Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools

Sommer B (2013)
Computational and Structural Biotechnology Journal 5(6): e201302014.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
Autor*in
Sommer, BjörnUniBi
Einrichtung
Technische Fakultät > AG Bioinformatik
Centrum für Biotechnologie
Erscheinungsjahr
2013
Zeitschriftentitel
Computational and Structural Biotechnology Journal
Band
5
Ausgabe
6
Art.-Nr.
e201302014
ISSN
2001-0370
Page URI
https://pub.uni-bielefeld.de/record/2576375

Zitieren

Sommer B. Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools. Computational and Structural Biotechnology Journal. 2013;5(6): e201302014.
Sommer, B. (2013). Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools. Computational and Structural Biotechnology Journal, 5(6), e201302014. doi:10.5936/csbj.201302014
Sommer, Björn. 2013. “Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools”. Computational and Structural Biotechnology Journal 5 (6): e201302014.
Sommer, B. (2013). Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools. Computational and Structural Biotechnology Journal 5:e201302014.
Sommer, B., 2013. Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools. Computational and Structural Biotechnology Journal, 5(6): e201302014.
B. Sommer, “Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools”, Computational and Structural Biotechnology Journal, vol. 5, 2013, : e201302014.
Sommer, B.: Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools. Computational and Structural Biotechnology Journal. 5, : e201302014 (2013).
Sommer, Björn. “Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools”. Computational and Structural Biotechnology Journal 5.6 (2013): e201302014.

6 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Extracellular loops 2 and 3 of the calcitonin receptor selectively modify agonist binding and efficacy.
Dal Maso E, Zhu Y, Pham V, Reynolds CA, Deganutti G, Hick CA, Yang D, Christopoulos A, Hay DL, Wang MW, Sexton PM, Furness SGB, Wootten D., Biochem Pharmacol 150(), 2018
PMID: 29454620
Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell.
Biere N, Ghaffar M, Doebbe A, Jäger D, Rothe N, Friedrich BM, Hofestädt R, Schreiber F, Kruse O, Sommer B., J Integr Bioinform 15(2), 2018
PMID: 30001212
Cryo-EM structure of the active, Gs-protein complexed, human CGRP receptor.
Liang YL, Khoshouei M, Deganutti G, Glukhova A, Koole C, Peat TS, Radjainia M, Plitzko JM, Baumeister W, Miller LJ, Hay DL, Christopoulos A, Reynolds CA, Wootten D, Sexton PM., Nature 561(7724), 2018
PMID: 30209400
Molecular modeling of the human P2Y14 receptor: A template for structure-based design of selective agonist ligands.
Trujillo K, Paoletta S, Kiselev E, Jacobson KA., Bioorg Med Chem 23(14), 2015
PMID: 25868749
Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries.
Jefferys E, Sands ZA, Shi J, Sansom MS, Fowler PW., J Chem Theory Comput 11(6), 2015
PMID: 26089745
The challenges of understanding glycolipid functions: An open outlook based on molecular simulations.
Manna M, Róg T, Vattulainen I., Biochim Biophys Acta 1841(8), 2014
PMID: 24406903

56 References

Daten bereitgestellt von Europe PubMed Central.

CELLmicrocosmos 2.2 MembraneEditor: a modular interactive shape-based software approach to solve heterogeneous Membrane Packing Problems
Sommer, Journal of Chemical Information and Modeling 5(), 2011
The fluid mosaic model of the structure of cell membranes
Singer, Science (Washington, DC, US) 175(), 1972
Molecular view of cholesterol flip-flop and chemical potential in different membrane environments.
Bennett WF, MacCallum JL, Hinner MJ, Marrink SJ, Tieleman DP., J. Am. Chem. Soc. 131(35), 2009
PMID: 19673519
Lipid rafts as a membrane-organizing principle
Lingwood, Science (Washington, DC, US) 327(), 2010
Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems.
Park K, Gotz AW, Walker RC, Paesani F., J Chem Theory Comput 8(8), 2012
PMID: 26592126
Scalable molecular dynamics with NAMD.
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K., J Comput Chem 26(16), 2005
PMID: 16222654
GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.
Hess B, Kutzner C, van der Spoel D, Lindahl E., J Chem Theory Comput 4(3), 2008
PMID: 26620784
CHARMM: the biomolecular simulation program.
Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M., J Comput Chem 30(10), 2009
PMID: 19444816
Two-dimensional packing problems: A survey
Lodi, Eur J Oper Res 141(), 2002

Wottawa, 1996
Setting up and running molecular dynamics simulations of membrane proteins.
Kandt C, Ash WL, Tieleman DP., Methods 41(4), 2007
PMID: 17367719
g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation.
Wolf MG, Hoefling M, Aponte-Santamaria C, Grubmuller H, Groenhof G., J Comput Chem 31(11), 2010
PMID: 20336801
GRIFFIN: A versatile methodology for optimization of protein-lipid interfaces for membrane protein simulations.
Staritzbichler R, Anselmi C, Forrest LR, Faraldo-Gomez JD., J Chem Theory Comput 7(4), 2011
PMID: 24707227
OPM database and PPM web server: resources for positioning of proteins in membranes.
Lomize MA, Pogozheva ID, Joo H, Mosberg HI, Lomize AL., Nucleic Acids Res. 40(Database issue), 2011
PMID: 21890895
Exploring the conformational space of Vpu from HIV-1: a versatile adaptable protein.
Kruger J, Fischer WB., J Comput Chem 29(14), 2008
PMID: 18432615

AUTHOR UNKNOWN, 2010
Model for the structure of the lipid bilayer.
Pastor RW, Venable RM, Karplus M., Proc. Natl. Acad. Sci. U.S.A. 88(3), 1991
PMID: 1992480
Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer.
Woolf TB, Roux B., Proteins 24(1), 1996
PMID: 8628736
Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations.
Petrache HI, Grossfield A, MacKenzie KR, Engelman DM, Woolf TB., J. Mol. Biol. 302(3), 2000
PMID: 10986130
Liquid-ordered phase formation in cholesterol/sphingomyelin bilayers: all-atom molecular dynamics simulations.
Zidar J, Merzel F, Hodoscek M, Rebolj K, Sepcic K, Macek P, Janezic D., J Phys Chem B 113(48), 2009
PMID: 19929009
CHARMM: a program for macromolecular energy, minimization, and dynamics calculations
Brooks, J Comput Chem 4(), 1983
Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity
Venable, Science (Washington, DC, US) 262(), 1993
Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.
Woolf TB, Roux B., Proc. Natl. Acad. Sci. U.S.A. 91(24), 1994
PMID: 7526400
Transmembrane helix structure, dynamics, and interactions: multi-nanosecond molecular dynamics simulations.
Shen L, Bassolino D, Stouch T., Biophys. J. 73(1), 1997
PMID: 9199766
A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer.
Tieleman DP, Berendsen HJ., Biophys. J. 74(6), 1998
PMID: 9635733
Setting up and optimization of membrane protein simulations.
Faraldo-Gomez JD, Smith GR, Sansom MS., Eur. Biophys. J. 31(3), 2002
PMID: 12029334
Molecular Description of Biological Membrane Components by Computer Aided Conformational Analysis
Brasseur, CRC 1(), 1990
Interaction of surfactin with membranes: a computational approach
Deleu, Langmuir 19(), 2003
ProtSqueeze: simple and effective automated tool for setting up membrane protein simulations.
Yesylevskyy SO., J Chem Inf Model 47(5), 2007
PMID: 17649971
Automated builder and database of protein/membrane complexes for molecular dynamics simulations.
Jo S, Kim T, Im W., PLoS ONE 2(9), 2007
PMID: 17849009
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank.
Tusnady GE, Dosztanyi Z, Simon I., Nucleic Acids Res. 33(Database issue), 2005
PMID: 15608195

Kellerer, 2004

Dyckhoff, 1992
Shape annealing solution to the constrained geometric knapsack problem
Cagan, Comput Aided Design 26(), 1994
A typology of cutting and packing problems
Dyckhoff, Eur J Oper Res 44(), 1990

Martello, 1990
Greedy genetic algorithm to Bounded Knapsack Problem. 3rd IEEE International Conference on Computer Science and Information Technology (ICCSIT), 2010
Kaystha, IEEE 6(), 2010
Conformational flexibility of o-phosphorylcholine and o-phosphorylethanolamine: a molecular dynamics study of solvation effects
Woolf, J Am Chem Soc 116(), 1994
The Protein Data Bank.
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE., Nucleic Acids Res. 28(1), 2000
PMID: 10592235
Databases in protein crystallography
Kleywegt, Acta Crystallogr, Sect D: Biol Crystallogr 54(), 1998
Ligand Depot: a data warehouse for ligands bound to macromolecules.
Feng Z, Chen L, Maddula H, Akcan O, Oughtred R, Berman HM, Westbrook J., Bioinformatics 20(13), 2004
PMID: 15059838

HIC-Up, 0

AUTHOR UNKNOWN, 2010
VMD: visual molecular dynamics.
Humphrey W, Dalke A, Schulten K., J Mol Graph 14(1), 1996
PMID: 8744570

AUTHOR UNKNOWN, 0

Grubmüller, 0
CHARMM-GUI: a web-based graphical user interface for CHARMM.
Jo S, Kim T, Iyer VG, Im W., J Comput Chem 29(11), 2008
PMID: 18351591

CHARMM-GUI, 0
CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes.
Jo S, Lim JB, Klauda JB, Im W., Biophys. J. 97(1), 2009
PMID: 19580743
Sphingomyelin-cholesterol domains in phospholipid membranes: atomistic simulation.
Pandit SA, Vasudevan S, Chiu SW, Mashl RJ, Jakobsson E, Scott HL., Biophys. J. 87(2), 2004
PMID: 15298913
Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking.
Martinez JM, Martinez L., J Comput Chem 24(7), 2003
PMID: 12692791
PACKMOL: a package for building initial configurations for molecular dynamics simulations.
Martinez L, Andrade R, Birgin EG, Martinez JM., J Comput Chem 30(13), 2009
PMID: 19229944
Large-scale active-set box-constrained optimization method with spectral projected gradients
Birgin, Comput Optim Appl 23(), 2002
Role of glycolipids in lipid rafts: a view through atomistic molecular dynamics simulations with galactosylceramide.
Hall A, Rog T, Karttunen M, Vattulainen I., J Phys Chem B 114(23), 2010
PMID: 20496924

Herrez, 2007
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates.
Tusnady GE, Dosztanyi Z, Simon I., Bioinformatics 21(7), 2004
PMID: 15539454
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