參考文獻 |
1. Elliott, E.W.; Fraiman, A. Using Chem-Wiki To Increase Student Collaboration through Online Lab Reporting. Journal of Chemical Education. 2009, 44, 54-56.
2. Wang, Z.; Wang, G. APD: the Antimicrobial Peptide Database. Nucleic Acids Research. 2004, 32, 590-592
3. Wang, G.; Li, X.; Wang, Z. APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Research. 2009, 37, 933-937.
4. WebMO Pro Home Page. http://www.webmo.net.
5. Kabsch, W.; Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983, 22, 2577-2637.
6. Jo, S.; Kim, T.; Im, W. Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations. PLoS ONE. 2007, 2, 880-889.
7. Jo, S.; Kim, T.; Iyer, V.G.; Im, W. CHARMM-GUI: A web-based graphical user interface for CHARMM. Journal of Computational Chemistry. 2008, 29, 1859-1865.
8. ChemAxon Home Page. http://www.chemaxon.com/product/mspace.html.
9. Van Der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. GROMACS: Fast, flexible, and free. Journal of Computational Chemistry. 2005, 26, 1701-1718.
10. Gridsphere: An Advanced Portal Framework Gridsphere Project Website. http://gridsphere.org.
11. Chia, E.; Shamsir, M. S.; Hussein, Z. A.; Hashim, S. Z. M. In GridMACS Portal: A Grid Web Portal for Molecular Dynamics Simulation Using GROMACS. Mathematical/Analytical Modelling and Computer Simulation. 2010, 10, 507-512.
12. Berman, H. M.; Battistuz, T.; Bhat, T. N.; Bluhm, W. F.; Bourne, P.E.; Burkhardt, K.; Feng, Z.; Gilliland, G. L.; Iype, L.; Jain, S.;Fagan, P.; Marvin, J.; Padilla, D.; Ravichandran, V.; Schneider, B.;Thanki, N.; Weissig, H.; Westbrook, J. D.; Zardecki, C. The Protein Data Bank. Acta CrystallogrD Biol Crystallogr. 2002, 58, 899-907.
13. Pauling, L.; Corey, R. B. Atomic Coordinates and Structure Factors for Two Helical Configurations of Polypeptide Chains. Proceedings of the National Academy of Sciences U.S.A.1951, 37, 235-240.
14. Pauling, L.; Corey, R. B. Configurations of Polypeptide Chains With Favored Orientations Around Single Bonds. Proceedings of the National Academy of Sciences U.S.A.1951, 37, 729-740.
15. Kabsch, W.; Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983, 22, 2577-2637.
16. Zhao, W.; Róg, T.; Gurtovenko, A. A.; Vattulainen, I.; Karttunen, M. Atomic-Scale Structure and Electrostatics of Anionic Palmitoyloleoylphosphatidylglycerol Lipid Bilayers with Na+ Counterions. Biophysical journal. 2007, 92, 1114-1124.
17. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids. 1987, Oxford, Clarendon Press.
18. Shinoda, W.; Okazaki, S. A Voronoi analysis of lipid area fluctuation in a bilayer. The Journal of Chemical Physics. 1998, 109, 1517-1521.
19. Allen, W. J.; Lemkul, J. A.; Bevan, D. R. GridMAT-MD: a grid-based membrane analysis tool for use with molecular dynamics. Journal of Computational Chemistry. 2009, 30, 1952-1958.
20. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The weighted histogram analysis method for free-energy calculations on biomolecules. I: The method. Journal of Computational Chemistry. 1992, 13, 1011-1021.
21. Shinoda, W.; Okazaki, S. A Voronoi analysis of lipid area fluctuation in a bilayer. The Journal of Chemical Physics. 1998, 109, 1517-1521.
22. Chodera, J.D.; Swope, W.C.; Pitera, J.W.; Seok, C.; Dill, K.A. Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. Journal of Chemical Theory and Computation. 2006, 3, 26-41.
23. Glasser, L.; Herráez, A.; Hanson, R. M. Interactive 3D Phase Diagrams Using Jmol. Journal of Chemical Education. 2009, 86, 566..
24. Cass, M. E.; Rzepa, H. S.; Rzepa, D. R.; Williams, C. K. The Use of the Free, Open-Source Program Jmol To Generate an Interactive Web Site To Teach Molecular Symmetry. Journal of Chemical Education. 2005, 82, 1736-1742.
25. Weiner, S. W.; Cerpovicz, P. F.; Dixon, D. W.; Harden, D. B.; Hobbs, D. S.; Gosnell, D. L. RasMol and Mage in the Undergraduate Biochemistry Curriculum. Journal of Chemical Education. 2000, 77, 401.
26. Kang, C.; Vanoye, C. G.; Welch, R.C.; Van Horn, W. D.; Sanders, C. R. Functional Delivery of a Membrane Protein into Oocyte Membranes Using Bicelles. Biochemistry. 2010, 49, 653-655.
27. Friemann, R.; Larsson, D. S. D.; Wang, Y.; van der Spoel, D. Molecular Dynamics Simulations of a Membrane Protein−Micelle Complex in Vacuo. Journal of the American Chemical Society. 2009, 131, 16606-16607.
28. Murzyn, K.; Róg, T.; Pasenkiewicz-Gierula, M. Phosphatidylethanolamine -Phosphatidylglycerol Bilayer as a Model of the Inner Bacterial Membrane. Biophysical journal. 2005, 88, 1091-1103.
29. Gopalakrishnan, G.; Thostrup, P.; Rouiller, I.; Lucido, A. L.; Belkaïd, W.; Colman, D. R.; Lennox, R. B. Lipid Bilayer Membrane-Triggered Presynaptic Vesicle Assembly. ACS Chemical Neuroscience. 2009, 1, 86-94.
30. Uran, S.; Larsen, A.; Jacobsen, P. B.; Skotland, T. Analysis of phospholipid species in human blood using normal-phase liquid chromatography coupled with electrospray ionization ion-trap tandem mass spectrometry. Journal of Chromatography B: Biomedical Sciences and Applications. 2001, 758, 265-275.
31. Dowhan, W. Molecular basis for membrane phospholipid diversity:Why are there so many lipids? Annual Review of Biochemistry. 1997, 66, 199-232.
32. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry. 2005, 26, 1781-1802.
33. Klauda, J. B.; Venable, R. M.; Freites, J. A.; O’Connor, J. W.; Tobias, D. J.; Mondragon-Ramirez, C.; Vorobyov, I.; MacKerell, A. D.; Pastor, R. W. Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. The Journal of Physical Chemistry B. 2010, 114, 7830-7843.
|