-
1
-
-
34447270231
-
Hydrophobic, hydrophilic, and charged amino acid networks within protein
-
Aftabuddin M, Kundu S. 2007. Hydrophobic, hydrophilic, and charged amino acid networks within protein. Biophys. J. 93:225-31
-
(2007)
Biophys. J.
, vol.93
, pp. 225-231
-
-
Aftabuddin, M.1
Kundu, S.2
-
2
-
-
0030786486
-
Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model
-
Agarwala R, Batzoglou S, Dancik V, Decatur SE, Hannenhalli S, et al. 1997. Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. J. Comput. Biol. 4:275-96
-
(1997)
J. Comput. Biol.
, vol.4
, pp. 275-296
-
-
Agarwala, R.1
Batzoglou, S.2
Dancik, V.3
Decatur, S.E.4
Hannenhalli, S.5
-
3
-
-
0346057951
-
Small-world communication of residues and significance for protein dynamics
-
Atilgan AR, Akan P, Baysal C. 2004. Small-world communication of residues and significance for protein dynamics. Biophys. J. 86:85-91
-
(2004)
Biophys. J.
, vol.86
, pp. 85-91
-
-
Atilgan, A.R.1
Akan, P.2
Baysal, C.3
-
4
-
-
80155184398
-
Subtle pH differences trigger single residue motions for moderating conformations of calmodulin
-
Atilgan AR, Aykut AO, Atilgan C. 2011. Subtle pH differences trigger single residue motions for moderating conformations of calmodulin. J. Chem. Phys. 135:155102
-
(2011)
J. Chem. Phys.
, vol.135
, pp. 155102
-
-
Atilgan, A.R.1
Aykut, A.O.2
Atilgan, C.3
-
5
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. 2001. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80:505-15
-
(2001)
Biophys. J.
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Jernigan, R.L.3
Demirel, M.C.4
Keskin, O.5
Bahar, I.6
-
6
-
-
34247580211
-
Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication
-
Atilgan AR, Turgut D, Atilgan C. 2007. Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication. Biophys. J. 92:3052-62
-
(2007)
Biophys. J.
, vol.92
, pp. 3052-3062
-
-
Atilgan, A.R.1
Turgut, D.2
Atilgan, C.3
-
7
-
-
73449126303
-
Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein
-
Atilgan C, Atilgan AR. 2009. Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein. PloS Comput. Biol. 5:e1000544
-
(2009)
PloS Comput. Biol.
, vol.5
-
-
Atilgan, C.1
Atilgan, A.R.2
-
8
-
-
77955680967
-
Manipulation of conformational change in proteins by single-residue perturbations
-
Atilgan C, Gerek ZN, Ozkan SB, Atilgan AR. 2010. Manipulation of conformational change in proteins by single-residue perturbations. Biophys. J. 99:933-43
-
(2010)
Biophys. J.
, vol.99
, pp. 933-943
-
-
Atilgan, C.1
Gerek, Z.N.2
Ozkan, S.B.3
Atilgan, A.R.4
-
10
-
-
0012015514
-
How much sequence variation can the functions of biological molecules tolerate?
-
ed. H Frauenfelder, J Deisenhofer, PG Wolynes Berlin: Dahlem Univ. Press
-
Baase WA, Gassner NC, Zhang X-J, Kuroki R, Weaver LH, et al. 1999. How much sequence variation can the functions of biological molecules tolerate? In Simplicity and Complexity in Proteins and Nucleic Acids, ed. H Frauenfelder, J Deisenhofer, PG Wolynes, pp. 297-311. Berlin: Dahlem Univ. Press
-
(1999)
Simplicity and Complexity in Proteins and Nucleic Acids
, pp. 297-311
-
-
Baase, W.A.1
Gassner, N.C.2
Zhang, X.-J.3
Kuroki, R.4
Weaver, L.H.5
-
11
-
-
33645747929
-
A constraint-based approach to fast and exact structure prediction in three-dimensional protein models
-
Backofen R, Will S. 2006. A constraint-based approach to fast and exact structure prediction in three-dimensional protein models. Constraints 11:5-30
-
(2006)
Constraints
, vol.11
, pp. 5-30
-
-
Backofen, R.1
Will, S.2
-
12
-
-
0036470527
-
Residue packing in proteins: Uniform distribution on a coarse-grained scale
-
Bagci Z, Jernigan RL, Bahar I. 2002. Residue packing in proteins: uniform distribution on a coarse-grained scale. J. Chem. Phys. 116:2269-76
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 2269-2276
-
-
Bagci, Z.1
Jernigan, R.L.2
Bahar, I.3
-
13
-
-
34547909602
-
Assortative mixing in protein contact networks and protein folding kinetics
-
Bagler G, Sinha S. 2007. Assortative mixing in protein contact networks and protein folding kinetics. Bioinformatics 23:1760-67
-
(2007)
Bioinformatics
, vol.23
, pp. 1760-1767
-
-
Bagler, G.1
Sinha, S.2
-
14
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar I, Atilgan AR, Erman B. 1997. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:173-81
-
(1997)
Fold. Des.
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
15
-
-
77952938726
-
Global dynamics of proteins: Bridging between structure and function
-
Bahar I, Lezon TR, Yang LW, Eyal E. 2010. Global dynamics of proteins: bridging between structure and function. Annu. Rev. Biophys. 39:23-42
-
(2010)
Annu. Rev. Biophys.
, vol.39
, pp. 23-42
-
-
Bahar, I.1
Lezon, T.R.2
Yang, L.W.3
Eyal, E.4
-
16
-
-
70149098505
-
Coarse-grained modeling of allosteric regulation in protein receptors
-
Balabin IA, Yang WT, Beratan DN. 2009. Coarse-grained modeling of allosteric regulation in protein receptors. Proc. Natl. Acad. Sci. USA 106:14253-58
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 14253-14258
-
-
Balabin, I.A.1
Yang, W.T.2
Beratan, D.N.3
-
17
-
-
67349157147
-
Graph spectra as a systematic tool in computational biology
-
Banerjee A, Jost J. 2009. Graph spectra as a systematic tool in computational biology. Discrete Appl. Math. 157:2425-31
-
(2009)
Discrete Appl. Math.
, vol.157
, pp. 2425-2431
-
-
Banerjee, A.1
Jost, J.2
-
18
-
-
0035479570
-
Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2
-
Baysal C, Atilgan AR. 2001. Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2. Proteins Struct. Funct. Genet. 45:62-70
-
(2001)
Proteins Struct. Funct. Genet.
, vol.45
, pp. 62-70
-
-
Baysal, C.1
Atilgan, A.R.2
-
19
-
-
0035342460
-
Elucidating the structural mechanisms for biological activity of the chemokine family
-
Baysal C, Atilgan AR. 2001. Elucidating the structural mechanisms for biological activity of the chemokine family. Proteins Struct. Funct. Genet. 43:150-60
-
(2001)
Proteins Struct. Funct. Genet.
, vol.43
, pp. 150-160
-
-
Baysal, C.1
Atilgan, A.R.2
-
20
-
-
77956285109
-
Optimal identification of semi-rigid domainsin macromolecules from molecular dynamics simulation
-
Bernhard S, Noe F. 2010. Optimal identification of semi-rigid domainsin macromolecules from molecular dynamics simulation. PLoS One 5:e10491
-
(2010)
PLoS One
, vol.5
-
-
Bernhard, S.1
Noe, F.2
-
21
-
-
80052213580
-
Dynamic heterogeneity in amorphous materials
-
Berthier L. 2011. Dynamic heterogeneity in amorphous materials. Physics 4:42
-
(2011)
Physics
, vol.4
, pp. 42
-
-
Berthier, L.1
-
22
-
-
80051959824
-
Simplifying the representation of complex free-energy landscapes using sketch-map
-
Ceriotti M, Tribello GA, Parrinello M. 2011. Simplifying the representation of complex free-energy landscapes using sketch-map. Proc. Natl. Acad. Sci. USA 108:13023-28
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 13023-13028
-
-
Ceriotti, M.1
Tribello, G.A.2
Parrinello, M.3
-
23
-
-
33144476007
-
Universal behavior of optimal paths in weighted networks with general disorder
-
Chen YP, Lopez E, Havlin S, Stanley HE. 2006. Universal behavior of optimal paths in weighted networks with general disorder. Phys. Rev. Lett. 96:068702
-
(2006)
Phys. Rev. Lett.
, vol.96
, pp. 068702
-
-
Chen, Y.P.1
Lopez, E.2
Havlin, S.3
Stanley, H.E.4
-
24
-
-
56449125182
-
Creative elements: Network-based predictions of active centres in proteins and cellular and social networks
-
Csermely P. 2008. Creative elements: network-based predictions of active centres in proteins and cellular and social networks. Trends Biochem. Sci. 33:569-76
-
(2008)
Trends Biochem. Sci.
, vol.33
, pp. 569-576
-
-
Csermely, P.1
-
25
-
-
84857131975
-
Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: Hypotheses and a comprehensive review
-
Csermely P, Sandhu KS, Hazai E, Hoksza Z, Kiss HJM, et al. 2012. Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review. Curr. Protein Pept. Sci. 13:19-33
-
(2012)
Curr. Protein Pept. Sci.
, vol.13
, pp. 19-33
-
-
Csermely, P.1
Sandhu, K.S.2
Hazai, E.3
Hoksza, Z.4
Kiss, H.J.M.5
-
26
-
-
84919842045
-
Coarse-grained models of proteins: Theory and applications
-
ed. A Kolinski New York: Springer
-
Czaplewski C, Liwo A, Makowski M, Oldziej S, Scheraga HA. 2011. Coarse-grained models of proteins: theory and applications. In Multiscale Approaches to Protein Modeling, ed. A Kolinski, pp. 35-84. New York: Springer
-
(2011)
Multiscale Approaches to Protein Modeling
, pp. 35-84
-
-
Czaplewski, C.1
Liwo, A.2
Makowski, M.3
Oldziej, S.4
Scheraga, H.A.5
-
27
-
-
59849093382
-
Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins
-
da Silveira CH, Pires DEV, Minardi RC, Ribeiro C, Veloso CJM, et al. 2009. Protein cutoff scanning: a comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins. Proteins Struct. Funct. Bioinform. 74:727-43
-
(2009)
Proteins Struct. Funct. Bioinform.
, vol.74
, pp. 727-743
-
-
Da Silveira, C.H.1
Pires, D.E.V.2
Minardi, R.C.3
Ribeiro, C.4
Veloso, C.J.M.5
-
28
-
-
80053903522
-
Characterizing protein motions from structure
-
David CC, Jacobs DJ. 2011. Characterizing protein motions from structure. J. Mol. Graph. Model. 31:41-56
-
(2011)
J. Mol. Graph. Model.
, vol.31
, pp. 41-56
-
-
David, C.C.1
Jacobs, D.J.2
-
29
-
-
0034663710
-
Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α-amylase inhibitor
-
Doruker P, Atilgan AR, Bahar I. 2000. Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to α-amylase inhibitor. Proteins Struct. Funct. Genet. 40:512-24
-
(2000)
Proteins Struct. Funct. Genet.
, vol.40
, pp. 512-524
-
-
Doruker, P.1
Atilgan, A.R.2
Bahar, I.3
-
30
-
-
77649199847
-
Dynamical transition of protein-hydration water
-
Doster W, Busch S, Gaspar AM, Appavou MS, Wuttke J, Scheer H. 2010. Dynamical transition of protein-hydration water. Phys. Rev. Lett. 104:098101
-
(2010)
Phys. Rev. Lett.
, vol.104
, pp. 098101
-
-
Doster, W.1
Busch, S.2
Gaspar, A.M.3
Appavou, M.S.4
Wuttke, J.5
Scheer, H.6
-
31
-
-
57349084047
-
Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron
-
Feng Y, Jernigan RL, Kloczkowski A. 2008. Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron. Proteins Struct. Funct. Bioinform. 73:730-41
-
(2008)
Proteins Struct. Funct. Bioinform.
, vol.73
, pp. 730-741
-
-
Feng, Y.1
Jernigan, R.L.2
Kloczkowski, A.3
-
33
-
-
33644873452
-
The database of macromolecular motions: New features added at the decade mark
-
Flores S, Echols N, Milburn D, Hespenheide B, Keating K, et al. 2006. The database of macromolecular motions: new features added at the decade mark. Nucleic Acids Res. 34:D296-301
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Flores, S.1
Echols, N.2
Milburn, D.3
Hespenheide, B.4
Keating, K.5
-
34
-
-
72849108234
-
Adaptations of proteins to cellular and subcellular pH
-
Garcia-Moreno B. 2009. Adaptations of proteins to cellular and subcellular pH. J. Biol. 8:98
-
(2009)
J. Biol.
, vol.8
, pp. 98
-
-
Garcia-Moreno, B.1
-
35
-
-
0000577041
-
Large-amplitude nonlinear motions in proteins
-
Garcia AE. 1992. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68:2696-99
-
(1992)
Phys. Rev. Lett.
, vol.68
, pp. 2696-2699
-
-
Garcia, A.E.1
-
36
-
-
78650217130
-
Cellular proteomes have broad distributions of protein stability
-
Ghosh K, Dill K. 2010. Cellular proteomes have broad distributions of protein stability. Biophys. J. 99:3996-4002
-
(2010)
Biophys. J.
, vol.99
, pp. 3996-4002
-
-
Ghosh, K.1
Dill, K.2
-
37
-
-
79961021741
-
Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements
-
Gupta AN, Vincent A, Neupane K, Yu H, Wang F, Woodside MT. 2011. Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements. Nat. Phys. 7:631-34
-
(2011)
Nat. Phys.
, vol.7
, pp. 631-634
-
-
Gupta, A.N.1
Vincent, A.2
Neupane, K.3
Yu, H.4
Wang, F.5
Woodside, M.T.6
-
38
-
-
68749107059
-
Protein sectors: Evolutionary units of three-dimensional structure
-
Halabi N, Rivoire O, Leibler S, Ranganathan R. 2009. Protein sectors: evolutionary units of three-dimensional structure. Cell 138:774-86
-
(2009)
Cell
, vol.138
, pp. 774-786
-
-
Halabi, N.1
Rivoire, O.2
Leibler, S.3
Ranganathan, R.4
-
39
-
-
37249032102
-
Dynamic personalities of proteins
-
Henzler-Wildman K, Kern D. 2007. Dynamic personalities of proteins. Nature 450:964-72
-
(2007)
Nature
, vol.450
, pp. 964-972
-
-
Henzler-Wildman, K.1
Kern, D.2
-
40
-
-
34347235156
-
Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins
-
Hilser VJ, Thompson EB. 2007. Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins. Proc. Natl. Acad. Sci. USA 104:8311-15
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 8311-8315
-
-
Hilser, V.J.1
Thompson, E.B.2
-
41
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen K. 1998. Analysis of domain motions by approximate normal mode calculations. Proteins Struct. Funct. Genet. 33:417-29
-
(1998)
Proteins Struct. Funct. Genet.
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
42
-
-
79960637431
-
Dynamic molecular processes mediate cellular mechanotransduction
-
Hoffman BD, Grashoff C, Schwartz MA. 2011. Dynamic molecular processes mediate cellular mechanotransduction. Nature 475:316-23
-
(2011)
Nature
, vol.475
, pp. 316-323
-
-
Hoffman, B.D.1
Grashoff, C.2
Schwartz, M.A.3
-
43
-
-
18144418170
-
Protein structural change upon ligand binding: Linear response theory
-
Ikeguchi M, Ueno J, Sato M, Kidera A. 2005. Protein structural change upon ligand binding: linear response theory. Phys. Rev. Lett. 94:078102
-
(2005)
Phys. Rev. Lett.
, vol.94
, pp. 078102
-
-
Ikeguchi, M.1
Ueno, J.2
Sato, M.3
Kidera, A.4
-
44
-
-
79961053709
-
Single-molecule experiments out of equilibrium
-
Jarzynski C. 2011. Single-molecule experiments out of equilibrium. Nat. Phys. 7:591-92
-
(2011)
Nat. Phys.
, vol.7
, pp. 591-592
-
-
Jarzynski, C.1
-
46
-
-
78649755348
-
The role of vicinal tyrosine residues in the function of Haemophilus influenzae ferric-binding protein A
-
Khambati HK, Moraes TF, Singh J, Shouldice SR, Yu RH, Schryvers AB. 2010. The role of vicinal tyrosine residues in the function of Haemophilus influenzae ferric-binding protein A. Biochem. J. 432:57-64
-
(2010)
Biochem. J.
, vol.432
, pp. 57-64
-
-
Khambati, H.K.1
Moraes, T.F.2
Singh, J.3
Shouldice, S.R.4
Yu, R.H.5
Schryvers, A.B.6
-
47
-
-
60849087655
-
Distance matrix-based approach to protein structure prediction
-
Kloczkowski A, Jernigan RL, Wu Z, Song G, Yang L, et al. 2009. Distance matrix-based approach to protein structure prediction. J. Struct. Funct. Genomics 10:67-81
-
(2009)
J. Struct. Funct. Genomics
, vol.10
, pp. 67-81
-
-
Kloczkowski, A.1
Jernigan, R.L.2
Wu, Z.3
Song, G.4
Yang, L.5
-
48
-
-
69449103989
-
Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model
-
Kurkcuoglu O, Turgut OT, Cansu S, Jernigan RL, Doruker P. 2009. Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model. Biophys. J. 97:1178-87
-
(2009)
Biophys. J.
, vol.97
, pp. 1178-1187
-
-
Kurkcuoglu, O.1
Turgut, O.T.2
Cansu, S.3
Jernigan, R.L.4
Doruker, P.5
-
49
-
-
54249105941
-
Surface sites for engineering allosteric control in proteins
-
Lee J, Natarajan M, Nashine VC, Socolich M, Vo T, et al. 2008. Surface sites for engineering allosteric control in proteins. Science 322:438-42
-
(2008)
Science
, vol.322
, pp. 438-442
-
-
Lee, J.1
Natarajan, M.2
Nashine, V.C.3
Socolich, M.4
Vo, T.5
-
50
-
-
79959704466
-
Exploration of the relationship between topology and designability of conformations
-
Leelananda SP, Towfic F, Jernigan RL, Kloczkowski A. 2011. Exploration of the relationship between topology and designability of conformations. J. Chem. Phys. 134:235101
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 235101
-
-
Leelananda, S.P.1
Towfic, F.2
Jernigan, R.L.3
Kloczkowski, A.4
-
51
-
-
0034901412
-
Are proteins well-packed?
-
Liang J, Dill KA. 2001. Are proteins well-packed? Biophys. J. 81:751-66
-
(2001)
Biophys. J.
, vol.81
, pp. 751-766
-
-
Liang, J.1
Dill, K.A.2
-
52
-
-
34248332629
-
Functional residues serve a dominant role in mediating the cooper-ativity of the protein ensemble
-
Liu T, Whitten ST, Hilser VJ. 2007. Functional residues serve a dominant role in mediating the cooper-ativity of the protein ensemble. Proc. Natl. Acad. Sci. USA 104:4347-52
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 4347-4352
-
-
Liu, T.1
Whitten, S.T.2
Hilser, V.J.3
-
53
-
-
0033536602
-
Evolutionarily conserved pathways of energetic connectivity in protein families
-
Lockless SW, Ranganathan R. 1999. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286:295-99
-
(1999)
Science
, vol.286
, pp. 295-299
-
-
Lockless, S.W.1
Ranganathan, R.2
-
56
-
-
30944460113
-
Fluctuating enzymes: Lessons from single-molecule studies
-
Min W, English BP, Luo GB, Cherayil BJ, Kou SC, Xie XS. 2005. Fluctuating enzymes: lessons from single-molecule studies. Acc. Chem. Res. 38:923-31
-
(2005)
Acc. Chem. Res.
, vol.38
, pp. 923-931
-
-
Min, W.1
English, B.P.2
Luo, G.B.3
Cherayil, B.J.4
Kou, S.C.5
Xie, X.S.6
-
57
-
-
33645102817
-
Interactions in native binding sites cause a large change in protein dynamics
-
Ming DM, Wall ME. 2006. Interactions in native binding sites cause a large change in protein dynamics. J. Mol. Biol. 358:213-23
-
(2006)
J. Mol. Biol.
, vol.358
, pp. 213-223
-
-
Ming, D.M.1
Wall, M.E.2
-
58
-
-
0038752085
-
Mixing patterns in networks
-
Newman MEJ. 2003. Mixing patterns in networks. Phys. Rev. E 67:026126
-
(2003)
Phys. Rev. e
, vol.67
, pp. 026126
-
-
Newman, M.E.J.1
-
59
-
-
70350025161
-
Nanosecond motions in proteins impose bounds on the timescale distributions of local dynamics
-
Okan OB, Atilgan AR, Atilgan C. 2009. Nanosecond motions in proteins impose bounds on the timescale distributions of local dynamics. Biophys. J. 97:2080-88
-
(2009)
Biophys. J.
, vol.97
, pp. 2080-2088
-
-
Okan, O.B.1
Atilgan, A.R.2
Atilgan, C.3
-
60
-
-
0029063717
-
The complexity and accuracy of discrete state models of protein structure
-
Park BH, Levitt M. 1995. The complexity and accuracy of discrete state models of protein structure. J. Mol. Biol. 249:493-507
-
(1995)
J. Mol. Biol.
, vol.249
, pp. 493-507
-
-
Park, B.H.1
Levitt, M.2
-
61
-
-
33646145523
-
Can conformational change be described by only a few normal modes?
-
Petrone P, Pande VS. 2006. Can conformational change be described by only a few normal modes? Biophys. J. 90:1583-93
-
(2006)
Biophys. J.
, vol.90
, pp. 1583-1593
-
-
Petrone, P.1
Pande, V.S.2
-
62
-
-
77954286692
-
ALADYN: A web server for aligning proteins by matching their large-scale motion
-
Potestio R, Aleksiev T, Pontiggia F, Cozzini S, Micheletti C. 2010. ALADYN: a web server for aligning proteins by matching their large-scale motion. Nucleic Acids Res. 38:W41-W45
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Potestio, R.1
Aleksiev, T.2
Pontiggia, F.3
Cozzini, S.4
Micheletti, C.5
-
63
-
-
0030850226
-
Ideal architecture of residue packing and its observation in protein structures
-
Raghunathan G, Jernigan RL. 1997. Ideal architecture of residue packing and its observation in protein structures. Protein Sci. 6:2072-83
-
(1997)
Protein Sci.
, vol.6
, pp. 2072-2083
-
-
Raghunathan, G.1
Jernigan, R.L.2
-
64
-
-
79955632669
-
Shape, flexibility and packing of proteins and nucleic acids in complexes
-
Rawat N, Biswas P. 2011. Shape, flexibility and packing of proteins and nucleic acids in complexes. Phys. Chem. Chem. Phys. 13:9632-43
-
(2011)
Phys. Chem. Chem. Phys.
, vol.13
, pp. 9632-9643
-
-
Rawat, N.1
Biswas, P.2
-
65
-
-
58149496872
-
Modeling the mechanical response of proteins to anisotropic deformation
-
Sacquin-Mora S, Lavery R. 2009. Modeling the mechanical response of proteins to anisotropic deformation. Chemphyschem 10:115-18
-
(2009)
Chemphyschem
, vol.10
, pp. 115-118
-
-
Sacquin-Mora, S.1
Lavery, R.2
-
66
-
-
61449196621
-
Folding, stability and shape of proteins in crowded environments: Experimental and computational approaches
-
Samiotakis A, Wittung-Stafshede P, Cheung MS. 2009. Folding, stability and shape of proteins in crowded environments: experimental and computational approaches. Int. J. Mol. Sci. 10:572-88
-
(2009)
Int. J. Mol. Sci.
, vol.10
, pp. 572-588
-
-
Samiotakis, A.1
Wittung-Stafshede, P.2
Cheung, M.S.3
-
67
-
-
34447499925
-
Ligand recombination and a hierarchy of solvent slaved dynamics: The origin of kinetic phases in heme proteins
-
Samuni U, Dantsker D, Roche CJ, Friedman JM. 2007. Ligand recombination and a hierarchy of solvent slaved dynamics: the origin of kinetic phases in heme proteins. Gene 398:234-48
-
(2007)
Gene
, vol.398
, pp. 234-248
-
-
Samuni, U.1
Dantsker, D.2
Roche, C.J.3
Friedman, J.M.4
-
68
-
-
77957937199
-
Atomic-level characterization of the structural dynamics of proteins
-
Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, et al. 2010. Atomic-level characterization of the structural dynamics of proteins. Science 330:341-46
-
(2010)
Science
, vol.330
, pp. 341-346
-
-
Shaw, D.E.1
Maragakis, P.2
Lindorff-Larsen, K.3
Piana, S.4
Dror, R.O.5
-
69
-
-
33847240145
-
Intracellular pH sensors: Design principles and functional significance
-
Srivastava J, Barber DL, Jacobson MP. 2007. Intracellular pH sensors: design principles and functional significance. Physiology 22:30-39
-
(2007)
Physiology
, vol.22
, pp. 30-39
-
-
Srivastava, J.1
Barber, D.L.2
Jacobson, M.P.3
-
72
-
-
0037219686
-
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
-
Suel GM, Lockless SW, Wall MA, Ranganathan R. 2003. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10:59-69
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 59-69
-
-
Suel, G.M.1
Lockless, S.W.2
Wall, M.A.3
Ranganathan, R.4
-
73
-
-
33745024278
-
Symmetry, form, and shape: Guiding principles for robustness in macromolec-ular machines
-
Tama F, Brooks CL. 2006. Symmetry, form, and shape: guiding principles for robustness in macromolec-ular machines. Annu. Rev. Biophys. Biomol. Struct. 35:115-33
-
(2006)
Annu. Rev. Biophys. Biomol. Struct.
, vol.35
, pp. 115-133
-
-
Tama, F.1
Brooks, C.L.2
-
74
-
-
0035044995
-
Conformational changeofproteins arising from normal mode calculations
-
Tama F, Sanejouand YH. 2001. Conformational changeofproteins arising from normal mode calculations. Protein Eng. 14:1-6
-
(2001)
Protein Eng.
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.H.2
-
75
-
-
79959937283
-
DEPTH: A web server to compute depth and predict small-molecule binding cavities in proteins
-
Tan KP, Varadarajan R, Madhusudhan MS. 2011. DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. Nucleic Acids Res. 39:W242-48
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Tan, K.P.1
Varadarajan, R.2
Madhusudhan, M.S.3
-
76
-
-
77957242403
-
Proteome-level interplay between folding and aggregation propensities of proteins
-
Tartaglia GG, Vendruscolo M. 2010. Proteome-level interplay between folding and aggregation propensities of proteins. J. Mol. Biol. 402:919-28
-
(2010)
J. Mol. Biol.
, vol.402
, pp. 919-928
-
-
Tartaglia, G.G.1
Vendruscolo, M.2
-
77
-
-
0029909384
-
An iterative method for extracting energy-like quantities from protein structures
-
Thomas PD, Dill KA. 1996. An iterative method for extracting energy-like quantities from protein structures. Proc. Natl. Acad. Sci. USA 93:11628-33
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 11628-11633
-
-
Thomas, P.D.1
Dill, K.A.2
-
78
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
Tirion MM. 1996. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1905-8
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
79
-
-
79951676668
-
Minimalist models for proteins: A comparative analysis
-
Tozzini V. 2010. Minimalist models for proteins: a comparative analysis. Q. Rev. Biophys. 43:333-71
-
(2010)
Q. Rev. Biophys.
, vol.43
, pp. 333-371
-
-
Tozzini, V.1
-
82
-
-
78650757173
-
Assortative mixing in close-packed spatial networks
-
Turgut D, Atilgan AR, Atilgan C. 2010. Assortative mixing in close-packed spatial networks. PLoS One 5:e15551
-
(2010)
PLoS One
, vol.5
-
-
Turgut, D.1
Atilgan, A.R.2
Atilgan, C.3
-
83
-
-
65649089458
-
Intra and inter-molecular communications through protein structure network
-
Vishveshwara S, Ghosh A, Hansia P. 2009. Intra and inter-molecular communications through protein structure network. Curr. Protein Pept. Sci. 10:146-60
-
(2009)
Curr. Protein Pept. Sci.
, vol.10
, pp. 146-160
-
-
Vishveshwara, S.1
Ghosh, A.2
Hansia, P.3
-
84
-
-
65649100094
-
Frameworks for understanding long-range intra-protein communication
-
Whitley MJ, Lee AL. 2009. Frameworks for understanding long-range intra-protein communication. Curr. Protein Pept. Sci. 10:116-27
-
(2009)
Curr. Protein Pept. Sci.
, vol.10
, pp. 116-127
-
-
Whitley, M.J.1
Lee, A.L.2
-
85
-
-
79959992592
-
A biophysical protein folding model accounts for most mutational fitness effects in viruses
-
Wylie CS, Shakhnovich EI. 2011. A biophysical protein folding model accounts for most mutational fitness effects in viruses. Proc. Natl. Acad. Sci. USA 108:9916-21
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 9916-9921
-
-
Wylie, C.S.1
Shakhnovich, E.I.2
-
86
-
-
61449160619
-
Coarse-grained models reveal functional dynamics-I. Elastic network models\theories, comparisons and perspectives
-
Yang L-W, Chng C-P. 2008. Coarse-grained models reveal functional dynamics-I. Elastic network models\theories, comparisons and perspectives. Bioinform. Biol. Insights 2:25-45
-
(2008)
Bioinform. Biol. Insights
, vol.2
, pp. 25-45
-
-
Yang, L.-W.1
Chng, C.-P.2
-
87
-
-
34547666968
-
How well can we understand large-scale protein motions using normal modes of elastic network models?
-
Yang L, Song G, Jernigan RL. 2007. How well can we understand large-scale protein motions using normal modes of elastic network models? Biophys. J. 93:920-29
-
(2007)
Biophys. J.
, vol.93
, pp. 920-929
-
-
Yang, L.1
Song, G.2
Jernigan, R.L.3
-
88
-
-
0034622725
-
Identifying the adaptive mechanism in globular proteins: Fluctuations in densely packed regions manipulate flexible parts
-
Yilmaz LS, Atilgan AR. 2000. Identifying the adaptive mechanism in globular proteins: fluctuations in densely packed regions manipulate flexible parts. J. Chem. Phys. 113:4454-64
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 4454-4464
-
-
Yilmaz, L.S.1
Atilgan, A.R.2
-
89
-
-
43949093427
-
Understanding protein evolution: From protein physics to Darwinian selection
-
Zeldovich KB, Shakhnovich EI. 2008. Understanding protein evolution: from protein physics to Darwinian selection. Annu. Rev. Phys. Chem. 59:105-27
-
(2008)
Annu. Rev. Phys. Chem.
, vol.59
, pp. 105-127
-
-
Zeldovich, K.B.1
Shakhnovich, E.I.2
-
90
-
-
79953899870
-
Single molecule force spectroscopy reveals that electrostatic interactions affect the mechanical stability of proteins
-
Zheng P, Cao Y, Bu TJ, Straus SK, Li HB. 2011. Single molecule force spectroscopy reveals that electrostatic interactions affect the mechanical stability of proteins. Biophys. J. 100:1534-41
-
(2011)
Biophys. J.
, vol.100
, pp. 1534-1541
-
-
Zheng, P.1
Cao, Y.2
Bu, T.J.3
Straus, S.K.4
Li, H.B.5
-
91
-
-
68149163617
-
Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model
-
Zheng WJ, Tekpinar M. 2009. Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model. BMC Struct. Biol. 9:45
-
(2009)
BMC Struct. Biol.
, vol.9
, pp. 45
-
-
Zheng, W.J.1
Tekpinar, M.2
|