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Darre L., Tek A., Baaden M, Pantano S..  2012.  Mixing atomistic and coarse grain solvation models for MD simulations: let WT4 handle the bulk. Jctc.
Laurin Y, Eyer J, Robert CH, Prévost C, Sacquin-Mora S.  2017.  Mobility and core-protein binding patterns of disordered C-terminal tails in β-tubulin isotypes.. Biochemistry. 56(12):1746–1756.
Bertucat G, Lavery R, Prévost C.  1998.  A model for parallel triple helix formation by RecA: single-single association with a homologous duplex via the minor groove. J. Biomol. Struct. Dyn.. 16:535–46.
Mazur AK, Petukhov M.G, Elyakova L.A.  1988.  Model of spatial random movement of depolymerase when interacting with the substrate. Biophysics. 23:417–421.
Laurent B., Murail S., Da Silva F., Corringer P.-J., Baaden M.  2012.  Modeling complex biological systems: From solution chemistry to membranes and channels. Pure Appl. Chem.. ASAP
Mazur AK.  2009.  Modeling DNA dynamics under steady deforming forces and torques. J. Chem. Theory Comput.. 5:2149–2157.
Cazals F, Dreyfus T, Robert CH.  2013.  Modeling macromolecular complexes: a journey across scales. Modeling in Computational Biology and Biomedicine: A Multidisciplinary Endeavor.
Petuhov M.G, Mazur AK.  1992.  Modeling of the possible binding modes of substrates in the active site of Taka-Amylase A. Mol. Biol.. 26:292–299.
Boyer B., Laurent B., Robert C.H, Prevost C..  2021.  Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom. Bio-protocol. 11:e4097.
Karaca E, Prévost C, Sacquin-Mora S.  2022.  Modeling the Dynamics of Protein-Protein Interfaces, How and Why? Molecules. 27:1841.
Baaden M, Borthakur MPratim, Casanova S, Coalson R, Freger V, Gonzalez M, Góra A, Hinds B, Hirunpinyopas W, Hummer G et al..  2018.  The modelling and enhancement of water hydrodynamics: general discussion.. Faraday Discuss. 209:273-285.
Brandner AF, Timr S, Melchionna S, Derreumaux P, Baaden M, Sterpone F.  2019.  Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics. Scientific Reports. 9:16450.
Hénin J, Shinoda W, Klein ML.  2009.  Models for phosphatidylglycerol lipids put to a structural test. J. Phys. Chem. B. 113:6958–6963.
Pasquali S., Gan H.H., Schlick T..  2005.  Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs. Nuc. Acids Res.. 33:1384–1398.
Kozhemyako VB, Rebrikov DV, Lukyanov SA, Bogdanova EA, Marin A, Mazur AK, Kovalchuk SN, Agafonova EV, Sova VV, Elyakova LA et al..  2004.  Molecular cloning of a mollusk glucanase. Comp. Biochem. Physiol.. 137:169–178.
Gagelin A, Largeau C, Masscheleyn S, Piel MS, Calderón-Mora D, Bouillaud F, Hénin J, Miroux B.  2023.  Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling.. Nat Commun. 14(1):2594.
Baaden M, Meier C, Sansom MSP.  2003.  A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA. J. Mol. Biol.. 331:177–189.
Mazur AK.  2001.  Molecular dynamics of minimal B-DNA. J. Comput. Chem.. 22:457–467.
Dorofeyev V.E, Mazur AK.  1991.  Molecular dynamics of polymers with fixed internal structure: Choice of models and methods. Russ. J. Phys. Chem.. 65:2548–2552.
Park S-M, Nguyen PHoang, Stock G.  2009.  Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent. J. Chem. Phys.. 131
Khalid S., Baaden M.  2010.  Molecular dynamics studies of outer membrane proteins : a story of barrels. :225–247.
Mazur AK.  2001.  Molecular dynamics studies of sequence-directed curvature in bending locus of Trypanosome kinetoplast DNA. J. Biomol. Struct. Dyn.. 18:832–843.
Sterpone F, Briganti G, Pierleoni C.  2001.  Molecular Dynamics Study of Spherical Aggregates of Chain Molecules at Different Degrees of Hydrophilicity in Water Solution. Langmuir. 17:5103–5110.
Sterpone F, Pierleoni C, Briganti G, Marchit M.  2004.  Molecular dynamics study of temperature dehydration of a C12E6 spherical micelle. Langmuir. 20:4311–4.
Baaden M, Schurhammer R, Wipff G.  2002.  Molecular dynamics study of the uranyl extraction by tri-n-butylphosphate (TBP): Demixing of water/''oil''/TBP solutions with a comparison of supercritical CO2 and chloroform. J. Phys. Chem. B. 106:434–441.