A molecular fragment cheminformatics roadmap for mesoscopic simulation

详细信息    查看全文

• 作者：Andreas Truszkowski (1)
  Mirco Daniel (2)
  Hubert Kuhn (3)
  Stefan Neumann (4)
  Christoph Steinbeck (5)
  Achim Zielesny (2)
  Matthias Epple (1)
  
  1. Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE) ; University of Duisburg-Essen ; Essen ; Germany
  2. Institute for Bioinformatics and Cheminformatics ; Westphalian University of Applied Sciences ; Recklinghausen ; Germany
  3. CAM-D Technologies ; Essen ; Germany
  4. GNWI - Gesellschaft fuer naturwissenschaftliche Informatik mbH ; Oer-Erkenschwick ; Germany
  5. Chemoinformatics and Metabolism ; European Bioinformatics Institute (EBI) ; Cambridge/Hinxton ; UK
  
• 关键词：Dissipative particle dynamics ; Computer simulation ; Molecular fragmentation ; fSmiles ; Fragment smiles ; Molecular fragment cheminformatics ; Molecular fragment dynamics ; Mesoscopic simulation ; Peptide representation ; Protein representation
• 刊名：Journal of Cheminformatics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：6
• 期：1
• 全文大小：3,006 KB
• 参考文献：1. Dirac, PAM (1929) Quantum mechanics of many-electron systems. Proc R Soc Lond Ser A 123: pp. 714-733 CrossRef
  2. Nobelprize.org: The Nobel Prize in Chemistry1998. [http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1998/ ]. Accessed: 23 Jan 2014.
  3. Nobelprize.org: The Nobel Prize in Chemistry2013. [http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2013/ ]. Accessed: 23 Jan 2014.
  4. Moore, G (1965) Cramming more components onto integrated circuits. Electronics 38: pp. 114-117
  5. Friesner, RA, Dunietz, BD (2001) Large-scale ab initio quantum chemical calculations on biological systems. Acc Chem Res 34: pp. 351-358 CrossRef
  6. Hansson, T, Oostenbrink, C, van Gunsteren, W (2002) Molecular dynamics simulations. Curr Opin Struct Biol 12: pp. 190-196 CrossRef
  7. Karplus, M, McCammon, JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9: pp. 646-652 CrossRef
  8. Murphy, RB, Philipp, DM, Friesner, RA (2000) Mechanics (qm/mm) method for large-scale modeling of chemistry in protein environments. J Comput Chem 21: pp. 1442-1457 CrossRef
  9. Hoogerbrugge, P, Koelman, J (1992) Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. EPL (Europhys Lett) 19: pp. 155-160 CrossRef
  10. Pagonabarraga, I (1998) Self-consistent dissipative particle dynamics algorithm. EPL (Europhys Lett) 42: pp. 377-382 CrossRef
  11. Koelman, J, Hoogerbrugge, P (1993) Dynamic simulations of hard-sphere suspensions under steady shear. EPL (Europhys Lett) 21: pp. 363-368 CrossRef
  12. Flekkoy, EG, Coveney, PV (1999) From molecular dynamics to dissipative particle dynamics. Phys Rev Lett 83: pp. 1775-1778 CrossRef
  13. Espanol, P, Warren, P (1995) Statistical mechanics of dissipative particle dynamics. EPL (Europhys Lett) 30: pp. 191-196 CrossRef
  14. Frenkel, D, Smit, B (2002:) Understanding molecular simulation: from algorithms to applications (computational science). Academic Press, Inc, San Diego
  15. Groot, RD, Warren, PB (1997) Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation. J Chem Phys 107: pp. 4423-4435 CrossRef
  16. Espanol, P (1995) Hydrodynamics from dissipative particle dynamics. Phys Rev E 52: pp. 1734-1742 CrossRef
  17. Schulz, S, Kuhn, H, Schmid, G (2004) Molecular modeling computer simulations of organic polymers: A novel computer simulation technique to characterize nanostructured materials. MRS Proceedings 788: pp. L10.5
  18. Ryjkina, E, Kuhn, H, Rehage, H, M眉ller, F, Peggau, J (2002) Molecular dynamic computer simulations of phase behavior of non-ionic surfactants. Angew Chem Int Ed 41: pp. 983-986 CrossRef
  19. Schulz, SG, Kuhn, H, Schmid, G, Mund, C, Venzmer, J (2004) Phase behavior of amphiphilic polymers: a dissipative particles dynamics study. Colloid Polym Sci 283: pp. 284-290 CrossRef
  20. Truszkowski, A, Epple, M, Fiethen, A, Zielesny, A, Kuhn, H (2013) Molecular fragment dynamics study on the water-air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants. J Colloid Interface Sci 410: pp. 140-145 CrossRef
  21. Leach, AR, Gillet, VJ (2003:) An Introduction to Chemoinformatics. Springer, Dordrecht
  22. Gasteiger, J, Engel, T (2003:) Chemoinformatics: A Textbook. Wiley-VCH Verlag GmbH & Co, Weinheim
  Handbook of chemoinformatics from data to knowledge. Wiley-VCH Verlag GmbH & Co, Weinheim
  23. Weininger, D, Weininger, A, Weininger, JL (1989) Smiles. 2. algorithm for generation of unique smiles notation. J Chem Inform Comput Sci 29: pp. 97-101 CrossRef
  24. Weininger, D (1988) Smiles, a chemical language and information system. 1. introduction to methodology and encoding rules. J Chem Inform Comput Sci 28: pp. 31-36 CrossRef
  25. Weininger, D (1990) Smiles. 3. depict. graphical depiction of chemical structures. J Chem Inform Comput Sci 30: pp. 237-243 CrossRef
  26. JChemPaint: Chemical 2D structure editor application/applet based on the chemistry development kit. [http://jchempaint.github.io]
  27. Steinbeck, C, Han, Y, Kuhn, S, Horlacher, O, Luttmann, E, Willighagen, E (2003) The chemistry development kit (cdk): an open-source java library for chemo- and bioinformatics. J Chem Inform Comput Sci 43: pp. 493-500 CrossRef
  28. Steinbeck, C, Hoppe, C, Kuhn, S, Floris, M, Guha, R, Willighagen, EL (2006) Recent developments of the chemistry development kit (cdk) - an open-source java library for chemo- and bioinformatics. Curr Pharm Des 12: pp. 2111-2120 CrossRef
  29. Berman, HM, Westbrook, J, Feng, Z, Gilliland, G, Bhat, TN, Weissig, H, Shindyalov, IN, Bourne, PE (2000) The protein data bank. Nucleic Acids Res 28: pp. 235-242 CrossRef
  30. Prli膰, A, Yates, A, Bliven, SE, Rose, PW, Jacobsen, J, Troshin, PV, Chapman, M, Gao, J, Koh, CH, Foisy, S, Holland, R, Rimsa, G, Heuer, ML, Brandst盲tter-M眉ller, H, Bourne, PE, Willis, S (2012) Biojava: an open-source framework for bioinformatics in 2012. Bioinformatics (Oxford, England) 28: pp. 2693-2695 CrossRef
  31. Jmol: an open-source Java viewer for chemical structures in 3D. [http://www.jmol.org ]
  32. Groot, RD (2003) Electrostatic interactions in dissipative particle dynamics-simulation of polyelectrolytes and anionic surfactants. J Chem Phys 118: pp. 11265 CrossRef
  33. Wayne, R, Sedgewick, K (2011:) Algorithms. Addison-Wesley, Boston
  34. Li, H, Fischle, W, Wang, W, Duncan, EM, Liang, L, Murakami-Ishibe, S, Allis, CD, Patel, DJ (2007) Structural basis for lower lysine methylation state-specific readout by mbt repeats of l3mbtl1 and an engineered phd finger. Mol Cell 28: pp. 677-691 CrossRef
  
• 刊物类别：Physics and Astronomy
• 刊物主题：Computer Applications in Chemistry
  Theoretical and Computational Chemistry
  Computational Biology/Bioinformatics
  Documentation and Information in Chemistry
  
• 出版者：Chemistry Central Ltd
• ISSN：1758-2946

文摘

Background Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. Results The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted fSMILES) with connected molecular fragments to represent a molecular structure. The fSMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Conclusions Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and conceptual usage hurdles. Molecular Fragment Cheminformatics may be regarded as a crucial accelerator to propagate MFD and similar mesoscopic simulation techniques in the molecular sciences. Graphical abstract A molecular fragment cheminformatics roadmap for mesoscopic simulation.