-
2
-
-
44949219079
-
Prediction of aggregation-prone regions in structured proteins
-
Tartaglia GG, Pawar AP, Campioni S, Dobson CM, Chiti F, et al. (2008) Prediction of aggregation-prone regions in structured proteins. J Mol Biol 380: 425-436.
-
(2008)
J Mol Biol
, vol.380
, pp. 425-436
-
-
Tartaglia, G.G.1
Pawar, A.P.2
Campioni, S.3
Dobson, C.M.4
Chiti, F.5
-
3
-
-
56349130674
-
Towards quantitative predictions in cell biology using chemical properties of proteins
-
Vendruscolo M, Tartaglia GG (2008) Towards quantitative predictions in cell biology using chemical properties of proteins. Mol Biosyst 4: 1170-1175.
-
(2008)
Mol Biosyst
, vol.4
, pp. 1170-1175
-
-
Vendruscolo, M.1
Tartaglia, G.G.2
-
4
-
-
63149130741
-
Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins
-
Niwa T, Ying BW, Saito K, Jin W, Takada S, et al. (2009) Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins. Proc Natl Acad Sci USA 106: 4201-4206.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 4201-4206
-
-
Niwa, T.1
Ying, B.W.2
Saito, K.3
Jin, W.4
Takada, S.5
-
6
-
-
43849103490
-
Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm
-
Ridgway D, Broderick G, Lopez-Campistrous A, Ru'aini M, Winter P, et al. (2008) Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm. Biophys J 94: 3748-3759.
-
(2008)
Biophys J
, vol.94
, pp. 3748-3759
-
-
Ridgway, D.1
Broderick, G.2
Lopez-Campistrous, A.3
Ru'aini, M.4
Winter, P.5
-
7
-
-
58149360317
-
Influence of macromolecular crowding on protein-protein association rates - a Brownian dynamics study
-
Wieczorek G, Zielenkiewicz P (2008) Influence of macromolecular crowding on protein-protein association rates - a Brownian dynamics study. Biophys J 95: 5030-5036.
-
(2008)
Biophys J
, vol.95
, pp. 5030-5036
-
-
Wieczorek, G.1
Zielenkiewicz, P.2
-
8
-
-
2342469914
-
Stochastic model of protein-protein interaction: Why signaling proteins need to be colocalized
-
Batada NN, Shepp LA, Siegmund DO (2004) Stochastic model of protein-protein interaction: Why signaling proteins need to be colocalized. Proc Natl Acad Sci U S A 101: 6445-6449.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 6445-6449
-
-
Batada, N.N.1
Shepp, L.A.2
Siegmund, D.O.3
-
10
-
-
0004232671
-
-
Princeton: Princeton University Press
-
Berg HC (1993) Random walks in biology. Princeton: Princeton University Press.
-
(1993)
Random Walks In Biology
-
-
Berg, H.C.1
-
11
-
-
0037086447
-
Addressing protein localization within the nucleus
-
Bickmore WA, Sutherland HGE (2002) Addressing protein localization within the nucleus. EMBO J 21: 1248-1254.
-
(2002)
EMBO J
, vol.21
, pp. 1248-1254
-
-
Bickmore, W.A.1
Sutherland, H.G.E.2
-
12
-
-
0035445626
-
Large-scale identification of mammalian proteins localized to nuclear sub-compartments
-
Sutherland HGE, Mumford GK, Newton K, Ford LV, Farrall R, et al. (2001) Large-scale identification of mammalian proteins localized to nuclear sub-compartments. Hum Mol Genet 10: 1995-2011.
-
(2001)
Hum Mol Genet
, vol.10
, pp. 1995-2011
-
-
Sutherland, H.G.E.1
Mumford, G.K.2
Newton, K.3
Ford, L.V.4
Farrall, R.5
-
13
-
-
33846010187
-
Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence
-
doi:10.1186/1471-2105-7-518
-
Du PF, Li YD (2006) Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence. BMC Bioinformatics 7: doi:10.1186/1471-2105-7-518.
-
(2006)
BMC Bioinformatics
, pp. 7
-
-
Du, P.F.1
Li, Y.D.2
-
14
-
-
33748476481
-
Electrostatic properties of protein-protein complexes
-
Kundrotas PJ, Alexov E (2006) Electrostatic properties of protein-protein complexes. Biophys J 91: 1724-1736.
-
(2006)
Biophys J
, vol.91
, pp. 1724-1736
-
-
Kundrotas, P.J.1
Alexov, E.2
-
15
-
-
36749060694
-
DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking
-
Gao Y, Douguet D, Tovchigrechko A, Vakser IA (2007) DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking. Proteins 69: 845-851.
-
(2007)
Proteins
, vol.69
, pp. 845-851
-
-
Gao, Y.1
Douguet, D.2
Tovchigrechko, A.3
Vakser, I.A.4
-
16
-
-
0003037157
-
Intraclass correlation coefficient. Encyclopedia of statistical sciences
-
editors
-
Kotz S, Johnson NL, Read CB, editors. (1983) Intraclass correlation coefficient. Encyclopedia of statistical sciences. New York: Wiley. vol. 4. pp. 212-217.
-
(1983)
New York: Wiley
, vol.4
, pp. 212-217
-
-
Kotz, S.1
Johnson, N.L.2
Read, C.B.3
-
17
-
-
48249153186
-
Intraclass correlations - uses in assessing rater reliability
-
Shrout PE, Fleiss JL (1979) Intraclass correlations - uses in assessing rater reliability. Psychol Bull 86: 420-428.
-
(1979)
Psychol Bull
, vol.86
, pp. 420-428
-
-
Shrout, P.E.1
Fleiss, J.L.2
-
18
-
-
4043171970
-
The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
-
Qiu D, Shenkin PS, Hollinger FP, Still WC (1997) The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J Phys Chem A 101: 3005-3014.
-
(1997)
J Phys Chem A
, vol.101
, pp. 3005-3014
-
-
Qiu, D.1
Shenkin, P.S.2
Hollinger, F.P.3
Still, W.C.4
-
19
-
-
41949100049
-
Recent advances in implicit solvent-based methods for biomolecular simulations
-
Chen JH, Brooks CL, Khandogin J (2008) Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol 18: 140-148.
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 140-148
-
-
Chen, J.H.1
Brooks, C.L.2
Khandogin, J.3
-
20
-
-
0037195486
-
Mathematical correlations for predicting protein retention times in hydrophobic interaction chromatography
-
Lienqueo ME, Mahn A, Asenjo JA (2002) Mathematical correlations for predicting protein retention times in hydrophobic interaction chromatography. J Chromatogr A 978: 71-79.
-
(2002)
J Chromatogr A
, vol.978
, pp. 71-79
-
-
Lienqueo, M.E.1
Mahn, A.2
Asenjo, J.A.3
-
21
-
-
59849088376
-
Methods of calculating protein hydrophobicity and their application in developing correlations to predict hydrophobic interaction chromatography retention
-
Mahn A, Lienqueo ME, Salgado JC (2009) Methods of calculating protein hydrophobicity and their application in developing correlations to predict hydrophobic interaction chromatography retention. J Chromatogr A 1216: 1838-1844.
-
(2009)
J Chromatogr A
, vol.1216
, pp. 1838-1844
-
-
Mahn, A.1
Lienqueo, M.E.2
Salgado, J.C.3
-
22
-
-
13844255387
-
Natively unfolded proteins
-
Fink AL (2005) Natively unfolded proteins. Curr Opin Struct Biol 15: 35-41.
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 35-41
-
-
Fink, A.L.1
-
24
-
-
69449106111
-
Negative membrane curvature as a cue for subcellular localization of a bacterial protein
-
Ramamurthi KS, Losick R (2009) Negative membrane curvature as a cue for subcellular localization of a bacterial protein. Proc Natl Acad Sci USA 106: 13541-13545.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 13541-13545
-
-
Ramamurthi, K.S.1
Losick, R.2
-
25
-
-
0033777047
-
Random walks and cell size
-
Agutter PS, Wheatley DN (2000) Random walks and cell size. Bioessays 22: 1018-1023.
-
(2000)
Bioessays
, vol.22
, pp. 1018-1023
-
-
Agutter, P.S.1
Wheatley, D.N.2
-
27
-
-
34547559704
-
PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
-
Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, et al. (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35: W522-W525.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Dolinsky, T.J.1
Czodrowski, P.2
Li, H.3
Nielsen, J.E.4
Jensen, J.H.5
-
29
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
30
-
-
0242443693
-
Force fields for protein simulations
-
Ponder JW, Case DA (2003) Force fields for protein simulations. Adv Protein Chem 66: 27-85.
-
(2003)
Adv Protein Chem
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
31
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen WL, Maxwell DS, TiradoRives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118: 11225-11236.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tiradorives, J.3
-
32
-
-
0029633168
-
GROMACS - A message-passing parallel molecular dynamics implementation
-
Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS - A message-passing parallel molecular dynamics implementation. Comp Phys Comm 91: 43-56.
-
(1995)
Comp Phys Comm
, vol.91
, pp. 43-56
-
-
Berendsen, H.J.C.1
van der Spoel, D.2
van Drunen, R.3
-
33
-
-
20544433165
-
Van der Waals volumes+radii
-
Bondi A (1964) Van der Waals volumes+radii. J Phys Chem 68: 441-452.
-
(1964)
J Phys Chem
, vol.68
, pp. 441-452
-
-
Bondi, A.1
-
34
-
-
33748546968
-
Intermolecular nonbonded contact distances in organic crystal structures: Comparison with distances expected from van der Waals radii
-
Rowland RS, Taylor R (1996) Intermolecular nonbonded contact distances in organic crystal structures: Comparison with distances expected from van der Waals radii. J Phys Chem 100: 7384-7391
-
(1996)
J Phys Chem
, vol.100
, pp. 7384-7391
-
-
Rowland, R.S.1
Taylor, R.2
|