-
1
-
-
0346220393
-
The role of dynamics in allosteric regulation
-
Kern D, Zuiderweg ERP (2003) The role of dynamics in allosteric regulation. Curr Opin Struct Biol 13:748-757.
-
(2003)
Curr Opin Struct Biol
, vol.13
, pp. 748-757
-
-
Kern, D.1
Zuiderweg, E.R.P.2
-
2
-
-
0031922657
-
Conformational dynamics and enzyme activity
-
Yon JM, Perahia D, Ghelis C (1998) Conformational dynamics and enzyme activity. Biochimie 80:33-42.
-
(1998)
Biochimie
, vol.80
, pp. 33-42
-
-
Yon, J.M.1
Perahia, D.2
Ghelis, C.3
-
3
-
-
33646943202
-
Molecular dynamics: Survey of methods for simulating the activity of proteins
-
Adcock SA, McCammon JA (2006) Molecular dynamics: Survey of methods for simulating the activity of proteins. Chem Rev 106:1589-1615.
-
(2006)
Chem Rev
, vol.106
, pp. 1589-1615
-
-
Adcock, S.A.1
McCammon, J.A.2
-
4
-
-
25844431698
-
Coarse-grained normal mode analysis in structural biology
-
DOI 10.1016/j.sbi.2005.08.007, PII S0959440X05001557, Carbohydrates and Glycoconjugates/Biophysical Methods
-
Bahar I, Rader AJ (2005) Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 15:586-592. (Pubitemid 41393491)
-
(2005)
Current Opinion in Structural Biology
, vol.15
, Issue.5
, pp. 586-592
-
-
Bahar, I.1
Rader, A.J.2
-
5
-
-
0029644728
-
Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases
-
Vonrhein C, Schlauderer GJ, Schulz GE (1995) Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. Structure 3:483-490.
-
(1995)
Structure
, vol.3
, pp. 483-490
-
-
Vonrhein, C.1
Schlauderer, G.J.2
Schulz, G.E.3
-
6
-
-
0029644168
-
Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding
-
Muller CW, Schlauderer GJ, Reinstein J, Schulz GE (1996) Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding. Structure 4:147-156. (Pubitemid 126658978)
-
(1996)
Structure
, vol.4
, Issue.2
, pp. 147-156
-
-
Muller, C.W.1
Schlauderer, G.J.2
Reinstein, J.3
Schulz, G.E.4
-
7
-
-
0029866802
-
Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP
-
DOI 10.1006/jmbi.1996.0080
-
Schlauderer GJ, Proba K, Schulz GE (1996) Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP. J Mol Biol 256:223-227. (Pubitemid 26105586)
-
(1996)
Journal of Molecular Biology
, vol.256
, Issue.2
, pp. 223-227
-
-
Schlauderer, G.J.1
Proba, K.2
Schulz, G.E.3
-
8
-
-
0029897810
-
The structure of bovine mitochondrial adenylate kinase: Comparison with isoenzymes in other compartments
-
Schlauderer GJ, Schulz GE (1996) The structure of bovine mitochondrial adenylate kinase: Comparison with isoenzymes in other compartments. Protein Sci 5:434-441.
-
(1996)
Protein Sci
, vol.5
, pp. 434-441
-
-
Schlauderer, G.J.1
Schulz, G.E.2
-
9
-
-
36849048228
-
Intrinsic motions along an enzymatic reaction trajectory
-
Henzler-Wildman KA, et al. (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature 450:838-844.
-
(2007)
Nature
, vol.450
, pp. 838-844
-
-
Henzler-Wildman, K.A.1
-
10
-
-
36749083505
-
Illuminating the mechanistic roles of enzyme conformational dynamics
-
Hanson JA, et al. (2007) Illuminating the mechanistic roles of enzyme conformational dynamics. Proc Natl Acad Sci USA 104:18055-18060.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 18055-18060
-
-
Hanson, J.A.1
-
12
-
-
33947431555
-
Essential dynamics sampling study of adenylate kinase: Comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions
-
DOI 10.1002/prot.21280
-
Snow C, Qi GY, Hayward S (2007) Essential dynamics sampling study of adenylate kinase: Comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions. Proteins 67:325-337. (Pubitemid 46449410)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.67
, Issue.2
, pp. 325-337
-
-
Snow, C.1
Qi, G.2
Hayward, S.3
-
13
-
-
48149084621
-
The atomistic mechanism of conformational transition in adenylate kinase: A TEE-REX molecular dynamics study
-
Kubitzki MB, de Groot BL (2008) The atomistic mechanism of conformational transition in adenylate kinase: A TEE-REX molecular dynamics study. Structure 16:1175-1182.
-
(2008)
Structure
, vol.16
, pp. 1175-1182
-
-
Kubitzki, M.B.1
De Groot, B.L.2
-
14
-
-
36849039429
-
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
-
Henzler-Wildman KA, et al. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450:913-916.
-
(2007)
Nature
, vol.450
, pp. 913-916
-
-
Henzler-Wildman, K.A.1
-
15
-
-
33846847773
-
Conformational Transitions of Adenylate Kinase: Switching by Cracking
-
DOI 10.1016/j.jmb.2006.11.085, PII S0022283606016445
-
Whitford PC, Miyashita O, Levy Y, Onuchic JN (2007) Conformational transitions of adenylate kinase: Switching by cracking. J Mol Biol 366:1661-1671. (Pubitemid 46215597)
-
(2007)
Journal of Molecular Biology
, vol.366
, Issue.5
, pp. 1661-1671
-
-
Whitford, P.C.1
Miyashita, O.2
Levy, Y.3
Onuchic, J.N.4
-
16
-
-
34548304871
-
Protein conformational transitions explored by mixed elastic network models
-
Zheng WJ, Brooks BR, Hummer G (2007) Protein conformational transitions explored by mixed elastic network models. Proteins 69:43-57.
-
(2007)
Proteins
, vol.69
, pp. 43-57
-
-
Zheng, W.J.1
Brooks, B.R.2
Hummer, G.3
-
17
-
-
37349101940
-
An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins
-
DOI 10.1002/prot.21570
-
Kirillova S, Cortes J, Stefaniu A, Simeon T (2008) An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins. Proteins 70:131-143. (Pubitemid 350293455)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.70
, Issue.1
, pp. 131-143
-
-
Kirillova, S.1
Cortes, J.2
Stefaniu, A.3
Simeon, T.4
-
18
-
-
24644483073
-
Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
-
DOI 10.1016/j.jmb.2005.07.031, PII S0022283605008193
-
Maragakis P, Karplus M (2005) Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase. J Mol Biol 352:807-822. (Pubitemid 41267070)
-
(2005)
Journal of Molecular Biology
, vol.352
, Issue.4
, pp. 807-822
-
-
Maragakis, P.1
Karplus, M.2
-
19
-
-
70349458094
-
A force field for virtual atom molecular mechanics of proteins
-
Korkut A, Hendrickson WA (2009) A force field for virtual atom molecular mechanics of proteins. Proc Natl Acad Sci USA 106:15667-15672.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 15667-15672
-
-
Korkut, A.1
Hendrickson, W.A.2
-
20
-
-
0036139410
-
EVA: Continuous automatic evaluation of protein structure prediction servers
-
Eyrich VA, et al. (2001) EVA: Continuous automatic evaluation of protein structure prediction servers. Bioinformatics 17:1242-1243. (Pubitemid 33735358)
-
(2001)
Bioinformatics
, vol.17
, Issue.12
, pp. 1242-1243
-
-
Eyrich, V.A.1
Marti-Renom, M.A.2
Przybylski, D.3
Madhusudhan, M.S.4
Fiser, A.5
Pazos, F.6
Valencia, A.7
Sali, A.8
Rost, B.9
-
21
-
-
0037441653
-
Structure validation by C alpha geometry: Phi, psi and C-beta deviation
-
Lovell SC, et al. (2003) Structure validation by C alpha geometry: Phi, psi and C-beta deviation. Proteins 50:437-450.
-
(2003)
Proteins
, vol.50
, pp. 437-450
-
-
Lovell, S.C.1
-
22
-
-
0030832809
-
Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches
-
DOI 10.1002/(SICI)1097-0134(199711)29:3<292::AID-PROT4>3.0.CO;2-D
-
Bahar I, Kaplan M, Jernigan RL (1997) Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins 29:292-308. (Pubitemid 27484221)
-
(1997)
Proteins: Structure, Function and Genetics
, vol.29
, Issue.3
, pp. 292-308
-
-
Bahar, I.1
Kaplan, M.2
Jernigan, R.L.3
-
23
-
-
0000933280
-
Transformations to optimize the superposition of similar structures
-
Hendrickson WA (1979) Transformations to optimize the superposition of similar structures. Acta Crystallogr A 35:158-163.
-
(1979)
Acta Crystallogr A
, vol.35
, pp. 158-163
-
-
Hendrickson, W.A.1
-
24
-
-
0026079373
-
The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 Å resolution
-
Diederichs K, Schulz GE (1991) The refined structure of the complex between adenylate kinase from beef-heart mitochondrial matrix and its substrate AMP at 1.85 Å resolution. J Mol Biol 217:541-549. (Pubitemid 121003300)
-
(1991)
Journal of Molecular Biology
, vol.217
, Issue.3
, pp. 541-549
-
-
Diederichs, K.1
Schulz, G.E.2
-
25
-
-
27744499156
-
Intrinsic dynamics of an enzyme underlies catalysis
-
DOI 10.1038/nature04105, PII N04105
-
Eisenmesser EZ, et al. (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438:117-121. (Pubitemid 41599831)
-
(2005)
Nature
, vol.438
, Issue.7064
, pp. 117-121
-
-
Eisenmesser, E.Z.1
Millet, O.2
Labeikovsky, W.3
Korzhnev, D.M.4
Wolf-Watz, M.5
Bosco, D.A.6
Skalicky, J.J.7
Kay, L.E.8
Kern, D.9
-
26
-
-
36549043024
-
Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
-
DOI 10.1016/j.sbi.2007.09.011, PII S0959440X07001534, Catalysis and Regulation /Protein
-
Bahar I, Chennubhotla C, Tobi D (2007) Intrinsic dynamics of enzymes in the unbound state and, relation to allosteric regulation. Curr Opin Struct Biol 17:633-640. (Pubitemid 350180409)
-
(2007)
Current Opinion in Structural Biology
, vol.17
, Issue.6
, pp. 633-640
-
-
Bahar, I.1
Chennubhotla, C.2
Tobi, D.3
-
27
-
-
45849131354
-
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
-
Lange OF, et al. (2008) Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 320:1471-1475.
-
(2008)
Science
, vol.320
, pp. 1471-1475
-
-
Lange, O.F.1
-
28
-
-
0028335096
-
Structural mechanisms for domain movements in proteins
-
DOI 10.1021/bi00188a001
-
Gerstein M, Lesk AM, Chothia C (1994) Structural mechanisms for domain movements in proteins. Biochemistry 33:6739-6749. (Pubitemid 24190795)
-
(1994)
Biochemistry
, vol.33
, Issue.22
, pp. 6739-6749
-
-
Gerstein, M.1
Lesk, A.M.2
Chothia, C.3
-
29
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan AR, et al. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80:505-515. (Pubitemid 32108200)
-
(2001)
Biophysical Journal
, vol.80
, Issue.1
, 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
-
31
-
-
0022419152
-
Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
-
Levitt M, Sander C, Stern PS (1985) Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol 181:423-447.
-
(1985)
J Mol Biol
, vol.181
, pp. 423-447
-
-
Levitt, M.1
Sander, C.2
Stern, P.S.3
-
32
-
-
0029560322
-
Hinge-bending motion in citrate synthase arising from normal mode calculations
-
DOI 10.1002/prot.340230410
-
Marques O, Sanejouand YH (1995) Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins 23:557-560. (Pubitemid 26009518)
-
(1995)
Proteins: Structure, Function and Genetics
, vol.23
, Issue.4
, pp. 557-560
-
-
Marques, O.1
Sanejouand, Y.-H.2
-
33
-
-
0030700726
-
Ligand-induced conformational changes in ras p21: A normal mode and energy minimization analysis
-
DOI 10.1006/jmbi.1997.1313
-
Ma J, Karplus M (1997) Ligand-induced conformational changes in ras p21: A normal mode and energy minimization analysis. J Mol Biol 274:114-131. (Pubitemid 27519461)
-
(1997)
Journal of Molecular Biology
, vol.274
, Issue.1
, pp. 114-131
-
-
Ma, J.1
Karplus, M.2
-
35
-
-
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
-
36
-
-
0026829432
-
TNPACK - A truncated Newton minimization package for large-scale problems: II. Implementation examples
-
DOI 10.1145/128745.150975
-
Schlick T, Fogelson A (1992) Tnpack-a Truncated Newton Minimization Package for large-scale problems. 2. Implementation examples.ACMTrans Math Software 18:71-111. (Pubitemid 23599656)
-
(1992)
ACM Transactions on Mathematical Software
, vol.18
, Issue.1
, pp. 71-111
-
-
Schlick, T.1
Fogelson, A.2
-
37
-
-
34547592557
-
MolProbity: All-atom contacts and structure validation for proteins and nucleic acids
-
Davis IW, et al. (2007) MolProbity: All-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375-W383.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Davis, I.W.1
|