Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools
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[1] S. Yesylevskyy. ProtSqueeze: Simple and Effective Automated Tool for Setting up Membrane Protein Simulations. , 2007 .
[2] H. Berendsen,et al. A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. , 1998, Biophysical journal.
[3] Jeffery B. Klauda,et al. CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. , 2009, Biophysical journal.
[4] Dusanka Janezic,et al. Liquid-ordered phase formation in cholesterol/sphingomyelin bilayers: all-atom molecular dynamics simulations. , 2009, The journal of physical chemistry. B.
[5] René Staritzbichler,et al. GRIFFIN: A versatile methodology for optimization of protein-lipid interfaces for membrane protein simulations. , 2011, Journal of chemical theory and computation.
[6] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[7] W. Im,et al. Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations , 2007, PloS one.
[8] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[9] José Mario Martínez,et al. PACKMOL: A package for building initial configurations for molecular dynamics simulations , 2009, J. Comput. Chem..
[10] Andrea Lodi,et al. Two-dimensional packing problems: A survey , 2002, Eur. J. Oper. Res..
[11] R M Venable,et al. Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity. , 1993, Science.
[12] B. Roux,et al. Structure, energetics, and dynamics of lipid–protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer , 1996, Proteins.
[13] Hyeon Joo,et al. OPM database and PPM web server: resources for positioning of proteins in membranes , 2011, Nucleic Acids Res..
[14] I. Vattulainen,et al. Role of glycolipids in lipid rafts: a view through atomistic molecular dynamics simulations with galactosylceramide. , 2010, The journal of physical chemistry. B.
[15] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[16] A. W. Götz,et al. Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems. , 2012, Journal of chemical theory and computation.
[17] Zukang Feng,et al. Ligand Depot: a data warehouse for ligands bound to macromolecules , 2004, Bioinform..
[18] Jens Krüger,et al. Exploring the conformational space of Vpu from HIV‐1: A versatile adaptable protein , 2008, J. Comput. Chem..
[19] B. Roux,et al. Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[20] Taehoon Kim,et al. CHARMM‐GUI: A web‐based graphical user interface for CHARMM , 2008, J. Comput. Chem..
[21] Zsuzsanna Dosztányi,et al. TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates , 2005, Bioinform..
[22] L. Shen,et al. Transmembrane helix structure, dynamics, and interactions: multi-nanosecond molecular dynamics simulations. , 1997, Biophysical journal.
[23] José Mario Martínez,et al. Large-Scale Active-Set Box-Constrained Optimization Method with Spectral Projected Gradients , 2002, Comput. Optim. Appl..
[24] R M Venable,et al. Model for the structure of the lipid bilayer. , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[25] José Mario Martínez,et al. Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking , 2003, J. Comput. Chem..
[26] Jonathan Cagan. Shape annealing solution to the constrained geometric knapsack problem , 1994, Comput. Aided Des..
[27] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[28] W F Drew Bennett,et al. Molecular view of cholesterol flip-flop and chemical potential in different membrane environments. , 2009, Journal of the American Chemical Society.
[29] Eric Jakobsson,et al. Sphingomyelin-cholesterol domains in phospholipid membranes: atomistic simulation. , 2004, Biophysical journal.
[30] Zsuzsanna Dosztányi,et al. PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank , 2004, Nucleic Acids Res..
[31] Harald Dyckhoff,et al. A typology of cutting and packing problems , 1990 .
[32] T. A. Jones,et al. Databases in protein crystallography. , 1998, Acta crystallographica. Section D, Biological crystallography.
[33] Christian Kandt,et al. Setting up and running molecular dynamics simulations of membrane proteins. , 2007, Methods.
[34] Paolo Toth,et al. Knapsack Problems: Algorithms and Computer Implementations , 1990 .
[35] Graham R. Smith,et al. Setting up and optimization of membrane protein simulations , 2002, European Biophysics Journal.
[36] Jens Krüger,et al. CELLmicrocosmos 2.2 MembraneEditor: A Modular Interactive Shape-Based Software Approach To Solve Heterogeneous Membrane Packing Problems , 2011, J. Chem. Inf. Model..
[37] D. Engelman,et al. Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations. , 2000, Journal of molecular biology.
[38] Maarten G. Wolf,et al. g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation , 2010, J. Comput. Chem..
[39] Suneeta Agarwal,et al. Notice of RetractionGreedy genetic algorithm to Bounded Knapsack Problem , 2010, 2010 3rd International Conference on Computer Science and Information Technology.
[40] Jianpeng Ma,et al. CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..
[41] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[42] Kai Simons,et al. Lipid Rafts As a Membrane-Organizing Principle , 2010, Science.
[43] R. Brasseur,et al. Interaction of Surfactin with Membranes: A Computational Approach , 2003 .
[44] S. Singer,et al. The fluid mosaic model of the structure of cell membranes. , 1972, Science.
[45] Benoît Roux,et al. Conformational Flexibility of o-Phosphorylcholine and o-Phosphorylethanolamine: A Molecular Dynamics Study of Solvation Effects , 1994 .