From sequence to 3D structure of hyperbranched molecules: Application to surface modified PAMAM dendrimers

Journal of Molecular Modeling

Volumn 17, Issue 11, 2011, Pages 2741-2749

  Barata, Teresa S ^a   Brocchini, Steve ^a   Teo, Ian ^b   Shaunak, Sunil ^b   Zloh, Mire ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b HAMMERSMITH HOSPITAL   (United Kingdom)

Author keywords

Dendrimer; Hyperbranched molecule; Molecular dynamics; Molecular modeling

Indexed keywords

DENDRIMER; POLYAMIDOAMINE;

ARTICLE; CHEMICAL INTERACTION; CHEMICAL STRUCTURE; MACROMOLECULE; METHODOLOGY; MOLECULAR MODEL; PRIORITY JOURNAL; THREE DIMENSIONAL IMAGING;

DENDRIMERS; MODELS, MOLECULAR; MOLECULAR CONFORMATION;

EID: 80255138817     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-0966-y     Document Type: Article

References (24)

1. S Svenson DA Tomalia 2005 Dendrimers in biomedical applications- reflections on the field Adv Drug Deliv Rev 57 2106 2129 10.1016/j.addr.2005.09. 018 1:CAS:528:DC%2BD2MXht12ksbzL (Pubitemid 41759389)
2. S Shaunak, et al. 2004 Polyvalent dendrimer glucosamine conjugates prevent scar tissue formation Nat Biotechnol 22 977 984 10.1038/nbt995 1:CAS:528:DC%2BD2cXmtFWru78%3D (Pubitemid 39014474)
3. N Malik, et al. 2000 Dendrimers: relationship between structure and biocompatibility in vitro and preliminary studies on the biodistribution of 125I-labelled polyamidoamine dendrimers in vivo J Control Release 65 133 148 10.1016/S0168-3659(99)00246-1 1:CAS:528:DC%2BD3cXhtl2qs7o%3D (Pubitemid 30122922)
4. JW Dear, et al. 2005 Dendrimer-enhanced MRI as a diagnostic and prognostic biomarker of sepsis-induced acute renal failure in aged mice Kidney Int 67 2159 2167 10.1111/j.1523-1755.2005.00321.x (Pubitemid 41623377)
5. BP Roberts, et al. 2008 The Dotted Cap Notation: a concise notation for describing variegated dendrimers New J Chem 32 1543 1554 10.1039/b800724a 1:CAS:528:DC%2BD1cXhtFems7%2FO
6. Brünger AT (1992) XPLOR. A System for X-ray Crystallography and NMR. Available from: http://nmr.cit.nih.gov/xplor-nih/doc/current/xplor/
7. CD Schwieters, et al. 2003 The Xplor-NIH NMR molecular structure determination package J Magn Reson 160 65 73 10.1016/S1090-7807(02)00014-9 1:CAS:528:DC%2BD3sXmslaquw%3D%3D
8. Barata TS et al (2010) Structural studies of biologically active glycosylated PAMAM dendrimers. J mol Model. doi: 10.1007/s00894-010-0907-1
9. Parameters CF (2010) Available from: http://mackerell.umaryland.edu/ CHARMM-ff-params.html
10. GL Morefield, et al. 2007 Synthetic Toll-like receptor 4 agonist enhances vaccine efficacy in an experimental model of toxic shock syndrome Clin Vaccine Immunol 14 1499 1504 10.1128/CVI.00153-07 1:CAS:528:DC%2BD2sXhtl2nurbJ (Pubitemid 350304045)
11. Available from: www.schrodinger.com
12. WL Jorgensen J Tirado-Rives 2005 Potential energy functions for atomic-level simulations of water and organic and biomolecular systems Proc Natl Acad Sci USA 102 6665 6670 10.1073/pnas.0408037102 1:CAS:528: DC%2BD2MXksVKgt7s%3D (Pubitemid 40675374)
13. F Mohamadi, et al. 1990 Macromodel-n integrated software system for modeling organic and bioorganic molecules using molecular mechanics J Comput Chem 11 440 467 10.1002/jcc.540110405 1:CAS:528:DyaK3cXktl2msLw%3D
14. JC Phillips, et al. 2005 Scalable molecular dynamics with NAMD J Comput Chem 26 1781 1802 10.1002/jcc.20289 1:CAS:528:DC%2BD2MXht1SlsbbJ (Pubitemid 43078511)
15. W Humphrey A Dalke K Schulten 1996 VMD: visual molecular dynamics J Mol Graph 14 33 38 10.1016/0263-7855(96)00018-5 1:CAS:528:DyaK28Xis12nsrg%3D (Pubitemid 26152973)
16. The Open Babel Package version 2.2.3 (accessed September 1, 2010)
17. AD MacKerell Jr N Banavali N Foloppe 2000 Development and current status of the CHARMM force field for nucleic acids Biopolymers 56 257 265 10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W 1:CAS:528:DC%2BD38XkvFGmtg%3D%3D (Pubitemid 34105873)
18. O Guvench, et al. 2008 Additive empirical force field for hexopyranose monosaccharides J Comput Chem 29 2543 2564 10.1002/jcc.21004 1:CAS:528:DC%2BD1cXhtlSrtrvO
19. SE Feller, et al. 1997 Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies Biophys J 73 2269 2279 10.1016/S0006-3495(97)78259-6 1:CAS:528:DyaK2sXntFylsLo%3D (Pubitemid 27471439)
20. K Vanommeslaeghe, et al. 2009 CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields J Comput Chem 31 671 690
21. The Open Babel Package, v. [cited 2010; Available from: http://openbabel.sourceforge.net/
22. RA Lippert, et al. 2007 A common avoidable source of error in molecular dynamics integrators J Chem Phys 126 046101 046102 10.1063/1.2431176 (Pubitemid 46379140)
23. KJ Bowers RO Dror DE Shaw 2006 The midpoint method for parallelization of particle simulations J Chem Phys 124 184109 184111 10.1063/1.2191489 (Pubitemid 43736791)
24. D Qiu, et al. 1997 The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii J Phys Chem A 101 3005 3014 10.1021/jp961992r 1:CAS:528:DyaK2sXitFWgs7w%3D (Pubitemid 127580882)