Scientific Publications

• Core Paper submitted on Nov-1-24 .. stay tuned!

If you use BioSpring in your research, and until the core BioSpring paper gets accepted, please cite the following references.

• Molza A-E, Férey N, Czjzek M, Le Rumeur E, Hubert J-F, Tek A, Laurent B, Baaden M, Delalande O (2014) Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly. Faraday Discuss 169:45–62.
• Tek A, Chavent M, Baaden M, Delalande O, Bourdot P, FG Katz B, Ferey N Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations. In: Cai W, Hong H, editors. Protein-Protein Interactions - Computational and Experimental Tools. IntechOpen; 2012.

• BioSpring is distributed under the CECILL-C license
• Over its 17 years of existence, BioSpring was funded by multiple sources. Most recently in particular the “Initiative d’Excellence” program from the French State, grants “DYNAMO,” ANR-11-LABX-0011, and “CACSICE,” ANR-11-EQPX-0008. We thank ANR for support of grants “MERLIN,” ANR-22-CE45-0032-04, “PIRATE,” ANR-21-CE45-0014 and “MINOMICS,” ANR- 19-CE45-0017. We thank Sesame Ile-de-France for cofunding the visualization platform of the IBPC institute used for testing some of the interactive use cases described in the manuscript and the CNRS Chemistry department for human resources funding.
• We thank past collaborators Sébastien Doutreligne, Xavier Martinez, Dominique Mias-Lucquin, Anne-Elisabeth Molza, Joao Rodriguez and Alex Tek who were essential in laying the foundations for this work.

• Delalande O, Férey N, Grasseau G, Baaden M (2009) Complex molecular assemblies at hand via interactive simulations. J. Comput. Chem. 30:2375–2387.
• Lanrezac A, Férey N, Baaden M (2021) Wielding the power of interactive molecular simulations. WIREs Comput Mol Sci 12:e1594.
• Baaden M (2022) Deep inside molecules — digital twins at the nanoscale. Virtual Reality & Intelligent Hardware 4:324–341.
• Baaden M (2024) MolPlay: Democratizing Interactive Molecular Simulations and Analyses with a Portable, Turnkey Platform. J. Phys. Chem. B 128:9132–9142.

• Lanrezac A, Laurent B, Santuz H, Férey N, Baaden M (2022) Fast and Interactive Positioning of Proteins within Membranes. Algorithms 15:415.
• Lanrezac A, Baaden M (2023) UNILIPID, a Methodology for Energetically Accurate Prediction of Protein Insertion into Implicit Membranes of Arbitrary Shape. Membranes 13:362.

• Delalande O, Ferey N, Laurent B, Gueroult M, Hartmann B, Baaden M (2010) Multi-resolution approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device. Pac Symp Biocomput:205–215.
• Saladin A, Amourda C, Poulain P, Férey N, Baaden M, Zacharias M, Delalande O, Prévost C (2010) Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Res 38:6313–6323.
• Da Costa G, Bondon A, Delalande O, Mouret L, Monti J-P (2013) Elucidation by NMR solution of neurotensin in small unilamellar vesicle environment: molecular surveys for neurotensin receptor recognition. J Biomol Struct Dyn 31:809–817.
• Paquet F, Delalande O, Goffinont S, Culard F, Loth K, Asseline U, Castaing B, Landon C (2014) Model of a DNA-protein complex of the architectural monomeric protein MC1 from Euryarchaea. PLoS One 9:e88809.
• Delalande O, Molza A-E, Morais RDS, Chéron A, Pollet É, Raguenes-Nicol C, Tascon C, Giudice E, Guilbaud M, Nicolas A, et al. (2018) Dystrophin’s central domain forms a complex filament that becomes disorganized by in-frame deletions. Journal of Biological Chemistry 293:6637–6646.
• Tashjian TF, Danilowicz C, Molza A-E, Nguyen BH, Prévost C, Prentiss M, Godoy VG (2019) Residues in the fingers domain of the translesion DNA polymerase DinB enable its unique participation in error-prone double-strand break repair. Journal of Biological Chemistry 294:7588–7600.
• Mias-Lucquin D, Dos Santos Morais R, Chéron A, Lagarrigue M, Winder SJ, Chenuel T, Pérez J, Appavou M-S, Martel A, Alviset G, et al. (2020) How the central domain of dystrophin acts to bridge F-actin to sarcolemmal lipids. Journal of Structural Biology 209:107411.
• Molza A-E, Westermaier Y, Moutte M, Ducrot P, Danilowicz C, Godoy-Carter V, Prentiss M, Robert CH, Baaden M, Prévost C (2022) Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Frontiers in Molecular Biosciences 9:826136.