-
1
-
-
0001740498
-
The Functioning of Molecular Switches in Three Dimensions
-
Oxford: Oxford University Press, Hall A
-
Wittinghofer A. The Functioning of Molecular Switches in Three Dimensions. GTPases 2000, 244-310. Oxford: Oxford University Press, Hall A.
-
(2000)
GTPases
, pp. 244-310
-
-
Wittinghofer, A.1
-
2
-
-
0001607723
-
Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold
-
553140, 6329717
-
Walker JE, Saraste M, Runswick MJ, Gay NJ. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. Embo J 1982, 1:945-951. 553140, 6329717.
-
(1982)
Embo J
, vol.1
, pp. 945-951
-
-
Walker, J.E.1
Saraste, M.2
Runswick, M.J.3
Gay, N.J.4
-
3
-
-
0025048136
-
The P-loop--a common motif in ATP- and GTP-binding proteins
-
10.1016/0968-0004(90)90281-F, 2126155
-
Saraste M, Sibbald PR, Wittinghofer A. The P-loop--a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci 1990, 15:430-434. 10.1016/0968-0004(90)90281-F, 2126155.
-
(1990)
Trends Biochem Sci
, vol.15
, pp. 430-434
-
-
Saraste, M.1
Sibbald, P.R.2
Wittinghofer, A.3
-
4
-
-
0036295212
-
Classification and evolution of P-loop GTPases and related ATPases
-
10.1006/jmbi.2001.5378, 11916378
-
Leipe DD, Wolf YI, Koonin EV, Aravind L. Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol 2002, 317:41-72. 10.1006/jmbi.2001.5378, 11916378.
-
(2002)
J Mol Biol
, vol.317
, pp. 41-72
-
-
Leipe, D.D.1
Wolf, Y.I.2
Koonin, E.V.3
Aravind, L.4
-
5
-
-
33746363486
-
Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits
-
10.1146/annurev.biochem.75.103004.142710, 16756506
-
Bhattacharyya RP, Remenyi A, Yeh BJ, Lim WA. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu Rev Biochem 2006, 75:655-680. 10.1146/annurev.biochem.75.103004.142710, 16756506.
-
(2006)
Annu Rev Biochem
, vol.75
, pp. 655-680
-
-
Bhattacharyya, R.P.1
Remenyi, A.2
Yeh, B.J.3
Lim, W.A.4
-
6
-
-
35649024916
-
Gα-Gβγ dissociation may be due to retraction of a buried lysine and disruption of an aromatic cluster by a GTP-sensing Arg-Trp pair
-
10.1110/ps.073098107, 2211685, 17962409
-
Neuwald AF. Gα-Gβγ dissociation may be due to retraction of a buried lysine and disruption of an aromatic cluster by a GTP-sensing Arg-Trp pair. Protein Science 2007, 16:2570-2577. 10.1110/ps.073098107, 2211685, 17962409.
-
(2007)
Protein Science
, vol.16
, pp. 2570-2577
-
-
Neuwald, A.F.1
-
7
-
-
0037398428
-
Ran's C-terminal, basic patch and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras and Ran GTPases
-
10.1101/gr.862303, 430177, 12671004
-
Neuwald AF, Kannan N, Poleksic A, Hata N, Liu JS. Ran's C-terminal, basic patch and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras and Ran GTPases. Genome Res 2003, 13:673-692. 10.1101/gr.862303, 430177, 12671004.
-
(2003)
Genome Res
, vol.13
, pp. 673-692
-
-
Neuwald, A.F.1
Kannan, N.2
Poleksic, A.3
Hata, N.4
Liu, J.S.5
-
8
-
-
33745848830
-
Bayesian shadows of molecular mechanisms cast in the light of evolution
-
Neuwald AF. Bayesian shadows of molecular mechanisms cast in the light of evolution. Trends Biochem Sciences 2006, 31:374-382.
-
(2006)
Trends Biochem Sciences
, vol.31
, pp. 374-382
-
-
Neuwald, A.F.1
-
9
-
-
0004182828
-
Monte Carlo Strategies in Scientific Computing
-
New York: Springer-Verlag
-
Liu JS. Monte Carlo Strategies in Scientific Computing. 2008, New York: Springer-Verlag.
-
(2008)
-
-
Liu, J.S.1
-
10
-
-
0032127912
-
GTPase-activating proteins: helping hands to complement an active site
-
10.1016/S0968-0004(98)01224-9, 9697416
-
Scheffzek K, Ahmadian MR, Wittinghofer A. GTPase-activating proteins: helping hands to complement an active site. Trends Biochem Sci 1998, 23:257-262. 10.1016/S0968-0004(98)01224-9, 9697416.
-
(1998)
Trends Biochem Sci
, vol.23
, pp. 257-262
-
-
Scheffzek, K.1
Ahmadian, M.R.2
Wittinghofer, A.3
-
11
-
-
67349190989
-
The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches
-
10.1016/j.jmb.2009.05.001, 2699579, 19427324
-
Neuwald AF. The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches. J Mol Biol 2009, 390:142-153. 10.1016/j.jmb.2009.05.001, 2699579, 19427324.
-
(2009)
J Mol Biol
, vol.390
, pp. 142-153
-
-
Neuwald, A.F.1
-
12
-
-
0028821639
-
Mutational analysis of Saccharomyces cerevisiae ARF1
-
10.1074/jbc.270.1.143, 7814365
-
Kahn RA, Clark J, Rulka C, Stearns T, Zhang CJ, Randazzo PA, Terui T, Cavenagh M. Mutational analysis of Saccharomyces cerevisiae ARF1. J Biol Chem 1995, 270:143-150. 10.1074/jbc.270.1.143, 7814365.
-
(1995)
J Biol Chem
, vol.270
, pp. 143-150
-
-
Kahn, R.A.1
Clark, J.2
Rulka, C.3
Stearns, T.4
Zhang, C.J.5
Randazzo, P.A.6
Terui, T.7
Cavenagh, M.8
-
13
-
-
0035068903
-
The structural GDP/GTP cycle of human Arf6
-
10.1093/embo-reports/kve043, 1083839, 11266366
-
Pasqualato S, Menetrey J, Franco M, Cherfils J. The structural GDP/GTP cycle of human Arf6. EMBO Rep 2001, 2:234-238. 10.1093/embo-reports/kve043, 1083839, 11266366.
-
(2001)
EMBO Rep
, vol.2
, pp. 234-238
-
-
Pasqualato, S.1
Menetrey, J.2
Franco, M.3
Cherfils, J.4
-
14
-
-
0023068346
-
Ras genes
-
10.1146/annurev.bi.56.070187.004023, 3304147
-
Barbacid M. ras genes. Annu Rev Biochem 1987, 56:779-827. 10.1146/annurev.bi.56.070187.004023, 3304147.
-
(1987)
Annu Rev Biochem
, vol.56
, pp. 779-827
-
-
Barbacid, M.1
-
15
-
-
0021126650
-
Biological properties of human c-Ha-ras1 genes mutated at codon 12
-
10.1038/312071a0, 6092966
-
Seeburg PH, Colby WW, Capon DJ, Goeddel DV, Levinson AD. Biological properties of human c-Ha-ras1 genes mutated at codon 12. Nature 1984, 312:71-75. 10.1038/312071a0, 6092966.
-
(1984)
Nature
, vol.312
, pp. 71-75
-
-
Seeburg, P.H.1
Colby, W.W.2
Capon, D.J.3
Goeddel, D.V.4
Levinson, A.D.5
-
16
-
-
0023256456
-
Prevalence of ras gene mutations in human colorectal cancers
-
10.1038/327293a0, 3587348
-
Bos JL, Fearon ER, Hamilton SR, Verlaan-de Vries M, van Boom JH, van der Eb AJ, Vogelstein B. Prevalence of ras gene mutations in human colorectal cancers. Nature 1987, 327:293-297. 10.1038/327293a0, 3587348.
-
(1987)
Nature
, vol.327
, pp. 293-297
-
-
Bos, J.L.1
Fearon, E.R.2
Hamilton, S.R.3
Verlaan-de Vries, M.4
van Boom, J.H.5
van der Eb, A.J.6
Vogelstein, B.7
-
17
-
-
0027057548
-
Role of proto-oncogene activation in carcinogenesis
-
10.2307/3431243, 1519627, 1486840
-
Anderson MW, Reynolds SH, You M, Maronpot RM. Role of proto-oncogene activation in carcinogenesis. Environ Health Perspect 1992, 98:13-24. 10.2307/3431243, 1519627, 1486840.
-
(1992)
Environ Health Perspect
, vol.98
, pp. 13-24
-
-
Anderson, M.W.1
Reynolds, S.H.2
You, M.3
Maronpot, R.M.4
-
18
-
-
0030005037
-
Mutant ras epitopes as targets for cancer vaccines
-
Abrams SI, Hand PH, Tsang KY, Schlom J. Mutant ras epitopes as targets for cancer vaccines. Semin Oncol 1996, 23:118-134.
-
(1996)
Semin Oncol
, vol.23
, pp. 118-134
-
-
Abrams, S.I.1
Hand, P.H.2
Tsang, K.Y.3
Schlom, J.4
-
19
-
-
0036866606
-
Arf, Arl, Arp and Sar proteins: a family of GTP-binding proteins with a structural device for 'front-back' communication
-
10.1093/embo-reports/kvf221, 1307594, 12429613
-
Pasqualato S, Renault L, Cherfils J. Arf, Arl, Arp and Sar proteins: a family of GTP-binding proteins with a structural device for 'front-back' communication. EMBO Rep 2002, 3:1035-1041. 10.1093/embo-reports/kvf221, 1307594, 12429613.
-
(2002)
EMBO Rep
, vol.3
, pp. 1035-1041
-
-
Pasqualato, S.1
Renault, L.2
Cherfils, J.3
-
20
-
-
41649087361
-
The retinitis pigmentosa 2 gene product is a GTPase-activating protein for Arf-like 3
-
10.1038/nsmb.1396, 18376416
-
Veltel S, Gasper R, Eisenacher E, Wittinghofer A. The retinitis pigmentosa 2 gene product is a GTPase-activating protein for Arf-like 3. Nat Struct Mol Biol 2008, 15:373-380. 10.1038/nsmb.1396, 18376416.
-
(2008)
Nat Struct Mol Biol
, vol.15
, pp. 373-380
-
-
Veltel, S.1
Gasper, R.2
Eisenacher, E.3
Wittinghofer, A.4
-
21
-
-
62549113471
-
The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops
-
10.1186/1472-6807-9-11, 2656535, 19265520
-
Neuwald AF. The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops. BMC Struct Biol 2009, 9:11. 10.1186/1472-6807-9-11, 2656535, 19265520.
-
(2009)
BMC Struct Biol
, vol.9
, pp. 11
-
-
Neuwald, A.F.1
-
22
-
-
58149177285
-
Structure and membrane interaction of myristoylated ARF1
-
10.1016/j.str.2008.10.020, 2659477, 19141284
-
Liu Y, Kahn RA, Prestegard JH. Structure and membrane interaction of myristoylated ARF1. Structure 2009, 17:79-87. 10.1016/j.str.2008.10.020, 2659477, 19141284.
-
(2009)
Structure
, vol.17
, pp. 79-87
-
-
Liu, Y.1
Kahn, R.A.2
Prestegard, J.H.3
-
23
-
-
34250872768
-
Orientation and motion of tryptophan interfacial anchors in membrane-spanning peptides
-
10.1021/bi700082v, 2532949, 17530863
-
van der Wel PC, Reed ND, Greathouse DV, Koeppe RE. Orientation and motion of tryptophan interfacial anchors in membrane-spanning peptides. Biochemistry 2007, 46:7514-7524. 10.1021/bi700082v, 2532949, 17530863.
-
(2007)
Biochemistry
, vol.46
, pp. 7514-7524
-
-
van der Wel, P.C.1
Reed, N.D.2
Greathouse, D.V.3
Koeppe, R.E.4
-
24
-
-
0026557830
-
The functions of tryptophan residues in membrane proteins
-
10.1093/protein/5.3.213, 1409540
-
Schiffer M, Chang CH, Stevens FJ. The functions of tryptophan residues in membrane proteins. Protein Eng 1992, 5:213-214. 10.1093/protein/5.3.213, 1409540.
-
(1992)
Protein Eng
, vol.5
, pp. 213-214
-
-
Schiffer, M.1
Chang, C.H.2
Stevens, F.J.3
-
25
-
-
0032552880
-
The preference of tryptophan for membrane interfaces
-
10.1021/bi980809c, 9778346
-
Yau WM, Wimley WC, Gawrisch K, White SH. The preference of tryptophan for membrane interfaces. Biochemistry 1998, 37:14713-14718. 10.1021/bi980809c, 9778346.
-
(1998)
Biochemistry
, vol.37
, pp. 14713-14718
-
-
Yau, W.M.1
Wimley, W.C.2
Gawrisch, K.3
White, S.H.4
-
26
-
-
70350057763
-
CH/Pi hydrogen bonds in organic and organometallic chemistry
-
Nishio M, Umezawa Y, Honda K, Tsuboyama S, Suezawa H. CH/Pi hydrogen bonds in organic and organometallic chemistry. CrystEngComm 2009, 11:1757-1788.
-
(2009)
CrystEngComm
, vol.11
, pp. 1757-1788
-
-
Nishio, M.1
Umezawa, Y.2
Honda, K.3
Tsuboyama, S.4
Suezawa, H.5
-
27
-
-
33644526287
-
Nomenclature for the human Arf family of GTP-binding proteins: ARF, ARL, and SAR proteins
-
10.1083/jcb.200512057, 2063696, 16505163
-
Kahn RA, Cherfils J, Elias M, Lovering RC, Munro S, Schurmann A. Nomenclature for the human Arf family of GTP-binding proteins: ARF, ARL, and SAR proteins. J Cell Biol 2006, 172:645-650. 10.1083/jcb.200512057, 2063696, 16505163.
-
(2006)
J Cell Biol
, vol.172
, pp. 645-650
-
-
Kahn, R.A.1
Cherfils, J.2
Elias, M.3
Lovering, R.C.4
Munro, S.5
Schurmann, A.6
-
28
-
-
0014694171
-
On N-H--S hydrogen bonds
-
10.1016/0022-2836(69)90102-8, 5367026
-
Donohue J. On N-H--S hydrogen bonds. J Mol Biol 1969, 45:231-235. 10.1016/0022-2836(69)90102-8, 5367026.
-
(1969)
J Mol Biol
, vol.45
, pp. 231-235
-
-
Donohue, J.1
-
29
-
-
70449574090
-
Nature of the N-H...S hydrogen bond
-
10.1021/jp907658w, 19831376
-
Biswal HS, Wategaonkar S. Nature of the N-H...S hydrogen bond. J Phys Chem A 2009, 113:12763-12773. 10.1021/jp907658w, 19831376.
-
(2009)
J Phys Chem A
, vol.113
, pp. 12763-12773
-
-
Biswal, H.S.1
Wategaonkar, S.2
-
30
-
-
0035851202
-
Regulation of the properties of the heme-NO complexes in nitric-oxide synthase by hydrogen bonding to the proximal cysteine
-
10.1074/jbc.M103907200, 11479310
-
Couture M, Adak S, Stuehr DJ, Rousseau DL. Regulation of the properties of the heme-NO complexes in nitric-oxide synthase by hydrogen bonding to the proximal cysteine. J Biol Chem 2001, 276:38280-38288. 10.1074/jbc.M103907200, 11479310.
-
(2001)
J Biol Chem
, vol.276
, pp. 38280-38288
-
-
Couture, M.1
Adak, S.2
Stuehr, D.J.3
Rousseau, D.L.4
-
31
-
-
67650751542
-
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences
-
10.1093/bioinformatics/btp342, 2732367, 19505947
-
Neuwald AF. Rapid detection, classification and accurate alignment of up to a million or more related protein sequences. Bioinformatics 2009, 25:1869-1875. 10.1093/bioinformatics/btp342, 2732367, 19505947.
-
(2009)
Bioinformatics
, vol.25
, pp. 1869-1875
-
-
Neuwald, A.F.1
-
32
-
-
35549007096
-
The CHAIN program: forging evolutionary links to underlying mechanisms
-
Neuwald AF. The CHAIN program: forging evolutionary links to underlying mechanisms. Trends Biochem Sciences 2007, 32:487-493.
-
(2007)
Trends Biochem Sciences
, vol.32
, pp. 487-493
-
-
Neuwald, A.F.1
-
33
-
-
0029119568
-
RASMOL: biomolecular graphics for all
-
10.1016/S0968-0004(00)89080-5, 7482707
-
Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem Sci 1995, 20:374. 10.1016/S0968-0004(00)89080-5, 7482707.
-
(1995)
Trends Biochem Sci
, vol.20
, pp. 374
-
-
Sayle, R.A.1
Milner-White, E.J.2
-
34
-
-
0346243924
-
Structural snapshots of the mechanism and inhibition of a guanine nucleotide exchange factor
-
10.1038/nature02197, 14654833
-
Renault L, Guibert B, Cherfils J. Structural snapshots of the mechanism and inhibition of a guanine nucleotide exchange factor. Nature 2003, 426:525-530. 10.1038/nature02197, 14654833.
-
(2003)
Nature
, vol.426
, pp. 525-530
-
-
Renault, L.1
Guibert, B.2
Cherfils, J.3
-
35
-
-
0035834688
-
Structures of yeast ARF2 and ARL1: distinct roles for the N terminus in the structure and function of ARF family GTPases
-
10.1074/jbc.M106660200, 11535602
-
Amor JC, Horton JR, Zhu X, Wang Y, Sullards C, Ringe D, Cheng X, Kahn RA. Structures of yeast ARF2 and ARL1: distinct roles for the N terminus in the structure and function of ARF family GTPases. J Biol Chem 2001, 276:42477-42484. 10.1074/jbc.M106660200, 11535602.
-
(2001)
J Biol Chem
, vol.276
, pp. 42477-42484
-
-
Amor, J.C.1
Horton, J.R.2
Zhu, X.3
Wang, Y.4
Sullards, C.5
Ringe, D.6
Cheng, X.7
Kahn, R.A.8
-
36
-
-
23644438026
-
Structural basis for the activation of cholera toxin by human ARF6-GTP
-
O'Neal CJ, Jobling MG, Holmes RK, Hol WG. Structural basis for the activation of cholera toxin by human ARF6-GTP. Science 2005, 309:1093-1096.
-
(2005)
Science
, vol.309
, pp. 1093-1096
-
-
O'Neal, C.J.1
Jobling, M.G.2
Holmes, R.K.3
Hol, W.G.4
-
37
-
-
0242266897
-
Structural basis for Arl1-dependent targeting of homodimeric GRIP domains to the Golgi apparatus
-
10.1016/S1097-2765(03)00356-3, 14580338
-
Panic B, Perisic O, Veprintsev DB, Williams RL, Munro S. Structural basis for Arl1-dependent targeting of homodimeric GRIP domains to the Golgi apparatus. Mol Cell 2003, 12:863-874. 10.1016/S1097-2765(03)00356-3, 14580338.
-
(2003)
Mol Cell
, vol.12
, pp. 863-874
-
-
Panic, B.1
Perisic, O.2
Veprintsev, D.B.3
Williams, R.L.4
Munro, S.5
-
38
-
-
0036565668
-
The complex of Arl2-GTP and PDE delta: from structure to function
-
10.1093/emboj/21.9.2095, 125981, 11980706
-
Hanzal-Bayer M, Renault L, Roversi P, Wittinghofer A, Hillig RC. The complex of Arl2-GTP and PDE delta: from structure to function. EMBO J 2002, 21:2095-2106. 10.1093/emboj/21.9.2095, 125981, 11980706.
-
(2002)
EMBO J
, vol.21
, pp. 2095-2106
-
-
Hanzal-Bayer, M.1
Renault, L.2
Roversi, P.3
Wittinghofer, A.4
Hillig, R.C.5
-
39
-
-
0034476959
-
Structural and biochemical properties show ARL3-GDP as a distinct GTP binding protein
-
10.1016/S0969-2126(00)00531-1, 11188688
-
Hillig RC, Hanzal-Bayer M, Linari M, Becker J, Wittinghofer A, Renault L. Structural and biochemical properties show ARL3-GDP as a distinct GTP binding protein. Structure 2000, 8:1239-1245. 10.1016/S0969-2126(00)00531-1, 11188688.
-
(2000)
Structure
, vol.8
, pp. 1239-1245
-
-
Hillig, R.C.1
Hanzal-Bayer, M.2
Linari, M.3
Becker, J.4
Wittinghofer, A.5
Renault, L.6
-
40
-
-
33747386160
-
An open conformation of switch I revealed by Sar1-GDP crystal structure at low Mg2+
-
10.1016/j.bbrc.2006.07.148, 16899220
-
Rao Y, Bian C, Yuan C, Li Y, Chen L, Ye X, Huang Z, Huang M. An open conformation of switch I revealed by Sar1-GDP crystal structure at low Mg2+. Biochem Biophys Res Commun 2006, 348:908-915. 10.1016/j.bbrc.2006.07.148, 16899220.
-
(2006)
Biochem Biophys Res Commun
, vol.348
, pp. 908-915
-
-
Rao, Y.1
Bian, C.2
Yuan, C.3
Li, Y.4
Chen, L.5
Ye, X.6
Huang, Z.7
Huang, M.8
-
41
-
-
0037136560
-
Structure of the Sec23/24-Sar1 pre-budding complex of the COPII vesicle coat
-
10.1038/nature01040, 12239560
-
Bi X, Corpina RA, Goldberg J. Structure of the Sec23/24-Sar1 pre-budding complex of the COPII vesicle coat. Nature 2002, 419:271-277. 10.1038/nature01040, 12239560.
-
(2002)
Nature
, vol.419
, pp. 271-277
-
-
Bi, X.1
Corpina, R.A.2
Goldberg, J.3
-
42
-
-
0033614004
-
Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation
-
10.1006/jmbi.1998.2401, 9917408
-
Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 1999, 285:1735-1747. 10.1006/jmbi.1998.2401, 9917408.
-
(1999)
J Mol Biol
, vol.285
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
43
-
-
77954306342
-
Multi-Harmony: detecting functional specificity from sequence alignment
-
10.1093/nar/gkq415, 2896201, 20525785
-
Brandt BW, Feenstra KA, Heringa J. Multi-Harmony: detecting functional specificity from sequence alignment. Nucleic Acids Res 2010, 38(Suppl):W35-40. 10.1093/nar/gkq415, 2896201, 20525785.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.SUPPL
-
-
Brandt, B.W.1
Feenstra, K.A.2
Heringa, J.3
-
44
-
-
77954554764
-
An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies
-
10.1186/1748-7188-5-29, 2914642, 20633297
-
Mazin PV, Gelfand MS, Mironov AA, Rakhmaninova AB, Rubinov AR, Russell RB, Kalinina OV. An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies. Algorithms Mol Biol 2010, 5:29. 10.1186/1748-7188-5-29, 2914642, 20633297.
-
(2010)
Algorithms Mol Biol
, vol.5
, pp. 29
-
-
Mazin, P.V.1
Gelfand, M.S.2
Mironov, A.A.3
Rakhmaninova, A.B.4
Rubinov, A.R.5
Russell, R.B.6
Kalinina, O.V.7
-
45
-
-
67149113261
-
Using evolutionary information to find specificity-determining and co-evolving residues
-
Kolesov G, Mirny LA. Using evolutionary information to find specificity-determining and co-evolving residues. Methods Mol Biol 2009, 541:421-448.
-
(2009)
Methods Mol Biol
, vol.541
, pp. 421-448
-
-
Kolesov, G.1
Mirny, L.A.2
-
46
-
-
68049104351
-
Ensemble approach to predict specificity determinants: benchmarking and validation
-
10.1186/1471-2105-10-207, 2716344, 19573245
-
Chakrabarti S, Panchenko AR. Ensemble approach to predict specificity determinants: benchmarking and validation. BMC Bioinformatics 2009, 10:207. 10.1186/1471-2105-10-207, 2716344, 19573245.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 207
-
-
Chakrabarti, S.1
Panchenko, A.R.2
-
47
-
-
72449178363
-
Partially-supervised protein subclass discovery with simultaneous annotation of functional residues
-
10.1186/1472-6807-9-68, 2777906, 19857261
-
Georgi B, Schultz J, Schliep A. Partially-supervised protein subclass discovery with simultaneous annotation of functional residues. BMC Struct Biol 2009, 9:68. 10.1186/1472-6807-9-68, 2777906, 19857261.
-
(2009)
BMC Struct Biol
, vol.9
, pp. 68
-
-
Georgi, B.1
Schultz, J.2
Schliep, A.3
-
48
-
-
46249099576
-
Characterization and prediction of residues determining protein functional specificity
-
10.1093/bioinformatics/btn214, 2718669, 18450811
-
Capra JA, Singh M. Characterization and prediction of residues determining protein functional specificity. Bioinformatics 2008, 24:1473-1480. 10.1093/bioinformatics/btn214, 2718669, 18450811.
-
(2008)
Bioinformatics
, vol.24
, pp. 1473-1480
-
-
Capra, J.A.1
Singh, M.2
-
49
-
-
44949137643
-
Determinants of protein function revealed by combinatorial entropy optimization
-
10.1186/gb-2007-8-11-r232, 2258190, 17976239
-
Reva B, Antipin Y, Sander C. Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol 2007, 8:R232. 10.1186/gb-2007-8-11-r232, 2258190, 17976239.
-
(2007)
Genome Biol
, vol.8
-
-
Reva, B.1
Antipin, Y.2
Sander, C.3
-
50
-
-
34548392746
-
Automated protein subfamily identification and classification
-
10.1371/journal.pcbi.0030160, 1950344, 17708678
-
Brown DP, Krishnamurthy N, Sjolander K. Automated protein subfamily identification and classification. PLoS Comput Biol 2007, 3:e160. 10.1371/journal.pcbi.0030160, 1950344, 17708678.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Brown, D.P.1
Krishnamurthy, N.2
Sjolander, K.3
-
51
-
-
33747859994
-
TreeDet: a web server to explore sequence space
-
10.1093/nar/gkl203, 1538789, 16844971
-
Carro A, Tress M, de Juan D, Pazos F, Lopez-Romero P, del Sol A, Valencia A, Rojas AM. TreeDet: a web server to explore sequence space. Nucleic Acids Res 2006, 34:W110-115. 10.1093/nar/gkl203, 1538789, 16844971.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Carro, A.1
Tress, M.2
de Juan, D.3
Pazos, F.4
Lopez-Romero, P.5
del Sol, A.6
Valencia, A.7
Rojas, A.M.8
-
52
-
-
32144442848
-
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios
-
10.1093/bioinformatics/bti766, 16278237
-
Pei J, Cai W, Kinch LN, Grishin NV. Prediction of functional specificity determinants from protein sequences using log-likelihood ratios. Bioinformatics 2006, 22:164-171. 10.1093/bioinformatics/bti766, 16278237.
-
(2006)
Bioinformatics
, vol.22
, pp. 164-171
-
-
Pei, J.1
Cai, W.2
Kinch, L.N.3
Grishin, N.V.4
-
53
-
-
1242339659
-
A family of evolution-entropy hybrid methods for ranking protein residues by importance
-
10.1016/j.jmb.2003.12.078, 15037084
-
Mihalek I, Res I, Lichtarge O. A family of evolution-entropy hybrid methods for ranking protein residues by importance. J Mol Biol 2004, 336:1265-1282. 10.1016/j.jmb.2003.12.078, 15037084.
-
(2004)
J Mol Biol
, vol.336
, pp. 1265-1282
-
-
Mihalek, I.1
Res, I.2
Lichtarge, O.3
-
54
-
-
0027764344
-
Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation
-
Livingstone CD, Barton GJ. Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput Appl Biosci 1993, 9:745-756.
-
(1993)
Comput Appl Biosci
, vol.9
, pp. 745-756
-
-
Livingstone, C.D.1
Barton, G.J.2
-
55
-
-
0036205440
-
DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family
-
10.1093/bioinformatics/18.3.500, 11934757
-
Gu X, Vander Velden K. DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics 2002, 18:500-501. 10.1093/bioinformatics/18.3.500, 11934757.
-
(2002)
Bioinformatics
, vol.18
, pp. 500-501
-
-
Gu, X.1
Vander Velden, K.2
-
56
-
-
37549049756
-
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting
-
10.1093/bioinformatics/btm537, 18024975
-
Ye K, Feenstra KA, Heringa J, Ijzerman AP, Marchiori E. Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. Bioinformatics 2008, 24:18-25. 10.1093/bioinformatics/btm537, 18024975.
-
(2008)
Bioinformatics
, vol.24
, pp. 18-25
-
-
Ye, K.1
Feenstra, K.A.2
Heringa, J.3
Ijzerman, A.P.4
Marchiori, E.5
-
57
-
-
0037407395
-
Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport
-
10.1038/nsb920, 12679809
-
Shiba T, Kawasaki M, Takatsu H, Nogi T, Matsugaki N, Igarashi N, Suzuki M, Kato R, Nakayama K, Wakatsuki S. Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport. Nat Struct Biol 2003, 10:386-393. 10.1038/nsb920, 12679809.
-
(2003)
Nat Struct Biol
, vol.10
, pp. 386-393
-
-
Shiba, T.1
Kawasaki, M.2
Takatsu, H.3
Nogi, T.4
Matsugaki, N.5
Igarashi, N.6
Suzuki, M.7
Kato, R.8
Nakayama, K.9
Wakatsuki, S.10
-
58
-
-
0030982264
-
Structure of RGS4 bound to AlF4--activated G(i alpha1): stabilization of the transition state for GTP hydrolysis
-
10.1016/S0092-8674(00)80204-4, 9108480
-
Tesmer JJ, Berman DM, Gilman AG, Sprang SR. Structure of RGS4 bound to AlF4--activated G(i alpha1): stabilization of the transition state for GTP hydrolysis. Cell 1997, 89:251-261. 10.1016/S0092-8674(00)80204-4, 9108480.
-
(1997)
Cell
, vol.89
, pp. 251-261
-
-
Tesmer, J.J.1
Berman, D.M.2
Gilman, A.G.3
Sprang, S.R.4
-
59
-
-
0030772378
-
The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants
-
10.1126/science.277.5324.333, 9219684
-
Scheffzek K, Ahmadian MR, Kabsch W, Wiesmuller L, Lautwein A, Schmitz F, Wittinghofer A. The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science 1997, 277(5324):333-338. 10.1126/science.277.5324.333, 9219684.
-
(1997)
Science
, vol.277
, Issue.5324
, pp. 333-338
-
-
Scheffzek, K.1
Ahmadian, M.R.2
Kabsch, W.3
Wiesmuller, L.4
Lautwein, A.5
Schmitz, F.6
Wittinghofer, A.7
-
60
-
-
0037177814
-
Functional overlap between retinitis pigmentosa 2 protein and the tubulin-specific chaperone cofactor C
-
10.1074/jbc.M200128200, 11847227
-
Bartolini F, Bhamidipati A, Thomas S, Schwahn U, Lewis SA, Cowan NJ. Functional overlap between retinitis pigmentosa 2 protein and the tubulin-specific chaperone cofactor C. J Biol Chem 2002, 277(17):14629-14634. 10.1074/jbc.M200128200, 11847227.
-
(2002)
J Biol Chem
, vol.277
, Issue.17
, pp. 14629-14634
-
-
Bartolini, F.1
Bhamidipati, A.2
Thomas, S.3
Schwahn, U.4
Lewis, S.A.5
Cowan, N.J.6
-
61
-
-
4143080261
-
Crystal structure of the actin binding domain of the cyclase-associated protein
-
10.1021/bi049071r, 15311924
-
Dodatko T, Fedorov AA, Grynberg M, Patskovsky Y, Rozwarski DA, Jaroszewski L, Aronoff-Spencer E, Kondraskina E, Irving T, Godzik A, et al. Crystal structure of the actin binding domain of the cyclase-associated protein. Biochemistry 2004, 43(33):10628-10641. 10.1021/bi049071r, 15311924.
-
(2004)
Biochemistry
, vol.43
, Issue.33
, pp. 10628-10641
-
-
Dodatko, T.1
Fedorov, A.A.2
Grynberg, M.3
Patskovsky, Y.4
Rozwarski, D.A.5
Jaroszewski, L.6
Aronoff-Spencer, E.7
Kondraskina, E.8
Irving, T.9
Godzik, A.10
-
62
-
-
77953241497
-
The structure of an Arf-ArfGAP complex reveals a Ca2+ regulatory mechanism
-
10.1016/j.cell.2010.03.051, 20510928
-
Ismail SA, Vetter IR, Sot B, Wittinghofer A. The structure of an Arf-ArfGAP complex reveals a Ca2+ regulatory mechanism. Cell 2010, 141(5):812-821. 10.1016/j.cell.2010.03.051, 20510928.
-
(2010)
Cell
, vol.141
, Issue.5
, pp. 812-821
-
-
Ismail, S.A.1
Vetter, I.R.2
Sot, B.3
Wittinghofer, A.4
|