-
1
-
-
0031283407
-
G proteins, effectors and GAP's: structure and mechanism
-
Sprang SR. G proteins, effectors and GAP's: structure and mechanism. Curr Opin Struct Biol 1997; 7: 849-856.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 849-856
-
-
Sprang, S.R.1
-
2
-
-
0035834388
-
The guanine nucleotide-binding switch in three dimensions
-
Vetter IR, Wittinghofer A. The guanine nucleotide-binding switch in three dimensions. Science 2001; 294: 1299-1304.
-
(2001)
Science
, vol.294
, pp. 1299-1304
-
-
Vetter, I.R.1
Wittinghofer, A.2
-
4
-
-
70350340728
-
The role of conformational ensembles in biomolecular recognition
-
Boehr DD, Nussinov R, Wright PE. The role of conformational ensembles in biomolecular recognition. Nat Chem Biol 2009; 5: 789-796.
-
(2009)
Nat Chem Biol
, vol.5
, pp. 789-796
-
-
Boehr, D.D.1
Nussinov, R.2
Wright, P.E.3
-
5
-
-
77951270272
-
Large conformational changes in proteins: signalling and other functions
-
Grant BJ, Gorfe AA, McCammon JA. Large conformational changes in proteins: signalling and other functions. Curr Opin Struct Biol 2010; 20: 142-147.
-
(2010)
Curr Opin Struct Biol
, vol.20
, pp. 142-147
-
-
Grant, B.J.1
Gorfe, A.A.2
McCammon, J.A.3
-
6
-
-
33749857564
-
GTPases of the prokaryotic translation apparatus
-
Hauryliuk VV. GTPases of the prokaryotic translation apparatus. Mol Biol 2006; 40: 688-701.
-
(2006)
Mol Biol
, vol.40
, pp. 688-701
-
-
Hauryliuk, V.V.1
-
7
-
-
36749037829
-
Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states
-
Yatime L, Méchulam Y, Blanquet S, Schmitt E. Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states. Proc Natl Acad Sci USA 2007; 104: 18445-18450.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 18445-18450
-
-
Yatime, L.1
Méchulam, Y.2
Blanquet, S.3
Schmitt, E.4
-
8
-
-
66549108297
-
Structure-function insights into prokaryotic and eukaryotic translation initiation
-
Myasnikov AG, Simonetti A, Marzi S, Klaholz BP. Structure-function insights into prokaryotic and eukaryotic translation initiation. Curr Opin Struct Biol 2009; 19: 300-309.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 300-309
-
-
Myasnikov, A.G.1
Simonetti, A.2
Marzi, S.3
Klaholz, B.P.4
-
9
-
-
71849102917
-
Eukaryotic and archaeal translation initiation factor 2: a heterotrimeric tRNA carrier
-
Schmitt E, Naveau M, Mechulam Y. Eukaryotic and archaeal translation initiation factor 2: a heterotrimeric tRNA carrier. FEBS Lett 2010; 584: 405-412.
-
(2010)
FEBS Lett
, vol.584
, pp. 405-412
-
-
Schmitt, E.1
Naveau, M.2
Mechulam, Y.3
-
10
-
-
0035355352
-
A subcomplex of three eIF3 subunits binds eIF1 and eIF5 and stimulates ribosome binding of mRNA and tRNA imet
-
Phan L, Schoenfeld LW, Valasek L, Nielsen KH, Hinnebusch AG. A subcomplex of three eIF3 subunits binds eIF1 and eIF5 and stimulates ribosome binding of mRNA and tRNA imet. EMBO J 2001; 20: 2954-2965.
-
(2001)
EMBO J
, vol.20
, pp. 2954-2965
-
-
Phan, L.1
Schoenfeld, L.W.2
Valasek, L.3
Nielsen, K.H.4
Hinnebusch, A.G.5
-
11
-
-
27144517608
-
The eIF1A c-terminal domain promotes initiation complex assembly, scanning and AUG selection in vivo
-
Fekete CA, Applefield DJ, Blakely SA, Shirokikh N, Pestova T, Lorsch JR, Hinnebusc AG. The eIF1A c-terminal domain promotes initiation complex assembly, scanning and AUG selection in vivo. EMBO J 2005; 24: 3588-301.
-
(2005)
EMBO J
, vol.24
, pp. 3588-3301
-
-
Fekete, C.A.1
Applefield, D.J.2
Blakely, S.A.3
Shirokikh, N.4
Pestova, T.5
Lorsch, J.R.6
Hinnebusc, A.G.7
-
12
-
-
0037439198
-
Domains of eIF1A that mediate binding to eIF2, eIF3 and eIF5B and promote ternary complex recruitment in vivo
-
Olsen DS, Savner EM, Mathew A, Zhang F, Krishnamoorthy T, Phan L, Hinnebusch AG. Domains of eIF1A that mediate binding to eIF2, eIF3 and eIF5B and promote ternary complex recruitment in vivo. EMBO J 2003; 22: 193-204.
-
(2003)
EMBO J
, vol.22
, pp. 193-204
-
-
Olsen, D.S.1
Savner, E.M.2
Mathew, A.3
Zhang, F.4
Krishnamoorthy, T.5
Phan, L.6
Hinnebusch, A.G.7
-
13
-
-
12344314307
-
A conformational change in the eukaryotic translation preinitiation complex and release of eIF1 signal recognition of the start codon
-
Maag D, Fekete CA, Gryczynski Z, Lorsch JR. A conformational change in the eukaryotic translation preinitiation complex and release of eIF1 signal recognition of the start codon. Mol Cell 2005; 17: 265-275.
-
(2005)
Mol Cell
, vol.17
, pp. 265-275
-
-
Maag, D.1
Fekete, C.A.2
Gryczynski, Z.3
Lorsch, J.R.4
-
14
-
-
0032572776
-
Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons
-
Pestova TV, Borukhov SI, Hellen CU. Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons. Nature 1998; 394: 854-859.
-
(1998)
Nature
, vol.394
, pp. 854-859
-
-
Pestova, T.V.1
Borukhov, S.I.2
Hellen, C.U.3
-
15
-
-
0037112055
-
The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection
-
Pestova TV, Kolupaeva VG. The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection. Genes Dev 2002; 16: 2906-2922.
-
(2002)
Genes Dev
, vol.16
, pp. 2906-2922
-
-
Pestova, T.V.1
Kolupaeva, V.G.2
-
16
-
-
34047263278
-
The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome
-
Passmore LA, Schmeing TM, Maag D, Applefield DJ, Acker MG, Algire MA, Lorsch JR, Ramakrishnan V. The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome. Mol Cell 2007; 26: 41-50.
-
(2007)
Mol Cell
, vol.26
, pp. 41-50
-
-
Passmore, L.A.1
Schmeing, T.M.2
Maag, D.3
Applefield, D.J.4
Acker, M.G.5
Algire, M.A.6
Lorsch, J.R.7
Ramakrishnan, V.8
-
17
-
-
0035794125
-
Eukaryotic translation initiation factor 5 functions as a GTPase-activating protein
-
Das S, Ghosh R, Maitra U. Eukaryotic translation initiation factor 5 functions as a GTPase-activating protein. J Biol Chem 2001; 276: 6720-6726.
-
(2001)
J Biol Chem
, vol.276
, pp. 6720-6726
-
-
Das, S.1
Ghosh, R.2
Maitra, U.3
-
18
-
-
0035191271
-
Eukaryotic translation initiation factor 5 (eIF5) acts as a classical GTPase-activator protein
-
Paulin FE, Campbell LE, O'Brien K, Loughlin J, Proud CG. Eukaryotic translation initiation factor 5 (eIF5) acts as a classical GTPase-activator protein. Curr Biol 2001; 11: 55-59.
-
(2001)
Curr Biol
, vol.11
, pp. 55-59
-
-
Paulin, F.E.1
Campbell, L.E.2
O'Brien, K.3
Loughlin, J.4
Proud, C.G.5
-
19
-
-
27744467413
-
Regulation of GTP hydrolysis prior to ribosomal AUG selection during eukaryotic translation initiation
-
Majumdar R, Maitra U. Regulation of GTP hydrolysis prior to ribosomal AUG selection during eukaryotic translation initiation. EMBO J 2005; 24: 3737-3746.
-
(2005)
EMBO J
, vol.24
, pp. 3737-3746
-
-
Majumdar, R.1
Maitra, U.2
-
20
-
-
26944435515
-
Pi release from eIF2, not GTP hydrolysis, is the step controlled by start-site selection during eukaryotic translation initiation
-
Algire MA, Maag D, Lorsch JR. Pi release from eIF2, not GTP hydrolysis, is the step controlled by start-site selection during eukaryotic translation initiation. Mol Cell 2005; 20: 251-262.
-
(2005)
Mol Cell
, vol.20
, pp. 251-262
-
-
Algire, M.A.1
Maag, D.2
Lorsch, J.R.3
-
21
-
-
34249069609
-
Dissociation of eIF1 from the 40S ribosomal subunit is a key step in start codon selection in vivo
-
Cheung YN, Maag D, Mitchell SF, Fekete CA, Algire MA, Takacs JE, Shirokikh N, Pestova T, Lorsch JR, Hinnebusch AG. Dissociation of eIF1 from the 40S ribosomal subunit is a key step in start codon selection in vivo. Genes Dev 2007; 21: 1217-1230.
-
(2007)
Genes Dev
, vol.21
, pp. 1217-1230
-
-
Cheung, Y.N.1
Maag, D.2
Mitchell, S.F.3
Fekete, C.A.4
Algire, M.A.5
Takacs, J.E.6
Shirokikh, N.7
Pestova, T.8
Lorsch, J.R.9
Hinnebusch, A.G.10
-
22
-
-
33744957161
-
Direct binding of translation initiation factor eif2γ-g domain to its gtpase-activating and gdp-gtp exchange factors eif5 and eif2bε{lunate}
-
Alone PV, Dever TE. Direct binding of translation initiation factor eif2γ-g domain to its gtpase-activating and gdp-gtp exchange factors eif5 and eif2bε{lunate}. J Biol Chem 2006; 281: 12636-12644.
-
(2006)
J Biol Chem
, vol.281
, pp. 12636-12644
-
-
Alone, P.V.1
Dever, T.E.2
-
23
-
-
0037007203
-
The large subunit of initiation factor alF2 is a close structural homologue of elongation factors
-
Schmitt E, Yatime L, Mechulam Y. The large subunit of initiation factor alF2 is a close structural homologue of elongation factors. EMBO J 2002; 21: 1821-1832.
-
(2002)
EMBO J
, vol.21
, pp. 1821-1832
-
-
Schmitt, E.1
Yatime, L.2
Mechulam, Y.3
-
24
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Mol Biol 2002; 9: 646-651.
-
(2002)
Nat Struct Mol Biol
, vol.9
, pp. 646-651
-
-
Karplus, M.1
McCammon, J.A.2
-
25
-
-
44649199260
-
Mapping the nucleotide and isoform dependent structural and dynamical features of Ras proteins
-
Gorfe AA, Grant BJ, McCammon JA. Mapping the nucleotide and isoform dependent structural and dynamical features of Ras proteins. Structure 2008; 16: 885-896.
-
(2008)
Structure
, vol.16
, pp. 885-896
-
-
Gorfe, A.A.1
Grant, B.J.2
McCammon, J.A.3
-
26
-
-
63549096871
-
Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics
-
Grant BJ, Gorfe AA, McCammon JA. Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Comp Biol 2009; 5: e1000325.
-
(2009)
PLoS Comp Biol
, vol.5
-
-
Grant, B.J.1
Gorfe, A.A.2
McCammon, J.A.3
-
27
-
-
78649801418
-
Conformational selection in G-proteins: Lessons from Ras and Rho
-
Grant BJ, McCammon JA, Gorfe AA. Conformational selection in G-proteins: Lessons from Ras and Rho. Biophys J 2010; 99: 87-89.
-
(2010)
Biophys J
, vol.99
, pp. 87-89
-
-
Grant, B.J.1
McCammon, J.A.2
Gorfe, A.A.3
-
28
-
-
78049448010
-
The distinct conformational dynamics of K-Ras and H-Ras A59G
-
Lukman S, Grant BJ, Gorfe AA, Grant GH, McCammon JA. The distinct conformational dynamics of K-Ras and H-Ras A59G. PLoS Comput Biol 2010; 6: e1000922.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Lukman, S.1
Grant, B.J.2
Gorfe, A.A.3
Grant, G.H.4
McCammon, J.A.5
-
29
-
-
67649850988
-
PROCAIN: protein profile comparison with assisting information
-
Wang Y, Sadreyev RI, Grishin NV. PROCAIN: protein profile comparison with assisting information. Nucl Acids Res 2009; 37: 3522-3530.
-
(2009)
Nucl Acids Res
, vol.37
, pp. 3522-3530
-
-
Wang, Y.1
Sadreyev, R.I.2
Grishin, N.V.3
-
30
-
-
11144236974
-
Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study
-
Lu B, Wong CF, McCammon JA. Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study. Prot Sci 2005; 14: 159-168.
-
(2005)
Prot Sci
, vol.14
, pp. 159-168
-
-
Lu, B.1
Wong, C.F.2
McCammon, J.A.3
-
31
-
-
52949113058
-
Computer simulations reveal a novel nucleotide-type binding orientation for ellipticine-based anticancer c-Kit kinase inhibitors
-
Thompson D, Miller C, McCarthy FO. Computer simulations reveal a novel nucleotide-type binding orientation for ellipticine-based anticancer c-Kit kinase inhibitors. Biochemistry 2008; 47: 10333-10344.
-
(2008)
Biochemistry
, vol.47
, pp. 10333-10344
-
-
Thompson, D.1
Miller, C.2
McCarthy, F.O.3
-
33
-
-
77954626097
-
Why an A-loop phospho-mimetic fails to activate PAK1: understanding an inaccessible kinase state by molecular dynamics simulations
-
Ng YW, Raghunathan D, Chan PM, Baskaran Y, Smith DJ, Lee CH, Verma C, Manser E. Why an A-loop phospho-mimetic fails to activate PAK1: understanding an inaccessible kinase state by molecular dynamics simulations. Structure 2010; 18: 879-890.
-
(2010)
Structure
, vol.18
, pp. 879-890
-
-
Ng, Y.W.1
Raghunathan, D.2
Chan, P.M.3
Baskaran, Y.4
Smith, D.J.5
Lee, C.H.6
Verma, C.7
Manser, E.8
-
34
-
-
17844400134
-
Structural mechanism of the recovery stroke in the myosin molecular motor
-
Fischer S, Windshügel B, Horak D, Holmes KC, Smith JC. Structural mechanism of the recovery stroke in the myosin molecular motor. Proc Natl Acad Sci USA 2005; 102: 6873-6878.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 6873-6878
-
-
Fischer, S.1
Windshügel, B.2
Horak, D.3
Holmes, K.C.4
Smith, J.C.5
-
35
-
-
33847270136
-
Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues
-
Yu H, Ma L, Yang Y, Cui Q. Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. PLoS Comput Biol 2007; 3: 214-230.
-
(2007)
PLoS Comput Biol
, vol.3
, pp. 214-230
-
-
Yu, H.1
Ma, L.2
Yang, Y.3
Cui, Q.4
-
36
-
-
50949099429
-
Allosteric communication in myosin V: From small conformational changes to large directed movements
-
Cecchini M, Houdusse A, Karplus M. Allosteric communication in myosin V: From small conformational changes to large directed movements. PLoS Comput Biol 2008; 4: e1000129.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Cecchini, M.1
Houdusse, A.2
Karplus, M.3
-
38
-
-
0032054612
-
Theory of biomolecular recognition
-
McCammon J. Theory of biomolecular recognition. Curr Opin Struct Biol 1998; 8: 245-249.
-
(1998)
Curr Opin Struct Biol
, vol.8
, pp. 245-249
-
-
McCammon, J.1
-
39
-
-
0036286654
-
Free energy simulations come of age: the protein-ligand recognition problem
-
Simonson T, Archontis G, Karplus M. Free energy simulations come of age: the protein-ligand recognition problem. Acc Chem Res 2002; 35: 430-437.
-
(2002)
Acc Chem Res
, vol.35
, pp. 430-437
-
-
Simonson, T.1
Archontis, G.2
Karplus, M.3
-
40
-
-
1642357706
-
The many roles of computation in drug discovery
-
Jorgensen WL. The many roles of computation in drug discovery. Science 2003; 303: 1813-1818.
-
(2003)
Science
, vol.303
, pp. 1813-1818
-
-
Jorgensen, W.L.1
-
41
-
-
63049135074
-
Significant applications of free energy calculations to chemistry and biology. In: Chipot C,Pohorille A. editors. NY: Springer Verlag; 2007,Chapter. 13, 463-501
-
Chipot C, Mark AE, Pande VS, Simonson T. Significant applications of free energy calculations to chemistry and biology. In: Chipot C, Pohorille A. editors. Free energy calculations: theory and applications in chemistry and biology. NY: Springer Verlag; 2007, Chapter. 13, 463-501.
-
Free energy calculations: theory and applications in chemistry and biology
-
-
Chipot, C.1
Mark, A.E.2
Pande, V.S.3
Simonson, T.4
-
42
-
-
76649086691
-
Alchemical free energy simulations for biological complexes: powerful but temperamental...
-
Aleksandrov A, Thompson D, Simonson T. Alchemical free energy simulations for biological complexes: powerful but temperamental... J Mol Recognit 2010; 23: 117-127.
-
(2010)
J Mol Recognit
, vol.23
, pp. 117-127
-
-
Aleksandrov, A.1
Thompson, D.2
Simonson, T.3
-
43
-
-
78649317138
-
Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ
-
Hritz J, Lappchen T, Oostenbrink C. Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ. Eur Biophys J 2010; 39: 1573-1580.
-
(2010)
Eur Biophys J
, vol.39
, pp. 1573-1580
-
-
Hritz, J.1
Lappchen, T.2
Oostenbrink, C.3
-
44
-
-
33747671419
-
2+ contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactions
-
2+ contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactions. J Biol Chem 2006; 281: 23792-23803.
-
(2006)
J Biol Chem
, vol.281
, pp. 23792-23803
-
-
Thompson, D.1
Simonson, T.2
-
45
-
-
69149097233
-
Nucleotide-dependent conformational states of actin
-
Pfaendtner J, Branduardi D, Parrinello M, Pollard TD, Voth GA. Nucleotide-dependent conformational states of actin. Proc Natl Acad Sci USA 2007; 106: 12723-12728.
-
(2007)
Proc Natl Acad Sci USA
, vol.106
, pp. 12723-12728
-
-
Pfaendtner, J.1
Branduardi, D.2
Parrinello, M.3
Pollard, T.D.4
Voth, G.A.5
-
46
-
-
0037417786
-
The missing link between thermodynamics and structure in F1-ATPase
-
Yang W, Gao YQ, Cui Q, Ma J, Karplus M. The missing link between thermodynamics and structure in F1-ATPase. Proc Natl Acad Sci USA 2003; 100: 874-879.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 874-879
-
-
Yang, W.1
Gao, Y.Q.2
Cui, Q.3
Ma, J.4
Karplus, M.5
-
47
-
-
26844546402
-
A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase
-
Gao YQ, Yang W, Karplus M. A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase. Cell 2005; 123: 195-205.
-
(2005)
Cell
, vol.123
, pp. 195-205
-
-
Gao, Y.Q.1
Yang, W.2
Karplus, M.3
-
48
-
-
0021582448
-
Ligand-receptor interactions
-
Tembe B, McCammon JA. Ligand-receptor interactions. Comp Chem 1984; 8: 281-283.
-
(1984)
Comp Chem
, vol.8
, pp. 281-283
-
-
Tembe, B.1
McCammon, J.A.2
-
49
-
-
79958158111
-
Free energy simulations of a GTPase: GTP and GDP binding to archaeal Initiation Factor 2
-
Satpati P, Clavaguéra C, Ohanessian G, Simonson T. Free energy simulations of a GTPase: GTP and GDP binding to archaeal Initiation Factor 2. J Phys Chem B 2011; 115: 6749-6763.
-
(2011)
J Phys Chem B
, vol.115
, pp. 6749-6763
-
-
Satpati, P.1
Clavaguéra, C.2
Ohanessian, G.3
Simonson, T.4
-
50
-
-
33644790001
-
Structural switch of the γ subunit in an archaeal aIF2 α γ heterodimer
-
Yatime L, Mechulam Y, Blanquet S, Schmitt E. Structural switch of the γ subunit in an archaeal aIF2 α γ heterodimer. Structure 2006; 14: 119-128.
-
(2006)
Structure
, vol.14
, pp. 119-128
-
-
Yatime, L.1
Mechulam, Y.2
Blanquet, S.3
Schmitt, E.4
-
51
-
-
0033810049
-
Modeling of loops in protein structures
-
Fiser A, Do RK, Sali A. Modeling of loops in protein structures. Prot Sci 2000; 9: 1753-1773.
-
(2000)
Prot Sci
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.2
Sali, A.3
-
52
-
-
38049034590
-
Comparative protein structure modeling with MODELLER
-
Eswar N, Marti-Renom MA, Webb B, Madhusudhan MS, Eramian D, Shen M, Pieper U, Sali A. Comparative protein structure modeling with MODELLER. Curr Prot Bioinf Suppl 2006; 15: 5.6.1-5.6.30.
-
(2006)
Curr Prot Bioinf Suppl
, vol.15
, pp. 561-5630
-
-
Eswar, N.1
Marti-Renom, M.A.2
Webb, B.3
Madhusudhan, M.S.4
Eramian, D.5
Shen, M.6
Pieper, U.7
Sali, A.8
-
53
-
-
34548846390
-
New insights into the interactions of the translation initiation factor 2 from archaea with guanine nucleotides and initiator tRNA
-
Nikonov O, Stolboushkina E, Nikulin A, Hasenohrl D, Blasi U, Manstein D, Fedorov R, Garber M, Nikonov S. New insights into the interactions of the translation initiation factor 2 from archaea with guanine nucleotides and initiator tRNA. J Mol Biol 2007; 373: 328-336.
-
(2007)
J Mol Biol
, vol.373
, pp. 328-336
-
-
Nikonov, O.1
Stolboushkina, E.2
Nikulin, A.3
Hasenohrl, D.4
Blasi, U.5
Manstein, D.6
Fedorov, R.7
Garber, M.8
Nikonov, S.9
-
54
-
-
0023818516
-
2+ and guanine nucleotide exchange factor on the binding of guanine nucleotides to eukaryotic Initiation Factor 2
-
2+ and guanine nucleotide exchange factor on the binding of guanine nucleotides to eukaryotic Initiation Factor 2. J Biol Chem 1988; 263: 5519-5525.
-
(1988)
J Biol Chem
, vol.263
, pp. 5519-5525
-
-
Panniers, R.1
Rowlands, A.G.2
Henshaw, E.3
-
55
-
-
33846823909
-
Particle mesh Ewald: an N log(N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L. Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J Chem Phys 1993; 98: 10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
56
-
-
33751143432
-
Free energy of ionic hydration
-
Hummer G, Pratt L, Garcia A. Free energy of ionic hydration. J Phys Chem 1996; 100: 1206-1215.
-
(1996)
J Phys Chem
, vol.100
, pp. 1206-1215
-
-
Hummer, G.1
Pratt, L.2
Garcia, A.3
-
57
-
-
0000123071
-
Removal of pressure and free energy artefacts in charged periodic systems via net charge corrections to the ewald potential
-
Bogusz S, Cheatham TE, Brooks BR. Removal of pressure and free energy artefacts in charged periodic systems via net charge corrections to the ewald potential. J Chem Phys 1998; 108: 7070-7084.
-
(1998)
J Chem Phys
, vol.108
, pp. 7070-7084
-
-
Bogusz, S.1
Cheatham, T.E.2
Brooks, B.R.3
-
58
-
-
0041784950
-
An all-atom empirical potential for molecular modelling and dynamics study of proteins
-
Mackerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck J, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. An all-atom empirical potential for molecular modelling and dynamics study of proteins. J Phys Chem B 1998; 102: 3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
Mackerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Smith, J.22
Stote, R.23
Straub, J.24
Watanabe, M.25
Wiorkiewicz-Kuczera, J.26
Yin, D.27
Karplus, M.28
more..
-
59
-
-
6344260593
-
An all-atom empirical energy force-field for the study of nucleic acids
-
Mackerell AD, Wiorkiewicz-Kuczera J, Karplus M. An all-atom empirical energy force-field for the study of nucleic acids. J Am Chem Soc 1995; 117: 11946-11975.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 11946-11975
-
-
Mackerell, A.D.1
Wiorkiewicz-Kuczera, J.2
Karplus, M.3
-
60
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen W, Chandrasekar J, Madura J, Impey R, Klein M. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983; 79: 926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.1
Chandrasekar, J.2
Madura, J.3
Impey, R.4
Klein, M.5
-
61
-
-
84986512474
-
Charmm: a program for macromolecular energy, minimization, and molecular dynamics calculations
-
Brooks B, Bruccoleri R, Olafson B, States D, Swaminathan S, Karplus M. Charmm: a program for macromolecular energy, minimization, and molecular dynamics calculations. J Comp Chem 1983; 4: 187-217.
-
(1983)
J Comp Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.1
Bruccoleri, R.2
Olafson, B.3
States, D.4
Swaminathan, S.5
Karplus, M.6
-
62
-
-
67650500988
-
CHARMM: the biomolecular simulation program
-
Brooks B, Brooks III, CL, Mackerell Jr, AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. CHARMM: the biomolecular simulation program. J Comp Chem 2009; 30: 1545-1614.
-
(2009)
J Comp Chem
, vol.30
, pp. 1545-1614
-
-
Brooks, B.1
Brooks III, C.L.2
Mackerell Jr, A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
63
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K. Scalable molecular dynamics with NAMD. J Comp Chem 2005; 26: 1781-1802.
-
(2005)
J Comp Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
64
-
-
0041754408
-
Free energy calculations. In: BeckerO, MackerellJr.,A,Roux B,Watanabe M. editor. NY: Marcel Dekker. 2001,Chapter 9
-
Simonson T. Free energy calculations. In: Becker O, Mackerell Jr., A, Roux B, Watanabe M. editor. Computational biochemistry & biophysics. NY: Marcel Dekker. 2001, Chapter 9, 169-197.
-
Computational biochemistry & biophysics
, pp. 169-197
-
-
Simonson, T.1
-
65
-
-
84872607890
-
Free energy of particle insertion. an exact analysis of the origin singularity for simple liquids
-
Simonson T. Free energy of particle insertion. an exact analysis of the origin singularity for simple liquids. Mol Phys 1993; 80: 441-447.
-
(1993)
Mol Phys
, vol.80
, pp. 441-447
-
-
Simonson, T.1
-
66
-
-
0034225199
-
Electrostatic free energy calculations for macromolecules: a hybrid molecular dynamics/continuum electrostatics approach
-
Simonson T. Electrostatic free energy calculations for macromolecules: a hybrid molecular dynamics/continuum electrostatics approach. J Phys Chem B 2000; 104: 6509-6513.
-
(2000)
J Phys Chem B
, vol.104
, pp. 6509-6513
-
-
Simonson, T.1
-
67
-
-
0026457728
-
Standard thermodynamic formation properties for the adenosine 5′-triphosphate series
-
Alberty RA, Goldberg RN. Standard thermodynamic formation properties for the adenosine 5′-triphosphate series. Biochemistry 1992; 31: 10610-10615.
-
(1992)
Biochemistry
, vol.31
, pp. 10610-10615
-
-
Alberty, R.A.1
Goldberg, R.N.2
-
68
-
-
0035895423
-
Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase
-
Archontis G, Simonson T, Karplus M. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. J Mol Biol 2001; 306: 307-327.
-
(2001)
J Mol Biol
, vol.306
, pp. 307-327
-
-
Archontis, G.1
Simonson, T.2
Karplus, M.3
-
69
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
-
Srinivasan J, Cheatham T, Cieplak P, Kollman P, Case DA. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J Am Chem Soc 1998; 120: 9401-9409.
-
(1998)
J Am Chem Soc
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.2
Cieplak, P.3
Kollman, P.4
Case, D.A.5
-
70
-
-
0034521981
-
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models
-
Kollman P, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham T. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000; 33: 889-897.
-
(2000)
Acc Chem Res
, vol.33
, pp. 889-897
-
-
Kollman, P.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham, T.15
-
71
-
-
62849122214
-
Free energy calculations: approximate methods for biological macromolecules. In: Chipot C,Pohorille A. editors. NY: Springer Verlag, 2007,Chapter 12, 423-462
-
Simonson T. Free energy calculations: approximate methods for biological macromolecules. In: Chipot C, Pohorille A. editors. Free energy calculations: theory and applications in chemistry and biology. NY: Springer Verlag, 2007, Chapter 12, 423-462.
-
Free energy calculations: theory and applications in chemistry and biology
-
-
Simonson, T.1
-
72
-
-
41949084672
-
Computation of noncovalent binding affinities
-
Dykstra C,Frenking G,Kim K,Scuseria G. editors. Amsterdam: Elsevier
-
McCammon J. Computation of noncovalent binding affinities. In: Dykstra C, Frenking G, Kim K, Scuseria G. editors. Theory and applications of computational chemistry. Amsterdam: Elsevier, 2005 pp 41-46.
-
(2005)
Theory and applications of computational chemistry
, pp. 41-46
-
-
McCammon, J.1
-
73
-
-
0032096837
-
Continuum solvation model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
-
Im W, Beglov D, Roux B. Continuum solvation model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Comp Phys Comm 1998; 111: 59-75.
-
(1998)
Comp Phys Comm
, vol.111
, pp. 59-75
-
-
Im, W.1
Beglov, D.2
Roux, B.3
-
74
-
-
0023779259
-
Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis
-
Gilson M, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins 1988; 4: 7-18.
-
(1988)
Proteins
, vol.4
, pp. 7-18
-
-
Gilson, M.1
Honig, B.2
-
77
-
-
0031604810
-
Vibrational study of phosphate modes in GDP and GTP and their interaction with magnesium in aqueous solution
-
Wang JH, Xiao DG, Deng H, Callender R, Webb MR. Vibrational study of phosphate modes in GDP and GTP and their interaction with magnesium in aqueous solution. Biospectroscopy 1998; 4: 219-227.
-
(1998)
Biospectroscopy
, vol.4
, pp. 219-227
-
-
Wang, J.H.1
Xiao, D.G.2
Deng, H.3
Callender, R.4
Webb, M.R.5
-
78
-
-
0001835759
-
3D search and research using the Cambridge crystallogaphic database
-
Allen F, Kennard O. 3D search and research using the Cambridge crystallogaphic database. Chem Des Autom News 1993; 8: 31-37.
-
(1993)
Chem Des Autom News
, vol.8
, pp. 31-37
-
-
Allen, F.1
Kennard, O.2
-
79
-
-
3543010528
-
Preparation and physico-chemical properties of the ternary complexes formed between adenosine 5-triphosphoric acid, bis(2-pyridyl)amine, and divalent metal ions. Crystal and molecular structures of the compounds containing MgII and CaII
-
Cini R, Burla MC, Nunzi A, Polidori GP, Zanazzi PF. Preparation and physico-chemical properties of the ternary complexes formed between adenosine 5-triphosphoric acid, bis(2-pyridyl)amine, and divalent metal ions. Crystal and molecular structures of the compounds containing MgII and CaII. J Chem Soc Dalton Trans 1984; 11: 2467-2476.
-
(1984)
J Chem Soc Dalton Trans
, vol.11
, pp. 2467-2476
-
-
Cini, R.1
Burla, M.C.2
Nunzi, A.3
Polidori, G.P.4
Zanazzi, P.F.5
-
80
-
-
34250613522
-
From nucleotides to ribozymes: a comparison of their metal ion binding properties
-
Freisinger E, Sigel R. From nucleotides to ribozymes: a comparison of their metal ion binding properties. Coord Chem Rev 2007; 251: 1834-1851.
-
(2007)
Coord Chem Rev
, vol.251
, pp. 1834-1851
-
-
Freisinger, E.1
Sigel, R.2
-
81
-
-
0032789936
-
Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding
-
Hendsch Z, Tidor B. Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding. Prot Sci 1999; 8: 1381-1392.
-
(1999)
Prot Sci
, vol.8
, pp. 1381-1392
-
-
Hendsch, Z.1
Tidor, B.2
-
82
-
-
0035451052
-
What are the dielectric 'constants' of proteins and how to validate electrostatic models?
-
Schutz CN, Warshel A. What are the dielectric 'constants' of proteins and how to validate electrostatic models? Proteins 2001; 44: 400-417.
-
(2001)
Proteins
, vol.44
, pp. 400-417
-
-
Schutz, C.N.1
Warshel, A.2
-
83
-
-
0035823823
-
Dielectric relaxation in an enzyme active site: molecular dynamics simulations intepreted with a macroscopic continuum model
-
Archontis G, Simonson T. Dielectric relaxation in an enzyme active site: molecular dynamics simulations intepreted with a macroscopic continuum model. J Am Chem Soc 2001; 123: 11047-11056.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 11047-11056
-
-
Archontis, G.1
Simonson, T.2
-
84
-
-
0037529067
-
Electrostatics and dynamics of proteins
-
Simonson T. Electrostatics and dynamics of proteins. Rep Prog Phys 2003; 66: 737-787.
-
(2003)
Rep Prog Phys
, vol.66
, pp. 737-787
-
-
Simonson, T.1
-
85
-
-
67650340734
-
Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins
-
Gao J, Bosco DA, Powers ET, Kelly JW. Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins. Nat Struct Mol Biol 2009; 16: 684-690.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 684-690
-
-
Gao, J.1
Bosco, D.A.2
Powers, E.T.3
Kelly, J.W.4
-
86
-
-
18744372751
-
Calculation of absolute protein ligand binding free energy from computer simulations
-
Woo H, Roux B. Calculation of absolute protein ligand binding free energy from computer simulations. Proc Natl Acad Sci USA 2005; 102: 6825-6830.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 6825-6830
-
-
Woo, H.1
Roux, B.2
-
87
-
-
77951557992
-
Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases
-
Aleksandrov A, Simonson T. Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases. J Biol Chem 2010; 285: 13807-13815.
-
(2010)
J Biol Chem
, vol.285
, pp. 13807-13815
-
-
Aleksandrov, A.1
Simonson, T.2
-
88
-
-
0242443693
-
Force fields for protein simulations
-
Ponder J, Case DA. Force fields for protein simulations. Adv Prot Chem 2003; 66: 27.
-
(2003)
Adv Prot Chem
, vol.66
, pp. 27
-
-
Ponder, J.1
Case, D.A.2
-
89
-
-
36749024620
-
Polarizable force fields: History, test cases, and prospects
-
Warshel A, Kato M, Pisliakov AV. Polarizable force fields: History, test cases, and prospects. J Chem Theory Comput 2007; 3: 2034-2045.
-
(2007)
J Chem Theory Comput
, vol.3
, pp. 2034-2045
-
-
Warshel, A.1
Kato, M.2
Pisliakov, A.V.3
-
90
-
-
0347062349
-
Xray structure refinement of proteins with the generalized Born solvent model
-
Moulinier L, Case DA, Simonson T. Xray structure refinement of proteins with the generalized Born solvent model. Acta Cryst D 2003; 59: 2094-2103.
-
(2003)
Acta Cryst D
, vol.59
, pp. 2094-2103
-
-
Moulinier, L.1
Case, D.A.2
Simonson, T.3
-
91
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucl Acids Res 2000; 28: 235-242.
-
(2000)
Nucl Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
92
-
-
0347949637
-
Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy
-
Swanson JMJ, Henchman RH, McCammon JA. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys J 2004; 86: 67-74.
-
(2004)
Biophys J
, vol.86
, pp. 67-74
-
-
Swanson, J.M.J.1
Henchman, R.H.2
McCammon, J.A.3
|