choonpeng's methodology [52 articles] Export

Recent papers added to choonpeng's library classified by the tag methodology. You can also see everyone's methodology.

	Role of Hydrogen Bonding and Helix−Lipid Interactions in Transmembrane Helix Association [My Copy] Journal of the American Chemical Society, Vol. 130, No. 20. (1 May 2008), pp. 6456-6462. by Jinhyuk Lee, Wonpil Im posted to methodology transmembrane by choonpeng on 2009-08-03 09:09:19 as along with 1 person and 1 group sobolevnrm baker-group
	Coarse-graining protein structures with local multivariate features from molecular dynamics. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 44. (6 November 2008), pp. 14026-14035. by Zhiyong Zhang, Willy Wriggers posted to methodology pca protein-dynamics by choonpeng on 2009-07-31 11:19:36 as along with 1 person and 1 group sobolevnrm baker-group
	Solvent-Free Lipid Bilayer Model Using Multiscale Coarse-Graining [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 13. (2 April 2009), pp. 4443-4455. by Sergei Izvekov, Gregory A. Voth posted to coarse-grained methodology transmembrane by choonpeng on 2009-07-27 11:43:15 as along with 3 people and 1 group flbarroso agrossfield sobolevnrm baker-group
	Relationships between three-body and two-body interactions in fluids and solids [My Copy] The Journal of Chemical Physics, Vol. 125, No. 14. (2006), 144509. by Liping Wang, Richard J. Sadus posted to methodology by choonpeng on 2009-06-23 11:19:29 as
	Role of nonadditive forces on the structure and properties of liquid water [My Copy] The Journal of Chemical Physics, Vol. 127, No. 15. (2007), 154509. by Jianhui Li, Zhongwu Zhou, Richard J. Sadus posted to methodology by choonpeng on 2009-06-23 11:07:27 as
	Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes [My Copy] Journal of Computational Physics, Vol. 23, No. 3. (March 1977), pp. 327-341. by J. Ryckaert, G. Ciccotti, H. Berendsen posted to methodology by choonpeng on 2009-06-14 06:58:48 as along with 8 people Vadikus dimka rpetrenko gcottone stephenbond bmduggan A_Coletta_Thesis ashaytan
	Simulation of the diffusional association of barnase and barstar [My Copy] Vol. 72, No. 5. (1 May 1997), pp. 1917-1929. by R. R. Gabdoulline, R. C. Wade posted to kinetics methodology protein-interaction by choonpeng on 2009-05-04 06:48:27 as along with 1 person Martin8223
	Brownian dynamics simulation of diffusion-influenced bimolecular reactions [My Copy] The Journal of Chemical Physics, Vol. 80, No. 4. (1984), pp. 1517-1524. by Scott H. Northrup, Stuart A. Allison, Andrew J. Mccammon posted to kinetics methodology by choonpeng on 2009-05-04 02:51:07 as along with 3 people stephenbond barry Martin8223
	Dynamic strength of molecularly bonded surfaces. [My Copy] The Journal of chemical physics, Vol. 125, No. 19. (21 November 2006) by F. Li, D. Leckband posted to methodology protein-interaction by choonpeng on 2009-04-16 09:51:05 as
	Feature-preserving adaptive mesh generation for molecular shape modeling and simulation [My Copy] Journal of Molecular Graphics and Modelling, Vol. 26 (2008), pp. 1370-1380. by Zeyun Yu, Michael J. Holst, Yuhui Cheng, Mccammon posted to methodology by choonpeng on 2009-03-01 07:24:51 as along with 2 people and 1 group carlk sobolevnrm baker-group
	Methodological Issues in Lipid Bilayer Simulations [My Copy] J. Phys. Chem. B, Vol. 107, No. 35. (4 September 2003), pp. 9424-9433. by C. Anezo, A. H. Devries, H. D. Holtje, D. P. Tieleman, S. J. Marrink posted to methodology by choonpeng on 2009-01-15 09:02:42 as along with 2 people agrossfield softsimu
	Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters [My Copy] The Journal of Chemical Physics, Vol. 105, No. 11. (1996), pp. 4871-4880. by D. P. Tieleman, H. J. C. Berendsen posted to methodology by choonpeng on 2009-01-09 10:23:03 as
	Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. [My Copy] Biophysical journal, Vol. 72, No. 5. (May 1997), pp. 2002-2013. by O. Berger, O. Edholm, F. Jähnig posted to methodology by choonpeng on 2009-01-08 06:32:06 as along with 3 people and 1 group Marine sunnytov robertvacha Molecular dynamics in MSU
	SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models [My Copy] Journal of Computational Chemistry, Vol. 13, No. 8. (1992), pp. 952-962. by Shuichi Miyamoto, Peter A. Kollman posted to methodology by choonpeng on 2009-01-05 05:37:53 as along with 8 people oteri Lombardo_7 A_Coletta_Thesis jwagoner tji softsimu ashaytan robertvacha
	P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation [My Copy] J. Chem. Theory Comput., Vol. 4, No. 1. (8 January 2008), pp. 116-122. by B. Hess posted to methodology by choonpeng on 2009-01-05 05:33:55 as along with 2 people r2s2 janneb
	A smooth particle mesh Ewald method [My Copy] The Journal of Chemical Physics, Vol. 103, No. 19. (1995), pp. 8577-8593. by Ulrich Essmann, Lalith Perera, Max L. Berkowitz, Tom Darden, Hsing Lee, Lee G. Pedersen posted to methodology by choonpeng on 2009-01-05 05:32:16 as along with 15 people and 2 groups jmparks rpetrenko A_Coletta_Thesis r2s2 charris5 pavanghatty sobolevnrm lillekatt and_ped10 easybakemuffin RamuAnandakrishnan ashaytan mikaellund 6rheology jteyra Structural Biology Group TorVergata baker-group
	Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues [My Copy] Journal of Computational Chemistry, Vol. 28, No. 3. (2007), pp. 689-697. by Zhitao Xu, Harry H. Luo, Peter D. Tieleman posted to methodology by choonpeng on 2009-01-02 10:25:41 as along with 1 person loison
	Setting up and running molecular dynamics simulations of membrane proteins. [My Copy] Methods (San Diego, Calif.), Vol. 41, No. 4. (April 2007), pp. 475-488. by Christian Kandt, Walter L. Ash, D. Peter Tieleman posted to methodology transmembrane by choonpeng on 2008-12-04 02:27:31 as along with 3 people and 2 groups arnaucordomi xdeupi sobolevnrm LabCompMed baker-group
	The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. [My Copy] The Journal of chemical physics, Vol. 128, No. 24. (28 June 2008) by W. G. Noid, J. W. Chu, G. S. Ayton, et al.V. Krishna, S. Izvekov, G. A. Voth, A. Das, H. C. Andersen posted to methodology multi-scale by choonpeng on 2008-11-27 09:12:39 as
	A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules [My Copy] Biophysical Journal, Vol. 95, No. 11. (01 December 2008), pp. 5073-5083. by Z. Zhang, L. Lu, W. Noid, V. Krishna, J. Pfaendtner, G. Voth posted to coarse-grained methodology pca by choonpeng on 2008-11-27 08:53:06 as along with 5 people and 2 groups okapi barry sobolevnrm agrossfield paulschlesinger structural_bioinformatics McCammon
	Phase Transition for a Hard Sphere System [My Copy] The Journal of Chemical Physics, Vol. 27, No. 5. (1957), pp. 1208-1209. by B. J. Alder, T. E. Wainwright posted to methodology by choonpeng on 2008-07-30 01:40:01 as along with 1 person stephenbond
	Molecular dynamics with coupling to an external bath [My Copy] The Journal of Chemical Physics, Vol. 81, No. 8. (1984), pp. 3684-3690. by H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Dinola, J. R. Haak posted to methodology by choonpeng on 2008-06-04 13:09:41 as along with 12 people and 1 group georgwachter A_Coletta_Thesis rdf r2s2 dsmueller Lombardo_7 gsub lillekatt allmensch jwagoner tji jteyra Structural Biology Group TorVergata
	Structure Prediction of Domain Insertion Proteins from Structures of Individual Domains [My Copy] Structure, Vol. 16, No. 4. (8 April 2008), pp. 513-527. by Monica Berrondo, Marc Ostermeier, Jeffrey J. Gray posted to methodology protein-domains by choonpeng on 2008-04-10 14:33:38 as along with 2 people zwang raik
	Comparison of multiple Amber force fields and development of improved protein backbone parameters. [My Copy] Proteins, Vol. 65, No. 3. (15 November 2006), pp. 712-725. by Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg, Carlos Simmerling posted to methodology by choonpeng on 2008-03-15 06:29:57 as along with 10 people arnaucordomi Vadikus bmduggan baaden lna allmensch kazemi barry GermanErlenkamp RamuAnandakrishnan
	Full correlation analysis of conformational protein dynamics [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Oliver F. Lange, Helmut Grubmüller posted to methodology pca by choonpeng on 2008-02-19 07:08:18 as along with 7 people and 1 group anuragsethi jeargle Diego_Prada softsimu barry sobolevnrm LamBras baker-group
	Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution. [My Copy] FEBS Lett, Vol. 470, No. 3. (31 March 2000), pp. 257-262. by J. Kleinjung, P. Bayley, F. Fraternali posted to ensemble methodology by choonpeng on 2008-02-12 00:39:01 as
	Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures. [My Copy] Biophys J, Vol. 90, No. 12. (15 June 2006), pp. 4558-4573. by K. L. Damm, H. A. Carlson posted to methodology by choonpeng on 2008-01-26 10:28:25 as along with 5 people mijam nickolay blackbart rabio higueruelo
	Investigation of Salt Bridge Stability in a Generalized Born Solvent Model [My Copy] Journal of Chemical Theory and Computation, Vol. 2, No. 1. (1 January 2006), pp. 115-127. by Raphael Geney, Melinda Layten, Roberto Gomperts, Viktor Hornak, Carlos Simmerling posted to methodology solvent-effects by choonpeng on 2008-01-23 04:07:27 as along with 2 people onufriev baaden
	Calculation of the solution properties of flexible macromolecules: methods and applications. [My Copy] Eur Biophys J, Vol. 32, No. 5. (August 2003), pp. 477-486. by J. García de la Torre, H. E. Pérez Sánchez, A. Ortega, et al.J. G. Hernández, M. X. Fernandes, F. G. Díaz, M. C. López Martínez posted to methodology modular by choonpeng on 2007-12-23 11:17:08 as
	Structural characterization of flexible proteins using small-angle X-ray scattering. [My Copy] J Am Chem Soc, Vol. 129, No. 17. (2 May 2007), pp. 5656-5664. by P. Bernadó, E. Mylonas, M. V. Petoukhov, M. Blackledge, D. I. Svergun posted to methodology protein-domains by choonpeng on 2007-11-06 07:13:29 as along with 1 person higueruelo
	Physical methods for structure, dynamics and binding in immunological research. [My Copy] Trends Immunol, Vol. 25, No. 12. (December 2004), pp. 700-707. by D. Morikis, J. D. Lambris posted to methodology modular by choonpeng on 2007-10-12 08:24:54 as along with 1 person dgront
	Residual dipolar couplings in NMR structure analysis. [My Copy] Annu Rev Biophys Biomol Struct, Vol. 33 (2004), pp. 387-413. by R. S. Lipsitz, N. Tjandra posted to methodology by choonpeng on 2007-10-05 07:20:30 as
	Exact Low-Force Kinetics from High-Force Single-Molecule Unfolding Events. [My Copy] Biophys J (17 August 2007) by Jeremiah Nummela, Ioan Andricioaei posted to force-probe-md methodology by choonpeng on 2007-08-29 06:23:31 as
	Liquid-structure forces and electrostatic modulation of biomolecular interactions in solution. [My Copy] J Phys Chem B, Vol. 111, No. 1. (11 January 2007), pp. 227-241. by S. A. Hassan posted to methodology solvent-effects by choonpeng on 2007-08-26 12:42:14 as along with 1 person flbarroso
	Effective energy function for proteins in solution. [My Copy] Proteins, Vol. 35, No. 2. (1 May 1999), pp. 133-152. by T. Lazaridis, M. Karplus posted to implicit-solvent methodology solvent-effects by choonpeng on 2007-08-26 12:27:05 as along with 6 people and 2 groups melo_mcr oceanwind marcius bluvsh1 hmk kgutwin BioinfoCIPF SGU-CIPF
	Interdomain contact regions and angles between adjacent short consensus repeat domains. [My Copy] J Mol Biol, Vol. 344, No. 5. (10 December 2004), pp. 1385-1396. by M. J. Lehtinen, S. Meri, T. S. Jokiranta posted to methodology modular by choonpeng on 2007-08-12 11:01:00 as
	VISTAL--a new 2D visualization tool of protein 3D structural alignments [My Copy] Bioinformatics, Vol. 22, No. 17. (1 September 2006), pp. 2166-2167. by Rachel Kolodny, Barry Honig posted to methodology by choonpeng on 2007-08-09 11:52:22 as along with 2 people dimka msierk
	Collective Langevin dynamics of conformational motions in proteins [My Copy] The Journal of Chemical Physics, Vol. 124, No. 21. (2006) by Oliver F. Lange, Helmut Grubmuller posted to methodology by choonpeng on 2007-07-17 10:35:56 as along with 1 person and 1 group sobolevnrm baker-group
	On the calculation of time correlation functions by potential scaling [My Copy] The Journal of Chemical Physics, Vol. 124, No. 3. (2006) by Chenyue Xing, Ioan Andricioaei posted to methodology by choonpeng on 2007-07-11 04:41:09 as along with 2 people blackbart jorgeramirez
	Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. [My Copy] J Mol Biol, Vol. 256, No. 3. (1 March 1996), pp. 623-644. by S. Miyazawa, R. L. Jernigan posted to methodology by choonpeng on 2007-07-01 10:06:26 as along with 4 people and 1 group okapi krapnik rabio joseph_x_zhou protein_Dyn
	Deriving effective mesoscale potentials from atomistic simulations [My Copy] Journal of Computational Chemistry, Vol. 24, No. 13. (2003), pp. 1624-1636. by Dirk Reith, Mathias Pütz, Florian Müller-Plathe posted to coarse-grained methodology by choonpeng on 2007-05-29 14:26:01 as
	Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches [My Copy] Proteins: Structure, Function, and Genetics, Vol. 29, No. 3. (1997), pp. 292-308. by I. Bahar, M. Kaplan, R. L. Jernigan posted to methodology by choonpeng on 2007-05-29 14:20:27 as
	Implementation of π-π interactions in molecular dynamics simulation [My Copy] Journal of Computational Chemistry, Vol. 28, No. 6. (2007), pp. 1091-1099. by Hitomi Yuki, Yoshikazu Tanaka, Masayuki Hata, Hidenori Ishikawa, Saburo Neya, Tyuji Hoshino posted to methodology protein-stability by choonpeng on 2007-03-04 15:18:04 as along with 1 person jwagoner
	Electrostatic potentials of proteins in water: a structured continuum approach. [My Copy] Bioinformatics, Vol. 23, No. 2. (15 January 2007) by A. Hildebrandt, R. Blossey, S. Rjasanow, O. Kohlbacher, H. P. Lenhof posted to methodology solvent-effects by choonpeng on 2007-02-23 16:11:43 as along with 1 person grahamc
	Three-body interactions improve the prediction of rate and mechanism in protein folding models. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 42. (19 October 2004), pp. 15088-15093. by M. R. Ejtehadi, S. P. Avall, S. S. Plotkin posted to methodology protein-folding by choonpeng on 2007-02-12 12:24:45 as
	Hierarchical clustering of the correlation patterns: New method of domain identification in proteins. [My Copy] Biophys Chem (24 August 2005) by S O O. Yesylevskyy, V N N. Kharkyanen, A P P. Demchenko posted to methodology protein-domains by choonpeng on 2006-12-29 01:35:39 as along with 2 people and 3 groups barry yongzhao structural_bioinformatics Bioinformatics TSRI_MGL
	Order N algorithm for computation of electrostatic interactions in biomolecular systems [My Copy] Proceedings of the National Academy of Sciences, Vol. 103, No. 51. (19 December 2006), pp. 19314-19319. by Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, J. Andrew Mccammon posted to methodology by choonpeng on 2006-12-20 05:20:40 as along with 5 people flbarroso dmitry_s_yershov stephenbond eyliu qwermish
	Dynamite: a simple way to gain insight into protein motions. [My Copy] Acta crystallographica. Section D, Biological crystallography, Vol. 60, No. Pt 12 Pt 1. (01 December 2004), pp. 2280-2287. by C. Paul Barrett, Benjamin A. Hall, Martin E. Noble posted to methodology web-server by choonpeng on 2006-11-03 12:21:24 as along with 4 people and 1 group arifor dimka aqeel yongzhao TSRI_MGL
	Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features [My Copy] Biopolymers, Vol. 22, No. 12. (December 1983), pp. 2577-2637. by Wolfgang Kabsch, Christian Sander posted to methodology by choonpeng on 2006-09-26 13:52:46 as along with 33 people dfdong barmak7282 Vadikus j3xucite scampos TLVincent maria_hauser pablocarb rpetrenko carlosjavierna mijam wqia007 dsmueller niallhaslam saunders jwm sebk Diego_Prada pjcite kaarsinogen lna chad_davis wouterboomsma penka ffranca dgront rabio gisle medic0747 martainn chgjb mschofie marti
	Knowledge-based protein secondary structure assignment [My Copy] Proteins: Structure, Function, and Genetics, Vol. 23, No. 4. (December 1995), pp. 566-579. by Dmitrij Frishman, Patrick Argos posted to methodology by choonpeng on 2006-09-19 05:43:35 as along with 4 people ashaytan3 rpetrenko marti saravan

Note: You may cite this page as: http://www.citeulike.org/user/choonpeng/tag/methodology

Result page: 1 2 Next

protein-folding	177
modular	117
coarse-grained	111
review	90
protein-interaction	87
protein-domains	83
force-probe-md	64
mechanotransduction	63
flagellar	61
methodology	52
protein-translocation	48
single-molecule-methods	48
allostery	45
cell-adhesion	43
signaling	43
high-t-md	40
ttss	29
nma	28
transmembrane	27
integrin	26
mechanical-unfolding	26
solvent-effects	24
protein-mechanics	22
books	21
protein-stability	19
pca	18
chaperone	16
cytoskeletal-dynamics	16
folding-nucleus	16
cooperativity	15
folding-intermediate	15
web-server	15
go-model	14
bioinformatics	13
ensemble	12
implicit-solvent	12
theoretical	11
software	10
self-assembly	9
denatured-state	8
crowding	7
diffusion	7
multi-scale	7
protein-degradation	7
ig-like	6
kinetics	6
computer-programming	5
protein-secretion	5
salt-bridge	5
protein-dynamics	4
structure-validation	3
science-presentation	1
science-writing	1

choonpeng's methodology [52 articles] Export

choonpeng's tags