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A
Mazur AK.  2009.  Analysis of accordion DNA stretching revealed by the gold cluster ruler. Phys. Rev. E. 80:010901.
Gill S.J, Robert C.H, Wyman J..  1988.  Analysis of allosteric systems. Biochemical Thermodynamics.
Gan H.H, Perow R.A, Roy S., , Yan S., Nicoletta A., D. Vafai SJ, Wang L., Noah J.E, Pasquali S. et al..  2002.  Analysis of Protein Sequence/Structure Similarity Relationships. Biophys. J.. 83:2781–2791.
Connelly PR, Robert CH, Briggs WE, Gill SJ.  1986.  Analysis of zeros of binding polynomials for tetrameric hemoglobins. Biophys. Chem.. 24:295–309.
Esque J, Sansom MSP, Baaden M, Oguey C.  2018.  Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network.. Sci Rep. 8(1):13540.
Mazur AK.  2010.  Anharmonic torsional stiffness of DNA revealed under small external torques. Phys. Rev. Lett.. 105:018102.
Oleinikova A, Brovchenko I, Krukau A, Mazur AK.  2008.  Anomalous diffusion of ions at the surface of hydrated DNA molecule. Europhys. Lett.. 82:46002.
Floquet N, Pasco S, Ramont L, Derreumaux P, Laronze JY, Nuzillard JM, Maquart FX, Alix AJP, Monboisse JC.  2004.  The antitumor properties of the alpha 3(IV)-(185-203) peptide from the NC1 domain of type IV collagen (tumstatin) are conformation-dependent. J. Biol. Chem.. 279:2091–2100.
Baaden M, Barboiu M, Borthakur MPratim, Chen C-L, Coalson R, Davis J, Freger V, Gong B, Hélix-Nielsen C, Hickey R et al..  2018.  Applications to water transport systems: general discussion.. Faraday Discuss. 209:389-414.
Kalimeri M, Derreumaux P, Sterpone F.  2015.  Are coarse-grained models apt to detect protein thermal stability? The case of \OPEP\ force field J. Non-cryst. Solids. 407:494–501.
Yun MR, Lavery R, Mousseau N, Zakrzewska K, Derreumaux P.  2006.  ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes. Proteins: Struct., Funct., Bioinf.. 63:967–975.
Chintapalli SV, Illingworth CJR, Upton GJG, Sacquin-Mora S, Reeves PJ, Mohammedali HS, Reynolds CA.  2014.  Assessing the effect of dynamics on the closed-loop protein-folding hypothesis. Journal of the Royal Society Interface. 11:20130935.
Barducci A, Bonomi M, Derreumaux P.  2011.  Assessing the Quality of the OPEP Coarse-Grained Force Field. J. Chem. Theory Comput.. 7:1928–1934.
Zhang T, Xu W, Mu Y, Derreumaux P.  2014.  Atomic and Dynamic Insights into the Beneficial Effect of the 1,4-Naphthoquinon-2-yl-L-tryptophan Inhibitor on Alzheimer's A beta 1-42 Dimer in Terms of Aggregation and Toxicity. Acs Chem. Neurosci.. 5:148–159.
Mazur AK, Maaloum M.  2014.  Atomic force microscopy study of DNA flexibility on short length scales: Smooth bending versus kinking. Nucleic. Acids. Res.. 42:14006–14012.
Hénin J, Brannigan G, Dailey WP, Eckenhoff RG, Klein ML.  2010.  An atomistic model for simulations of the general anesthetic isoflurane. J. Phys. Chem. B. 114:604–612.
Krieger E., Leger L., Durrieu M.P., Taib N., Bond P., Laguerre M., Lavery R., Sansom M.S.P., Baaden M.  2007.  Atomistic modeling of the membrane-embedded synaptic fusion complex: a grand challenge project on the DEISA HPC infrastructure. ParCo 2007, Parallel Computing: Architectures, Algorithms and Applications. 38:729–736.
Danilowicz C, Hermans L, Coljee V, Prévost C, Prentiss M.  2017.  ATP hydrolysis provides functions that promote rejection of pairings between different copies of long repeated sequences. Nucleic Acids Res. 45:8448-8462.
Schneider S., Saladin A, Fiorucci S., Prévost C, Zacharias M.  2012.  ATTRACT and PTOOLS: Open source programs for protein-protein docking. Methods Mol. Biol.. 819:221–232.
Nguyen HLinh, Thu TThi Minh, Truong PMinh, Lan PDang, Man VHoang, Nguyen PHoang, Tu LAnh, Chen Y-C, Li MSuan.  2016.  Aβ41 Aggregates More Like Aβ40 than Like Aβ42: In Silico and in Vitro Study. The Journal of Physical Chemistry B. 120:7371–7379.
B
Timsit Y, Vilbois E., Moras D..  1991.  Base-pairing shift in the major groove of (CA)n tracts by B-DNA crystal structures. Nature. 354:167–170.
Charon S., Taly A, Rodrigo J., Perret P., Goeldner M..  2011.  Binding modes of noncompetitive GABA-channel blockers revisited using engineered affinity-labeling reactions combined with new docking studies. J. Agric. Food Chem.. 59:2803–2807.
Graille M, Sacquin-Mora S, Taly A.  2023.  Best Practices of Using AI-Based Models in Crystallography and Their Impact in Structural Biology. J Chem Inf Model.
Coincon M, Heitz A, Chiche L, Derreumaux P.  2005.  The beta alpha beta alpha beta alpha elementary Supersecondary structure of the Rossmann fold from porcine lactate dehydrogenase exhibits characteristics of a molten globule. Proteins: Struct., Funct., Bioinf.. 60:740–745.
Liang C, Derreumaux P, Mousseau N, Wei G.  2008.  The beta-strand-loop-beta-strand conformation is marginally populated in beta(2)-microglobulin (20-41) peptide in solution as revealed by replica exchange molecular dynamics simulations. Biophys. J.. 95:510–517.

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