":"2018","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024072213203798700_c53","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1007\/s10822-018-0154-6","article-title":"Blinded predictions of standard binding free energies: Lessons learned from the SAMPL6 challenge","volume":"32","year":"2018","journal-title":"J.\u00a0Comput.-Aided Mol. Des."},{"key":"2024072213203798700_c54","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1007\/s10822-017-0083-9","article-title":"Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations","volume":"32","year":"2018","journal-title":"J.\u00a0Comput.-Aided Mol. Des."},{"key":"2024072213203798700_c55","doi-asserted-by":"publisher","first-page":"2556","DOI":"10.1016\/j.jmb.2017.06.016","article-title":"Pushing the limits of detection of weak binding using fragment-based drug discovery: Identification of new cyclophilin binders","volume":"429","year":"2017","journal-title":"J.\u00a0Mol. Biol."},{"key":"2024072213203798700_c56","doi-asserted-by":"publisher","first-page":"1101","DOI":"10.1007\/s10822-016-9969-1","article-title":"Blinded predictions of distribution coefficients in the SAMPL5 challenge","volume":"30","year":"2016","journal-title":"J.\u00a0Comput.-Aided Mol. Des."},{"key":"2024072213203798700_c57","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1007\/s10822-016-9933-0","article-title":"Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge","volume":"31","year":"2017","journal-title":"J.\u00a0Comput.-Aided Mol. Des."},{"key":"2024072213203798700_c58","doi-asserted-by":"publisher","first-page":"4890","DOI":"10.1016\/j.bmc.2016.07.044","article-title":"Blinded predictions of binding modes and energies of HSP90-\u03b1 ligands for the 2015 D3R grand challenge","volume":"24","year":"2016","journal-title":"Bioorg. Med. Chem."},{"key":"2024072213203798700_c59","unstructured":"BioSimSpace: Exscientia branch, https:\/\/github.com\/Exscientia\/biosimspace."},{"key":"2024072213203798700_c60","unstructured":"C. J.\n            Woods\n           and J.Michel, \u201cProtoMS 2.1: A Monte Carlo free,\u201d Energy Program; https:\/\/protoms.org, 2006."},{"key":"2024072213203798700_c61","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1021\/ct600069r","article-title":"Efficient generalized Born models for Monte Carlo simulations","volume":"2","year":"2006","journal-title":"J.\u00a0Chem. Theory Comput."},{"key":"2024072213203798700_c62","unstructured":"Calendar versioning, https:\/\/calver.org, 2024."},{"key":"2024072213203798700_c63","doi-asserted-by":"publisher","first-page":"3914","DOI":"10.21105\/joss.03914","article-title":"MetaWards: A flexible metapopulation framework for modelling disease spread","volume":"7","year":"2022","journal-title":"J.\u00a0Open Source Softw."},{"key":"2024072213203798700_c64","unstructured":"Conda-Forge Community (2015). \u201cThe conda-forge project: Community-based software distribution built on the conda package format and ecosystem,\u201d Zenodo, https:\/\/doi.org\/10.5281\/ZENODO.4774216"},{"key":"2024072213203798700_c65","unstructured":"OpenBioSim Conda Channel: https:\/\/anaconda.org\/openbiosim, 2024."},{"key":"2024072213203798700_c66","unstructured":"OpenBioSim archive channel: https:\/\/openbiosim.blob.core.windows.net\/archive\/index.html, 2024."},{"key":"2024072213203798700_c67","unstructured":"Sire Changelog: https:\/\/sire.openbiosim.org\/changelog, 2024."},{"key":"2024072213203798700_c68","unstructured":"Sire: Usage analytics, https:\/\/siremol.org\/analytics\/oschart.html, 2024."}],"container-title":["The Journal of Chemical Physics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.aip.org\/aip\/jcp\/article-pdf\/doi\/10.1063\/5.0200458\/20064977\/202503_1_5.0200458.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/pubs.aip.org\/aip\/jcp\/article-pdf\/doi\/10.1063\/5.0200458\/20064977\/202503_1_5.0200458.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.aip.org\/aip\/jcp\/article-pdf\/doi\/10.1063\/5.0200458\/20064977\/202503_1_5.0200458.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,27]],"date-time":"2025-05-27T20:20:49Z","timestamp":1748377249000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.aip.org\/jcp\/article\/160\/20\/202503\/3295373\/Sire-An-interoperability-engine-for-prototyping"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,28]]},"references-count":68,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2024,5,28]]}},"URL":"https:\/\/doi.org\/10.1063\/5.0200458","relation":{},"ISSN":["0021-9606","1089-7690"],"issn-type":[{"value":"0021-9606","type":"print"},{"value":"1089-7690","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,5,28]]},"published":{"date-parts":[[2024,5,28]]},"article-number":"202503"}}