Shape: automatic conformation prediction of carbohydrates using a genetic algorithm
Tóm tắt
Từ khóa
Tài liệu tham khảo
Pérez S, Mulloy B: Prospects for Glycoinformatics. Cur Opin Struct Biol. 2005, 15: 517-10.1016/j.sbi.2005.08.005.
Koca J, Pérez S, Imberty A: Conformational Analysis and Flexibility of Carbohydrates Using the CICADA Approach with MM3. J Comp Chem. 1995, 16: 296-10.1002/jcc.540160305.
Rosen J: Prediction of 3D structures of oligosaccharides - methodological development and studies on saccharide antigens of interest for vaccine design. PhD thesis. 2005, University of Gothenburg
Nahmany A, Strino F, Rosen J, Kemp GJL, Nyholm PG: The use of genetic algorithm search for molecular mechanics (MM3)-based conformational analysis of oligosaccharides. Carb Res. 2005, 340: 1059-10.1016/j.carres.2004.12.037.
Frank M, Gutbrod P, Hassayoun C, Lieth von der C-W: Dynamic Molecules: molecular dynamics for everyone. An internet-based access to molecular dynamic simulations: basic concepts. J Mol Model. 2003, 9: 308-10.1007/s00894-003-0144-y.
Mitchell T: Machine Learning. 2007, P.O. Box 182604. Columbus, OH 43272, USA: McGraw-Hill
Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ: Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function. J Comp Chem. 1998, 19: 1639-10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B.
Jones G, Willett P, Glen R, Leach A, Taylor R: Development and validation of a genetic algorithm for flexible docking. J Mol Bio. 1997, 267: 727-10.1006/jmbi.1996.0897.
Jones G, Willett P, Glen RC: GASP: genetic algorithm superimposition program. Pharmacophore Perception, Development, and Use in Drug Design. Edited by: Güner OF. 1999, La Jolla: International University Line, 85-
Pérez S, Imberty A, Engelsen SB, Gruza J, Mazeau K, Jimenez-Barbero J, Poveda A, Espinosa JF, van Eyck BP, Johanson G, French AD, Kouwijzer ML, Grootenius PD, Bernardi A, Raimondi L, Senderowitz H, Durier V, Vergoten G, Rasmussen K: A comparison and chemometric analysis of several molecular mechanics force fields and parameter sets applied to carbohydrates. Carb Res. 1998, 314: 141-10.1016/S0008-6215(98)00305-X.
Allinger NL, Yuh YH, Lii JH: Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 1. J Am Chem Soc. 1989, 111: 8551-10.1021/ja00205a001.
Lii JH, Allinger NL: Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 2. Vibrational Frequencies and Thermodynamics. J Am Chem Soc. 1989, 111: 8566-10.1021/ja00205a002.
Lii JH, Allinger NL: Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 3. The van der Waals Potentials and Crystal Data for Aliphatic and Aromatic Hydrocarbons. J Am Chem Soc. 1989, 111: 8576-10.1021/ja00205a003.
Center for Computational Chemistry, University of Georgia. [ http://europa.chem.uga.edu/ ]
Allinger NL, Chen K, Lii JH: An improved force field (MM4) for saturated hydrocarbons. J Comp Chem. 1996, 17: 642-10.1002/(SICI)1096-987X(199604)17:5/6<642::AID-JCC6>3.0.CO;2-U.
TINKER - Software Tools for Molecular Design. [ http://dasher.wustl.edu/tinker/ ]
Lindahl E, Hess B, Spoel van der D: GROMACS 3.0: A package for molecular simulation and trajectory analysis. J Mol Model. 2001, 7: 306-
Case DA, Chetham TE, Darden T, Gohlke H, Merz KM, Onufriev A, Simmerling C, Wang B, Woods R: The Amber biomolecular simulation programs. J Comp Chem. 2005, 26: 1668-10.1002/jcc.20290.
Rosen J: A java library for simple use of the MM3 force field [Manuscript]. [ https://sourceforge.net/projects/mm3java/files/mm3java-preprint.pdf/download ]
Steinbeck C, Han Y, Kuhn S, Horlancker O, Luttman E, Willihagen E: The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. J Chem Inf Comp Sci. 2003, 43: 493-
Jmol: an open-source Java viewer for chemical structures in 3D. [ http://www.jmol.org/ ]
JOElib - A Java based chemoinformatics library. [ http://www.ra.cs.uni-tuebingen.de/software/joelib/ ]
Open Babel: The Open Source Chemistry Toolkit. [ http://openbabel.sourceforge.net/wiki/ ]
Djurdjevic DP, Biggs MJ: Ab Initio Protein Fol Prediction Using Evolutionary Algorithms: Influence of Design and Control Parameters on Performance. J Comp Chem. 2006, 27: 1177-10.1002/jcc.20440.
Rosen J, Robobi A, Nyholm PG: Conformation of the branched O-specific polysaccharide of Shigella dysenteriae type 2. Carb Res. 2002, 337: 1633-10.1016/S0008-6215(02)00089-7.
Nikitin IV, Genin AL, Vainstein EF, Kushnerev MI, Kochetkov NK: Molecular structure of the O-specific polysaccharide of Shigella dysenteriae type 2. Dokl Akad Nauk SSSR. 1984, 1133-
Rosen J, Robobi A, Nyholm PG: The conformations of the O-specific polysaccharides of Shigella dysenteriae type 4 and Escherichia coli O159 studied with molecular mechanics (MM3) filtered systematic search. Carb Res. 2004, 339: 961-10.1016/j.carres.2003.11.018.
Strino F, Nahmany A, Rosen J, Kemp GJL, Sà-Correia I, Nyholm PG: Conformation of the exo-polysaccharide of Burkholderia cepacia predicted with Molecular Mechanics (MM3) using Genetic Algorithm search. Carb Res. 2005, 340: 1019-10.1016/j.carres.2004.12.031.
Cioci G, Rivet A, Koca J, Pérez S: Conformational analysis of complex oligosaccharides: the CICADA approach to the uromodulin O-glycans. Carb Res. 2004, 339: 949-10.1016/j.carres.2003.12.022.
GNU General Public License. [ http://www.gnu.org/copyleft/gpl.html ]