Cellulose-builder: A toolkit for building crystalline structures of cellulose

Journal of Computational Chemistry

Volumn 33, Issue 14, 2012, Pages 1338-1346

  Gomes, Thiago C F ^a   Skaf, Munir S ^a  

^a UNIVERSITY OF CAMPINAS   (Brazil)

Author keywords

Bash programming language; cellulose crystalline structures; hydrophobic and hydrophilic surfaces of cellulose; plant cell wall elementary fibrils; software; starting configurations for simulations

Indexed keywords

CARTESIAN COORDINATE; CELLULOSE CRYSTALLINE STRUCTURE; CRYSTALLINE STRUCTURE; CRYSTALLOGRAPHIC DIRECTIONS; DIFFERENT SIZES; HYDROPHOBIC AND HYDROPHILIC; MOLECULAR DYNAMICS SIMULATIONS; PERIODIC BOUNDARY CONDITIONS; PLANT CELL WALL; PROTEIN DATA BANK; SIMULATION PACKAGES; USER FRIENDLY PROGRAM;

COMPUTER PROGRAMMING LANGUAGES; COMPUTER SOFTWARE; CRYSTALLINE MATERIALS; MOLECULAR DYNAMICS; MONOLAYERS; PLANT CELL CULTURE;

CELLULOSE;

CELLULOSE;

CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; CRYSTALLIZATION; REVIEW;

CELLULOSE; CRYSTALLIZATION; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; SOFTWARE;

EID: 84860003834     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.22959     Document Type: Review

References (33)

1. Y. Nishiyama, P. Langan, H. Chanzy, J. Am. Chem. Soc. 2002, 124, 9074.
2. Y. Nishiyama, J. Sugiyama, H. Chanzy, P. Langan, J. Am. Chem. Soc. 2003, 125, 14300.
3. P. Langan, Y. Nishiyama, H. Chanzy, Biomacromolecules 2001, 2, 401.
4. M. Wada, H. Chanzy, Y. Nishiyama, P. Langan, Macromolecules 2004, 37, 8548.
5. M. S. Baird, A. C. W. O'Sullivan, B. Banks, Cellulose 1998, 5, 89.
6. R. J. Vietor, K. Mazeau, M. Lakin, Biopolymers 2000, 54, 342.
7. J. F. Matthews, C. E. Skopec, P. E. Mason, P. Zuccato, R. W. Torget, J. Sugiyama, M. E. Himmel, J. W. Brady, Carbohydr. Res. 2006, 341, 138.
8. H. Miyamoto, M. Ago, C. Yamane, M. Seguchi, K. Ueda, K. Okajima, Carbohydr Res 2011, 346, 807.
9. Y. Ding, M. E. Himmel, J. Agr. Food Chem. 2006, 54, 597.
10. S. P. S. Chundawat, G. T. Beckham, M. E. Himmel, B. E. Dale, Annu. Rev. Biom. Eng. 2011, 2, 121.
11. L. Zhong, J. F. Matthews, M. F. Crowley, T. Rignall, C. Talon, J. M. Cleary, R. C. Walker, G. Chukkapall, C. McCabe, M. R. Nimlos, C. L. Brooks, III, M. E. Himmel, J. W. Brady, Cellulose 2008, 15, 261.
12. L. Zhong, J. F. Matthews, P. I. Hansen, M. F. Crowley, J. M. Cleary, R. C. Walker, M. R. Nimlos, C. L. Books, III, W. S. Adney, M. E. Himmel, J. W. Brady, Carbohydr. Res. 2009, 344, 1984.
13. C. M. Payne, M. E. Himmel, M. F. Crowley, G. T. Beckham, J. Phys. Chem. Lett. 2011, 2, 1546.
14. L. Petridis, X. Jiancong, M. F. Crowley, J. C. Smith, X. Cheng, In Computational Modeling in Lignocellulosic Biofuel Production. M. R. Nimlos, M. F. Crowley (Eds), ACS Symposium Series, 2010, vol. 1052, Chapter 3, 55.
15. H. M. Cho, A. S. Gross, J.-W. Chu, J. Am. Chem. Soc. 2011, 133, 14033.
16. R. P. Swatloski, S. K. Spear, J. D. Holbrey, R. D. Roger, J. Am. Chem. Soc. 2002, 124, 4974.
17. S. Zhu, Y. Wu, Q. Chen, Z. Yu, C. Wang, S. Jin, Y. Ding, G. Wu, G., Green Chem. 2006, 8, 325.
18. W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graphics 1996, 14, 33.
19. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, K. Schulten, J. Comput. Chem. 2005, 26, 1781.
20. B. R. Brooks, C. L. Brooks, III, A. D. Mackerell, Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus, J. Comp. Chem. 2009, 30, 1545.
21. D. A. Case, T. A. Darden, T. E. Cheatham, III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, R. C. Walker, W. Zhang, K. M. Merz, B. P. Roberts, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossvai, K. F. Wong, F. Paesani, J. Vanicek, J. Liu, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D. R. Roe, D. H. Mathews, M. G. Seetin, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A Kovalenko, P. A. Kollman, AMBER 11, University of California, San Francisco, 2010.
22. L. Martínez, R. Andrade, E. G. Birgin, J. M. Martínez, J. Comput. Chem. 2009, 30, 2157.
23. C. Newham, B. Rosenblatt, Learning the Bash Shell; O'Reilly & Associates: Cambridge, 1998.
24. C. Albing, J. P. Vossen, C. Newham, Bash Cookbook; O'Reilly Media: Sebastopol, 2007.
25. A. Robbins, N. H. F. Beebe, Classic Shell Scripting; O'Reilly Media: Beijing, 2005.
26. O. Guvench, S. N. Greene, G. Kamath, J. W. Brady, R. M. Venable, R. W. Pastor, A. D. MacKerell Jr., J. Comp. Chem. 2008, 29, 2543.
27. O. Guvench, E. Hatcher, A. D. MacKerell Jr., J. Chem. Theory Comput. 2009, 5, 2353.
28. J. P. Glusker, M. Lewis, M. Rossi, Crystal Structure Analysis for Chemists and Biologists; Wiley-VCH: New York, 1994.
29. M. F. C. Ladd, R. A. Palmer, Structure Determination by X-ray Crystallography; Plenum Press: New York, 1994.
30. T. Hahn, International Tables for Crystallography; Springer: Dordrecht, 2005; Volume A.
31. B. B. Buchanan, W. Gruissem, R. L. Jones, Biochemistry and Molecular Biology of Plants; American Society of Plant Physiologists: Rockville, 2000.
32. Q. Li, S. Renneckar, Biomacromolecules 2011, 12, 650.
33. G. Vaaje-Kolstad, B. Westereng, S. J. Horn, Z. Liu, H. Zhai, M. Sørlie, V. G. H. Eijsink, Science 2010, 330, 219.