-
1
-
-
84862983938
-
Conservation of complex knotting and slipknotting patterns in proteins
-
Sulkowska, J. I., Rawdon, E. J., Millett, K. C., Onuchic, J. N. and Stasiak, A. (2012) Conservation of complex knotting and slipknotting patterns in proteins. Proc. Natl. Acad. Sci. U. S. A., 109, E1715-E1723.
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. E1715-E1723
-
-
Sulkowska, J.I.1
Rawdon, E.J.2
Millett, K.C.3
Onuchic, J.N.4
Stasiak, A.5
-
2
-
-
0028421135
-
Are there knots in proteins?
-
Mansfield, M. L. (1994) Are there knots in proteins? Nat. Struct. Biol., 1, 213-214.
-
(1994)
Nat. Struct. Biol.
, vol.1
, pp. 213-214
-
-
Mansfield, M.L.1
-
4
-
-
0034710671
-
A deeply knotted protein structure and how it might fold
-
Taylor, W. R. (2000) A deeply knotted protein structure and how it might fold. Nature, 406, 916-919.
-
(2000)
Nature
, vol.406
, pp. 916-919
-
-
Taylor, W.R.1
-
5
-
-
33749347406
-
Intricate knots in proteins: Function and evolution
-
Virnau, P., Mirny, L. A. and Kardar, M. (2006) Intricate knots in proteins: Function and evolution. PLoS Comput. Biol., 2, e122.
-
(2006)
PLoS Comput. Biol.
, vol.2
, pp. e122
-
-
Virnau, P.1
Mirny, L.A.2
Kardar, M.3
-
6
-
-
77954565450
-
A Stevedore's protein knot
-
Bölinger, D., Sulkowska, J. I., Hsu, H. P., Mirny, L. A., Kardar, M., Onuchic, J. N. and Virnau, P. (2010) A Stevedore's protein knot. PLoS Comput. Biol., 6, e1000731.
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. e1000731
-
-
Bölinger, D.1
Sulkowska, J.I.2
Hsu, H.P.3
Mirny, L.A.4
Kardar, M.5
Onuchic, J.N.6
Virnau, P.7
-
7
-
-
78650549526
-
Structure and folding of a designed knotted protein
-
King, N. P., Jacobitz, A. W., Sawaya, M. R., Goldschmidt, L. and Yeates, T. O. (2010) Structure and folding of a designed knotted protein. Proc. Natl. Acad. Sci. U. S. A., 107, 20732-20737.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 20732-20737
-
-
King, N.P.1
Jacobitz, A.W.2
Sawaya, M.R.3
Goldschmidt, L.4
Yeates, T.O.5
-
8
-
-
34548575206
-
Identification of rare slipknots in proteins and their implications for stability and folding
-
King, N. P., Yeates, E. O. and Yeates, T. O. (2007) Identification of rare slipknots in proteins and their implications for stability and folding. J. Mol. Biol., 373, 153-66.
-
(2007)
J. Mol. Biol.
, vol.373
, pp. 153-166
-
-
King, N.P.1
Yeates, E.O.2
Yeates, T.O.3
-
9
-
-
73649114614
-
Jamming proteins with slipknots and their free energy landscape
-
Sulkowska, J. I., Sulkowski, P. and Onuchic, J. N. (2009) Jamming proteins with slipknots and their free energy landscape. Phys. Rev. Lett., 103, 268103.
-
(2009)
Phys. Rev. Lett.
, vol.103
, pp. 268103
-
-
Sulkowska, J.I.1
Sulkowski, P.2
Onuchic, J.N.3
-
10
-
-
33646904782
-
Statistics of knots, geometry of conformations, and evolution of proteins
-
Lua, R. C. and Grosberg, A. Y. (2006) Statistics of knots, geometry of conformations, and evolution of proteins. PLoS Comput. Biol., 2, e45.
-
(2006)
PLoS Comput. Biol.
, vol.2
, pp. e45
-
-
Lua, R.C.1
Grosberg, A.Y.2
-
11
-
-
34648820435
-
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases
-
Tkaczuk, K. L. et al. (2007) Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. Bioinformatics, 8, 73.
-
(2007)
Bioinformatics
, vol.8
, pp. 73
-
-
Tkaczuk, K.L.1
-
12
-
-
34047180474
-
The folding mechanics of a knotted protein
-
Wallin, S., Zeldovich, K. B. and Shakhnovich, E. I. (2007) The folding mechanics of a knotted protein. J. Mol. Biol., 368, 884-893.
-
(2007)
J. Mol. Biol.
, vol.368
, pp. 884-893
-
-
Wallin, S.1
Zeldovich, K.B.2
Shakhnovich, E.I.3
-
13
-
-
58149374561
-
Stabilizing effect of knots on proteins
-
Sulkowska, J. I., Sulkowski, P., Szymczak, P. and Cieplak, M. (2008) Stabilizing effect of knots on proteins. Proc. Natl. Acad. Sci. U. S. A., 105, 19714-19719.
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, pp. 19714-19719
-
-
Sulkowska, J.I.1
Sulkowski, P.2
Szymczak, P.3
Cieplak, M.4
-
14
-
-
78049235694
-
Knotted versus unknotted proteins: Evidence of knot-promoting loops
-
Potestio, R., Micheletti, C. and Orland, H. (2010) Knotted versus unknotted proteins: evidence of knot-promoting loops. PLoS Comput. Biol., 6, e1000864.
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. e1000864
-
-
Potestio, R.1
Micheletti, C.2
Orland, H.3
-
15
-
-
77957699207
-
Untying knots in proteins
-
Sulkowska, J. I., Sulkowski, P., Szymczak, P. and Cieplak, M. (2010) Untying knots in proteins. J. Am. Chem. Soc., 132, 13954-13956.
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 13954-13956
-
-
Sulkowska, J.I.1
Sulkowski, P.2
Szymczak, P.3
Cieplak, M.4
-
16
-
-
79954594752
-
A topological framework for the computation of the Homfly polynomial and its application to proteins
-
Comoglio, F. and Rinadli, M. (2011) A topological framework for the computation of the Homfly polynomial and its application to proteins. PLoS One, 6, e18693.
-
(2011)
PLoS One
, vol.6
, pp. e18693
-
-
Comoglio, F.1
Rinadli, M.2
-
17
-
-
84868107440
-
Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot
-
Li, W., Terakawa, T., Wang, W. and Takada, S., (2012) Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot. Proc. Natl. Acad. Sci. U. S. A., 109, 17789-17794.
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 17789-17794
-
-
Li, W.1
Terakawa, T.2
Wang, W.3
Takada, S.4
-
18
-
-
84879230918
-
Tightening and untying the knot in Human Carbonic Anhydrase III
-
Dzubiella, J. (2013) Tightening and untying the knot in Human Carbonic Anhydrase III. J. Phys. Chem. Lett., 4, 1829-1833.
-
(2013)
J. Phys. Chem. Lett.
, vol.4
, pp. 1829-1833
-
-
Dzubiella, J.1
-
19
-
-
84876001589
-
Folding pathways of a knotted protein with a realistic atomistic force field
-
Beccara, S., Skrbic, T., Covino, R., Micheletti, C. and Faccioli, P. (2013) Folding pathways of a knotted protein with a realistic atomistic force field. PLoS Comput. Biol., 9, e1003002.
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1003002
-
-
Beccara, S.1
Skrbic, T.2
Covino, R.3
Micheletti, C.4
Faccioli, P.5
-
20
-
-
77952415889
-
Experimental detection of knotted conformations in denatured proteins
-
Mallam, A. L., Rogers, J. M. and Jackson, S. E. (2010) Experimental detection of knotted conformations in denatured proteins. Proc. Natl. Acad. Sci. U. S. A., 107, 8189-8194.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 8189-8194
-
-
Mallam, A.L.1
Rogers, J.M.2
Jackson, S.E.3
-
21
-
-
84856113243
-
Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins
-
Mallam, A. L. and Jackson, S. E. (2011) Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins. Nat. Chem. Biol., 8, 147-153.
-
(2011)
Nat. Chem. Biol.
, vol.8
, pp. 147-153
-
-
Mallam, A.L.1
Jackson, S.E.2
-
22
-
-
84863470496
-
Mechanically untying a protein slipknot: Multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations
-
He, C., Genchev, G. Z., Lu, H. and Li, H. (2012) Mechanically untying a protein slipknot: multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations. J. Am. Chem. Soc., 134, 10428-10435.
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 10428-10435
-
-
He, C.1
Genchev, G.Z.2
Lu, H.3
Li, H.4
-
23
-
-
84872200194
-
Hysteresis as a marker for complex, overlapping landscapes in proteins
-
Andrews, B. T., Capraro, D. T., Sulkowska, J. I., Onuchic, J. N. and Jennings, P. A. (2013) Hysteresis as a marker for complex, overlapping landscapes in proteins. J. Phys. Chem. Lett., 4, 180-188.
-
(2013)
J. Phys. Chem. Lett.
, vol.4
, pp. 180-188
-
-
Andrews, B.T.1
Capraro, D.T.2
Sulkowska, J.I.3
Onuchic, J.N.4
Jennings, P.A.5
-
24
-
-
84891903281
-
Protein folidng on the ribosome studied using NMR spectroscopy
-
Waudby, C. A., Launay, H., Cabrita, L. D. and Christodoulou, J. (2013) Protein folidng on the ribosome studied using NMR spectroscopy. Prog. Nucl. Magn. Reson. Spectrosc., 74, 57-75.
-
(2013)
Prog. Nucl. Magn. Reson. Spectrosc.
, vol.74
, pp. 57-75
-
-
Waudby, C.A.1
Launay, H.2
Cabrita, L.D.3
Christodoulou, J.4
-
25
-
-
13244258252
-
Linear random knots and their scaling behaviour
-
Millett, K., Dobay, A. and Stasiak, A. (2005) Linear random knots and their scaling behaviour. Macromolecules, 38, 601-606.
-
(2005)
Macromolecules
, vol.38
, pp. 601-606
-
-
Millett, K.1
Dobay, A.2
Stasiak, A.3
-
26
-
-
84875395499
-
Identifying knots in proteins
-
Millett, K. C., Rawdon, E. J., Stasiak, A. and Sulkowska, J. I. (2012) Identifying knots in proteins. Biochem. Soc. Trans., 41, 533-537.
-
(2012)
Biochem. Soc. Trans.
, vol.41
, pp. 533-537
-
-
Millett, K.C.1
Rawdon, E.J.2
Stasiak, A.3
Sulkowska, J.I.4
-
27
-
-
0004598743
-
Self-entanglement in ring polymers
-
Koniaris, K. and Muthukumar, M. (1991) Self-entanglement in ring polymers. J. Chem. Phys., 95, 2873-2881.
-
(1991)
J. Chem. Phys.
, vol.95
, pp. 2873-2881
-
-
Koniaris, K.1
Muthukumar, M.2
-
28
-
-
84876239078
-
JSmol and the next-generation web-based representation of 3D molecular structure as applied to Proteopedia
-
Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013) JSmol and the next-generation web-based representation of 3D molecular structure as applied to Proteopedia. Israel J. Chem. 53, 207-216.
-
(2013)
Israel J. Chem
, vol.53
, pp. 207-216
-
-
Hanson, R.M.1
Prilusky, J.2
Renjian, Z.3
Nakane, T.4
Sussman, J.L.5
-
29
-
-
84875384720
-
Knot localization in proteins
-
Rawdon, E. J., Millett, K. C., Sulkowska, J. I. and Stasiak, A. (2013) Knot localization in proteins. Biochem. Soc. Trans., 41, 538-541.
-
(2013)
Biochem. Soc. Trans.
, vol.41
, pp. 538-541
-
-
Rawdon, E.J.1
Millett, K.C.2
Sulkowska, J.I.3
Stasiak, A.4
-
30
-
-
84876578144
-
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures
-
Sillitoe, I., Cuff, A. L., Dessailly, B. H., Dawson, N. L., Furnham, N., Lee, D., Lees, J. G., Lewis, T. E., Studer, R. A., Rentzsch, R. et al. (2013) New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res., 41, D490-D498.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D490-D498
-
-
Sillitoe, I.1
Cuff, A.L.2
Dessailly, B.H.3
Dawson, N.L.4
Furnham, N.5
Lee, D.6
Lees, J.G.7
Lewis, T.E.8
Studer, R.A.9
Rentzsch, R.10
-
31
-
-
84876579771
-
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource
-
Velankar, S., Dana, J. M., Jacobsen, J. et al. (2013) SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. Nucleic Acids Res., 41, D483-D489.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D483-D489
-
-
Velankar, S.1
Dana, J.M.2
Jacobsen, J.3
-
32
-
-
84868098919
-
Energy landscape of knotted protein folding
-
Sulkowska, J. I., Noel, J. K. and Onuchic, J. N. (2012) Energy landscape of knotted protein folding. Proc. Natl. Acad. Sci. U. S. A., 109, 17783-17788.
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 17783-17788
-
-
Sulkowska, J.I.1
Noel, J.K.2
Onuchic, J.N.3
-
33
-
-
34547563369
-
Protein knot server: Detection of knots in protein structures
-
Kolesov, G., Virnau, P., Kardar, M. and Mirny, L. A. (2007) Protein knot server: detection of knots in protein structures. Nucleic Acids Res., 35, W425-W428.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. W425-W428
-
-
Kolesov, G.1
Virnau, P.2
Kardar, M.3
Mirny, L.A.4
-
34
-
-
84864420695
-
Pknot v. 2: The protein KNOT web server
-
Yan-Long, Lai, Chih-Chieh, Chen and Jenn-Kang, Hwang (2012) pKNOT v. 2: the protein KNOT web server. Nucleic Acids Res., 40, W228-W231.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W228-W231
-
-
Yan-Long, L.1
Chih-Chieh, C.2
Jenn-Kang, H.3
-
35
-
-
84865154095
-
PyKnot: A PyMOL tool for the discovery and analysis of knots in proteins
-
Lua, R. (2012), PyKnot: a PyMOL tool for the discovery and analysis of knots in proteins. Bioinformatics, 28, 2069-2071.
-
(2012)
Bioinformatics
, vol.28
, pp. 2069-2071
-
-
Lua, R.1
-
36
-
-
84861147882
-
Rknots: Topological analysis of knotted biopolymers with R
-
Comoglio, F. and Rinaldi, M. (2012) Rknots: topological analysis of knotted biopolymers with R. Bioinformatics, 28, 1400-1401.
-
(2012)
Bioinformatics
, vol.28
, pp. 1400-1401
-
-
Comoglio, F.1
Rinaldi, M.2
|