-
1
-
-
66349117989
-
Thermally denatured state determines refolding in lipase: Mutational analysis
-
S. Ahmad, and N.M. Rao Thermally denatured state determines refolding in lipase: mutational analysis Protein Sci. 18 2009 1183 1196
-
(2009)
Protein Sci.
, vol.18
, pp. 1183-1196
-
-
Ahmad, S.1
Rao, N.M.2
-
2
-
-
47049084664
-
Thermostable Bacillus subtilis lipases: In vitro evolution and structural insight
-
S. Ahmad, M.Z. Kamal, R. Sankaranarayanan, and N.M. Rao Thermostable Bacillus subtilis lipases: in vitro evolution and structural insight J. Mol. Biol. 381 2008 324 340
-
(2008)
J. Mol. Biol.
, vol.381
, pp. 324-340
-
-
Ahmad, S.1
Kamal, M.Z.2
Sankaranarayanan, R.3
Rao, N.M.4
-
3
-
-
34447620778
-
Using molecular dynamics simulations to provide new insights into protein structure on the nanosecond timescale: Comparison with experimental data and biological inferences for the hyaluronan-binding link module of TSG-6
-
A. Almond, C.D. Blundell, V.A. Higman, A.D. MacKerell, and A.J. Day Using molecular dynamics simulations to provide new insights into protein structure on the nanosecond timescale: Comparison with experimental data and biological inferences for the hyaluronan-binding link module of TSG-6 J. Chem. Theory Comput. 3 2007 1 16
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 1-16
-
-
Almond, A.1
Blundell, C.D.2
Higman, V.A.3
Mackerell, A.D.4
Day, A.J.5
-
5
-
-
77952094752
-
Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering
-
P. Bernadó Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering Eur. Biophys. J. 39 2010 769 780
-
(2010)
Eur. Biophys. J.
, vol.39
, pp. 769-780
-
-
Bernadó, P.1
-
6
-
-
34249910312
-
Network analysis of protein dynamics
-
C. Böde, I.A. Kovács, M.S. Szalay, R. Palotai, T. Korcsmáros, and P. Csermely Network analysis of protein dynamics FEBS Lett. 581 2007 2776 2782
-
(2007)
FEBS Lett.
, vol.581
, pp. 2776-2782
-
-
Böde, C.1
Kovács, I.A.2
Szalay, M.S.3
Palotai, R.4
Korcsmáros, T.5
Csermely, P.6
-
7
-
-
54549098184
-
Target flexibility: An emerging consideration in drug discovery and design
-
P. Cozzini, G.E. Kellogg, F. Spyrakis, D.J. Abraham, G. Costantino, A. Emerson, F. Fanelli, H. Gohlke, L.A. Kuhn, and G.M. Morris Target flexibility: an emerging consideration in drug discovery and design J. Med. Chem. 51 2008 6237 6255
-
(2008)
J. Med. Chem.
, vol.51
, pp. 6237-6255
-
-
Cozzini, P.1
Kellogg, G.E.2
Spyrakis, F.3
Abraham, D.J.4
Costantino, G.5
Emerson, A.6
Fanelli, F.7
Gohlke, H.8
Kuhn, L.A.9
Morris, G.M.10
-
8
-
-
0036219887
-
A physical approach to protein structure prediction
-
S. Crivelli, E. Eskow, B. Bader, V. Lamberti, R. Byrd, R. Schnabel, and T. Head-Gordon A physical approach to protein structure prediction Biophys. J. 82 2002 36 49
-
(2002)
Biophys. J.
, vol.82
, pp. 36-49
-
-
Crivelli, S.1
Eskow, E.2
Bader, B.3
Lamberti, V.4
Byrd, R.5
Schnabel, R.6
Head-Gordon, T.7
-
9
-
-
0343742614
-
Automated design of the surface positions of protein helices
-
B.I. Dahiyat, D.B. Gordon, and S.L. Mayo Automated design of the surface positions of protein helices Protein Sci. 6 1997 1333 1337
-
(1997)
Protein Sci.
, vol.6
, pp. 1333-1337
-
-
Dahiyat, B.I.1
Gordon, D.B.2
Mayo, S.L.3
-
10
-
-
41149175561
-
Revisiting the correlation between proteins' thermoresistance and organisms' thermophilicity
-
Y. Dehouck, B. Folch, and M. Rooman Revisiting the correlation between proteins' thermoresistance and organisms' thermophilicity Protein Eng. Des. Sel. 21 2008 275 278
-
(2008)
Protein Eng. Des. Sel.
, vol.21
, pp. 275-278
-
-
Dehouck, Y.1
Folch, B.2
Rooman, M.3
-
11
-
-
30744478915
-
Protein flexibility: Its role in structure and mechanism revealed by molecular simulations
-
G. Dodson, and C.S. Verma Protein flexibility: its role in structure and mechanism revealed by molecular simulations Cell. Mol. Life Sci. 63 2006 207 219
-
(2006)
Cell. Mol. Life Sci.
, vol.63
, pp. 207-219
-
-
Dodson, G.1
Verma, C.S.2
-
13
-
-
84856397848
-
A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking
-
S. Forli, and A.J. Olson A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking J. Med. Chem. 55 2012 623 638
-
(2012)
J. Med. Chem.
, vol.55
, pp. 623-638
-
-
Forli, S.1
Olson, A.J.2
-
14
-
-
61649098586
-
Statics of the ribosomal exit tunnel: Implications for cotranslational peptide folding, elongation regulation, and antibiotics binding
-
S. Fulle, and H. Gohlke Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding J. Mol. Biol. 387 2009 502 517
-
(2009)
J. Mol. Biol.
, vol.387
, pp. 502-517
-
-
Fulle, S.1
Gohlke, H.2
-
15
-
-
70349299861
-
Constraint counting on RNA structures: Linking flexibility and function
-
S. Fulle, and H. Gohlke Constraint counting on RNA structures: linking flexibility and function Methods 49 2009 181 188
-
(2009)
Methods
, vol.49
, pp. 181-188
-
-
Fulle, S.1
Gohlke, H.2
-
16
-
-
3042806330
-
Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach
-
H. Gohlke, L.A. Kuhn, and D.A. Case Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach Proteins 56 2004 322 337
-
(2004)
Proteins
, vol.56
, pp. 322-337
-
-
Gohlke, H.1
Kuhn, L.A.2
Case, D.A.3
-
17
-
-
84858951932
-
Improving protein flexibility predictions by combining statistical sampling with a mean-field virtual pebble game
-
Gonzalez, L.C.; Livesay, D.R.; and Jacobs, D.J. (2011). Improving protein flexibility predictions by combining statistical sampling with a mean-field virtual pebble game. Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 294-298.
-
(2011)
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
, pp. 294-298
-
-
Gonzalez, L.C.1
Livesay, D.R.2
And Jacobs, D.J.3
-
18
-
-
84863155751
-
Calculating ensemble averaged descriptions of protein rigidity without sampling
-
L.C. González, H. Wang, D.R. Livesay, and D.J. Jacobs Calculating ensemble averaged descriptions of protein rigidity without sampling PLoS ONE 7 2012 e29176
-
(2012)
PLoS ONE
, vol.7
, pp. 29176
-
-
González, L.C.1
Wang, H.2
Livesay, D.R.3
Jacobs, D.J.4
-
19
-
-
0242720597
-
Uncovering network systems within protein structures
-
L.H. Greene, and V.A. Higman Uncovering network systems within protein structures J. Mol. Biol. 334 2003 781 791
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 781-791
-
-
Greene, L.H.1
Higman, V.A.2
-
20
-
-
0037022347
-
Flexibility and packing in proteins
-
B. Halle Flexibility and packing in proteins Proc. Natl. Acad. Sci. USA 99 2002 1274 1279
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 1274-1279
-
-
Halle, B.1
-
21
-
-
84867508210
-
Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS)
-
M. Hammel Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS) Eur. Biophys. J. 41 2012 789 799
-
(2012)
Eur. Biophys. J.
, vol.41
, pp. 789-799
-
-
Hammel, M.1
-
22
-
-
37249032102
-
Dynamic personalities of proteins
-
K. Henzler-Wildman, and D. Kern Dynamic personalities of proteins Nature 450 2007 964 972
-
(2007)
Nature
, vol.450
, pp. 964-972
-
-
Henzler-Wildman, K.1
Kern, D.2
-
23
-
-
0025789054
-
Side-chain clusters in protein structures and their role in protein folding
-
J. Heringa, and P. Argos Side-chain clusters in protein structures and their role in protein folding J. Mol. Biol. 220 1991 151 171
-
(1991)
J. Mol. Biol.
, vol.220
, pp. 151-171
-
-
Heringa, J.1
Argos, P.2
-
24
-
-
0036888379
-
Identifying protein folding cores from the evolution of flexible regions during unfolding
-
B.M. Hespenheide, A.J. Rader, M.F. Thorpe, and L.A. Kuhn Identifying protein folding cores from the evolution of flexible regions during unfolding J. Mol. Graph. Model. 21 2002 195 207
-
(2002)
J. Mol. Graph. Model.
, vol.21
, pp. 195-207
-
-
Hespenheide, B.M.1
Rader, A.J.2
Thorpe, M.F.3
Kuhn, L.A.4
-
25
-
-
33947716119
-
A semiempirical free energy force field with charge-based desolvation
-
R. Huey, G.M. Morris, A.J. Olson, and D.S. Goodsell A semiempirical free energy force field with charge-based desolvation J. Comput. Chem. 28 2007 1145 1152
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 1145-1152
-
-
Huey, R.1
Morris, G.M.2
Olson, A.J.3
Goodsell, D.S.4
-
26
-
-
0000785338
-
Generic rigidity percolation: The pebble game
-
D.J. Jacobs, and M.F. Thorpe Generic rigidity percolation: The pebble game Phys. Rev. Lett. 75 1995 4051 4054
-
(1995)
Phys. Rev. Lett.
, vol.75
, pp. 4051-4054
-
-
Jacobs, D.J.1
Thorpe, M.F.2
-
27
-
-
21244483843
-
Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity
-
D.J. Jacobs, and S. Dallakyan Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity Biophys. J. 88 2005 903 915
-
(2005)
Biophys. J.
, vol.88
, pp. 903-915
-
-
Jacobs, D.J.1
Dallakyan, S.2
-
29
-
-
1542285840
-
Network rigidity at finite temperature: Relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems
-
D.J. Jacobs, S. Dallakyan, G.G. Wood, and A. Heckathorne Network rigidity at finite temperature: Relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 68 2003
-
(2003)
Phys. Rev. E. Stat. Nonlin. Soft Matter Phys.
, vol.68
-
-
Jacobs, D.J.1
Dallakyan, S.2
Wood, G.G.3
Heckathorne, A.4
-
30
-
-
78651277458
-
A series of PDB related databases for everyday needs
-
R.P. Joosten, T.A. te Beek, E. Krieger, M.L. Hekkelman, R.W. Hooft, R. Schneider, C. Sander, and G. Vriend A series of PDB related databases for everyday needs Nucleic Acids Res. 39 Database issue 2011 D411 D419
-
(2011)
Nucleic Acids Res.
, vol.39
, Issue.DATABASE ISSUE
-
-
Joosten, R.P.1
Te Beek, T.A.2
Krieger, E.3
Hekkelman, M.L.4
Hooft, R.W.5
Schneider, R.6
Sander, C.7
Vriend, G.8
-
31
-
-
79954629700
-
A proof of the molecular conjecture
-
N. Katoh, and S. Tanigawa A proof of the molecular conjecture Discrete Comput. Geom. 45 2011 647 700
-
(2011)
Discrete Comput. Geom.
, vol.45
, pp. 647-700
-
-
Katoh, N.1
Tanigawa, S.2
-
32
-
-
29544432479
-
Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: A molecular dynamics study
-
G. Kieseritzky, G. Morra, and E.W. Knapp Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study J. Biol. Inorg. Chem. 11 2006 26 40
-
(2006)
J. Biol. Inorg. Chem.
, vol.11
, pp. 26-40
-
-
Kieseritzky, G.1
Morra, G.2
Knapp, E.W.3
-
33
-
-
79958837339
-
An introduction to NMR-based approaches for measuring protein dynamics
-
I.R. Kleckner, and M.P. Foster An introduction to NMR-based approaches for measuring protein dynamics Biochim. Biophys. Acta 1814 2011 942 968
-
(2011)
Biochim. Biophys. Acta
, vol.1814
, pp. 942-968
-
-
Kleckner, I.R.1
Foster, M.P.2
-
34
-
-
46749096337
-
Starting structure dependence of NMR order parameters derived from MD simulations: Implications for judging force-field quality
-
A.N. Koller, H. Schwalbe, and H. Gohlke Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality Biophys. J. 95 2008 L04 L06
-
(2008)
Biophys. J.
, vol.95
-
-
Koller, A.N.1
Schwalbe, H.2
Gohlke, H.3
-
35
-
-
84876532652
-
CNA web server: Rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo)stability, and function
-
D.M. Krüger, P.C. Rathi, C. Pfleger, and H. Gohlke CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo)stability, and function Nucleic Acids Res. 41 2013 W340 W348
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Krüger, D.M.1
Rathi, P.C.2
Pfleger, C.3
Gohlke, H.4
-
37
-
-
84985649741
-
Vibrational approach to the dynamics of an alpha-helix
-
R.M. Levy, and M. Karplus Vibrational approach to the dynamics of an alpha-helix Biopolymers 18 1979 2465 2495
-
(1979)
Biopolymers
, vol.18
, pp. 2465-2495
-
-
Levy, R.M.1
Karplus, M.2
-
38
-
-
30344476409
-
Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair
-
D.R. Livesay, and D.J. Jacobs Conserved quantitative stability/ flexibility relationships (QSFR) in an orthologous RNase H pair Proteins 62 2006 130 143
-
(2006)
Proteins
, vol.62
, pp. 130-143
-
-
Livesay, D.R.1
Jacobs, D.J.2
-
40
-
-
27744445169
-
Protein flexibility using constraints from molecular dynamics simulations
-
T. Mamonova, B. Hespenheide, R. Straub, M.F. Thorpe, and M. Kurnikova Protein flexibility using constraints from molecular dynamics simulations Phys. Biol. 2 2005 S137 S147
-
(2005)
Phys. Biol.
, vol.2
-
-
Mamonova, T.1
Hespenheide, B.2
Straub, R.3
Thorpe, M.F.4
Kurnikova, M.5
-
41
-
-
84876551539
-
Constraint Network Analysis (CNA): A Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function
-
C. Pfleger, P.C. Rathi, D.L. Klein, S. Radestock, and H. Gohlke Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function J. Chem. Inf. Model. 53 2013 1007 1015
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 1007-1015
-
-
Pfleger, C.1
Rathi, P.C.2
Klein, D.L.3
Radestock, S.4
Gohlke, H.5
-
42
-
-
84872307122
-
Global and local indices for characterizing biomolecular flexibility and rigidity
-
C. Pfleger, S. Radestock, E. Schmidt, and H. Gohlke Global and local indices for characterizing biomolecular flexibility and rigidity J. Comput. Chem. 34 2013 220 233
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 220-233
-
-
Pfleger, C.1
Radestock, S.2
Schmidt, E.3
Gohlke, H.4
-
43
-
-
36749120002
-
Theory of hydrophobic effect
-
L.R. Pratt, and D. Chandler Theory of hydrophobic effect J. Chem. Phys. 67 1977 3683 3704
-
(1977)
J. Chem. Phys.
, vol.67
, pp. 3683-3704
-
-
Pratt, L.R.1
Chandler, D.2
-
44
-
-
75449086680
-
Thermostability in rubredoxin and its relationship to mechanical rigidity
-
A.J. Rader Thermostability in rubredoxin and its relationship to mechanical rigidity Phys. Biol. 7 2009 16002
-
(2009)
Phys. Biol.
, vol.7
, pp. 16002
-
-
Rader, A.J.1
-
45
-
-
0346492917
-
Folding core predictions from network models of proteins
-
A.J. Rader, and I. Bahar Folding core predictions from network models of proteins Polymer (Guildf.) 45 2004 659 668
-
(2004)
Polymer (Guildf.)
, vol.45
, pp. 659-668
-
-
Rader, A.J.1
Bahar, I.2
-
47
-
-
61649103550
-
Exploiting the link between protein rigidity and thermostability for data-driven protein engineering
-
S. Radestock, and H. Gohlke Exploiting the link between protein rigidity and thermostability for data-driven protein engineering Eng. Life Sci. 8 2008 507 522
-
(2008)
Eng. Life Sci.
, vol.8
, pp. 507-522
-
-
Radestock, S.1
Gohlke, H.2
-
48
-
-
79952487469
-
Protein rigidity and thermophilic adaptation
-
S. Radestock, and H. Gohlke Protein rigidity and thermophilic adaptation Proteins 79 2011 1089 1108
-
(2011)
Proteins
, vol.79
, pp. 1089-1108
-
-
Radestock, S.1
Gohlke, H.2
-
49
-
-
0026731991
-
Hydrogen exchange in native and denatured states of hen egg-white lysozyme
-
S.E. Radford, M. Buck, K.D. Topping, C.M. Dobson, and P.A. Evans Hydrogen exchange in native and denatured states of hen egg-white lysozyme Proteins 14 1992 237 248
-
(1992)
Proteins
, vol.14
, pp. 237-248
-
-
Radford, S.E.1
Buck, M.2
Topping, K.D.3
Dobson, C.M.4
Evans, P.A.5
-
50
-
-
84860835198
-
Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio
-
P.C. Rathi, S. Radestock, and H. Gohlke Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio J. Biotechnol. 159 2012 135 144
-
(2012)
J. Biotechnol.
, vol.159
, pp. 135-144
-
-
Rathi, P.C.1
Radestock, S.2
Gohlke, H.3
-
51
-
-
0027256739
-
Hydrogen bonding, hydrophobicity, packing, and protein folding
-
G.D. Rose, and R. Wolfenden Hydrogen bonding, hydrophobicity, packing, and protein folding Annu. Rev. Biophys. Biomol. Struct. 22 1993 381 415
-
(1993)
Annu. Rev. Biophys. Biomol. Struct.
, vol.22
, pp. 381-415
-
-
Rose, G.D.1
Wolfenden, R.2
-
52
-
-
84872301054
-
The relationship between catalytic activity, structural flexibility and conformational stability as deduced from the analysis of mesophilic-thermophilic enzyme pairs and protein engineering studies
-
F. Robb, G. Antranikian, D. Grogan, A. Driessen, CRC Press London, New York
-
R. Sterner, and E. Brunner The relationship between catalytic activity, structural flexibility and conformational stability as deduced from the analysis of mesophilic-thermophilic enzyme pairs and protein engineering studies F. Robb, G. Antranikian, D. Grogan, A. Driessen, Thermophiles: Biology and Technology at High Temperatures 2008 CRC Press London, New York 25 38
-
(2008)
Thermophiles: Biology and Technology at High Temperatures
, pp. 25-38
-
-
Sterner, R.1
Brunner, E.2
-
54
-
-
0036139093
-
Why are proteins marginally stable?
-
D.M. Taverna, and R.A. Goldstein Why are proteins marginally stable? Proteins 46 2002 105 109
-
(2002)
Proteins
, vol.46
, pp. 105-109
-
-
Taverna, D.M.1
Goldstein, R.A.2
-
55
-
-
0037666888
-
Implications of protein flexibility for drug discovery
-
S.J. Teague Implications of protein flexibility for drug discovery Nat. Rev. Drug Discov. 2 2003 527 541
-
(2003)
Nat. Rev. Drug Discov.
, vol.2
, pp. 527-541
-
-
Teague, S.J.1
-
56
-
-
0021093473
-
Continuous deformations in random networks
-
M.F. Thorpe Continuous deformations in random networks J. Non-Cryst. Solids 57 1983 355 370
-
(1983)
J. Non-Cryst. Solids
, vol.57
, pp. 355-370
-
-
Thorpe, M.F.1
-
57
-
-
41349118690
-
Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E: Stat.; Nonlinear
-
M. Vendruscolo, N.V. Dokholyan, E. Paci, and M. Karplus Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E: Stat.; Nonlinear Soft Matter Physiol. 65 2002 1 4
-
(2002)
Soft Matter Physiol.
, vol.65
, pp. 1-4
-
-
Vendruscolo, M.1
Dokholyan, N.V.2
Paci, E.3
Karplus, M.4
-
58
-
-
27744521303
-
Counting out to the flexibility of molecules
-
W. Whiteley Counting out to the flexibility of molecules Phys. Biol. 2 2005 S116 S126
-
(2005)
Phys. Biol.
, vol.2
-
-
Whiteley, W.1
-
59
-
-
0035815288
-
Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation
-
M.A. Young, S. Gonfloni, G. Superti-Furga, B. Roux, and J. Kuriyan Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation Cell 105 2001 115 126
-
(2001)
Cell
, vol.105
, pp. 115-126
-
-
Young, M.A.1
Gonfloni, S.2
Superti-Furga, G.3
Roux, B.4
Kuriyan, J.5
-
60
-
-
0034595671
-
How soft is a protein? A protein dynamics force constant measured by neutron scattering
-
G. Zaccai How soft is a protein? A protein dynamics force constant measured by neutron scattering Science 288 2000 1604 1607
-
(2000)
Science
, vol.288
, pp. 1604-1607
-
-
Zaccai, G.1
|