-
1
-
-
0030815986
-
RNA editing in kinetoplastid protozoa
-
Stuart, K., Allen, T. E., Heidmann, S., and Seiwert, S. D. (1997) RNA editing in kinetoplastid protozoa. Microbiol. Mol. Biol. Rev. 61, 105.
-
(1997)
Microbiol. Mol. Biol. Rev
, vol.61
, pp. 105
-
-
Stuart, K.1
Allen, T.E.2
Heidmann, S.3
Seiwert, S.D.4
-
2
-
-
33646870148
-
Compositionally and functionally distinct editosomes in Trypanosoma brucei
-
Panigrahi, A. K., Ernst, N. L., Domingo, G. J., Fleck, M., Salavati, R., and Stuart, K. D. (2006) Compositionally and functionally distinct editosomes in Trypanosoma brucei. RNA 12, 1038-1049.
-
(2006)
RNA
, vol.12
, pp. 1038-1049
-
-
Panigrahi, A.K.1
Ernst, N.L.2
Domingo, G.J.3
Fleck, M.4
Salavati, R.5
Stuart, K.D.6
-
3
-
-
0027102742
-
Formation of guide RNA/ messenger RNA chimeric molecules in vitro, the initial step of RNA editing, is dependent on an anchor sequence
-
Blum, B., and Simpson, L. (1992) Formation of guide RNA/ messenger RNA chimeric molecules in vitro, the initial step of RNA editing, is dependent on an anchor sequence. Proc. Natl. Acad. Sci. U.S.A. 89, 11944-11948.
-
(1992)
Proc. Natl. Acad. Sci. U.S.A
, vol.89
, pp. 11944-11948
-
-
Blum, B.1
Simpson, L.2
-
4
-
-
0029942430
-
Direct visualization of uridylate deletion in vitro suggests a mechanism for kinetoplastid RNA editing
-
Seiwert, S. D., Heidmann, S., and Stuart, K. (1996) Direct visualization of uridylate deletion in vitro suggests a mechanism for kinetoplastid RNA editing. Cell 84, 831.
-
(1996)
Cell
, vol.84
, pp. 831
-
-
Seiwert, S.D.1
Heidmann, S.2
Stuart, K.3
-
5
-
-
0037371743
-
Uridine insertion/deletion RNA editing in trypanosome mitochondria: A complex business
-
Simpson, L., Sbicego, S., and Aphasizhev, R. (2003) Uridine insertion/deletion RNA editing in trypanosome mitochondria: A complex business. RNA 9, 265.
-
(2003)
RNA
, vol.9
, pp. 265
-
-
Simpson, L.1
Sbicego, S.2
Aphasizhev, R.3
-
6
-
-
13244290067
-
Complex management: RNA editing in trypanosomes
-
Stuart, K. D., Schnaufer, A., Ernst, N. L., and Panigrahi, A. K. (2005) Complex management: RNA editing in trypanosomes. Trends Biochem. Sci. 30, 97.
-
(2005)
Trends Biochem. Sci
, vol.30
, pp. 97
-
-
Stuart, K.D.1
Schnaufer, A.2
Ernst, N.L.3
Panigrahi, A.K.4
-
7
-
-
4744374004
-
High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1
-
Deng, J., Schnaufer, A., Salavati, R., Stuart, K. D., and Hol, W. G. (2004) High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1. J. Mol. Biol. 343, 601-613.
-
(2004)
J. Mol. Biol
, vol.343
, pp. 601-613
-
-
Deng, J.1
Schnaufer, A.2
Salavati, R.3
Stuart, K.D.4
Hol, W.G.5
-
8
-
-
0035896357
-
An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei
-
Schnaufer, A., Panigrahi, A. K., Panicucci, B., Igo, R. P., Jr., Wirtz, E., Salavati, R., and Stuart, K. (2001) An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei. Science 291, 2159-2162.
-
(2001)
Science
, vol.291
, pp. 2159-2162
-
-
Schnaufer, A.1
Panigrahi, A.K.2
Panicucci, B.3
Igo Jr., R.P.4
Wirtz, E.5
Salavati, R.6
Stuart, K.7
-
9
-
-
0035164020
-
Association of Two Novel Proteins, TbMP52 and TbMP48, with the Trypanosoma brucei RNA Editing Complex
-
Panigrahi, A. K., Gygi, S. P., Ernst, N. L., Igo, R. P., Jr., Palazzo, S. S., Schnaufer, A., Weston, D. S., Carmean, N., Salavati, R., Aebersold, R., and Stuart, K. D. (2001) Association of Two Novel Proteins, TbMP52 and TbMP48, with the Trypanosoma brucei RNA Editing Complex. Mol. Cell. Biol. 21, 380.
-
(2001)
Mol. Cell. Biol
, vol.21
, pp. 380
-
-
Panigrahi, A.K.1
Gygi, S.P.2
Ernst, N.L.3
Igo Jr., R.P.4
Palazzo, S.S.5
Schnaufer, A.6
Weston, D.S.7
Carmean, N.8
Salavati, R.9
Aebersold, R.10
Stuart, K.D.11
-
10
-
-
9944230069
-
The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases
-
Shuman, S., and Lima, C. D. (2004) The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases. Curr. Opin. Struct. Biol. 14, 757-764.
-
(2004)
Curr. Opin. Struct. Biol
, vol.14
, pp. 757-764
-
-
Shuman, S.1
Lima, C.D.2
-
11
-
-
0038228666
-
X-Ray Crystallography Reveals a Large Conformational Change during Guanyl Transfer by mRNA Capping Enzymes
-
Håkansson, K., Doherty, A. J., Shuman, S., and Wigley, D. B. (1997) X-Ray Crystallography Reveals a Large Conformational Change during Guanyl Transfer by mRNA Capping Enzymes. Cell 89, 545-553.
-
(1997)
Cell
, vol.89
, pp. 545-553
-
-
Håkansson, K.1
Doherty, A.J.2
Shuman, S.3
Wigley, D.B.4
-
12
-
-
0037126846
-
2+-dependent Nucleotidyl Transfer Catalyzed by T4 DNA and RNA Ligases
-
2+-dependent Nucleotidyl Transfer Catalyzed by T4 DNA and RNA Ligases. J. Biol. Chem. 277, 1695-1704.
-
(2002)
J. Biol. Chem
, vol.277
, pp. 1695-1704
-
-
Cherepanov, A.V.1
de Vries, S.2
-
13
-
-
33749080322
-
RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward
-
Nandakumar, J., Shuman, S., and Lima, C. D. (2006) RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward. Cell 127, 71.
-
(2006)
Cell
, vol.127
, pp. 71
-
-
Nandakumar, J.1
Shuman, S.2
Lima, C.D.3
-
14
-
-
47749142459
-
Functional and Structural Insights Revealed by Molecular Dynamics Simulations of an Essential RNA Editing Ligase in Trypanosoma brucei
-
Amaro, R. E., Swift, R. V., and McCammon, J. A. (2007) Functional and Structural Insights Revealed by Molecular Dynamics Simulations of an Essential RNA Editing Ligase in Trypanosoma brucei. PLoS Neglected Trop. Dis. 1, e68.
-
(2007)
PLoS Neglected Trop. Dis. 1
-
-
Amaro, R.E.1
Swift, R.V.2
McCammon, J.A.3
-
15
-
-
39149142191
-
DNA and RNA ligases: Structural variations and shared mechanisms
-
Pascal, J. M. (2008) DNA and RNA ligases: Structural variations and shared mechanisms. Curr. Opin. Struct. Biol. 18, 96-105.
-
(2008)
Curr. Opin. Struct. Biol
, vol.18
, pp. 96-105
-
-
Pascal, J.M.1
-
16
-
-
0036280718
-
Molecular dynamics applied to nucleic acids
-
Norberg, J., and Nilsson, L. (2002) Molecular dynamics applied to nucleic acids. Acc. Chem. Res. 35, 465-472.
-
(2002)
Acc. Chem. Res
, vol.35
, pp. 465-472
-
-
Norberg, J.1
Nilsson, L.2
-
17
-
-
41949124146
-
Molecular dynamics simulations of nucleic acid-protein complexes
-
MacKerell, A. D., and Nilsson, L. (2008) Molecular dynamics simulations of nucleic acid-protein complexes. Curr. Opin. Struct. Biol. 18, 1-6.
-
(2008)
Curr. Opin. Struct. Biol
, vol.18
, pp. 1-6
-
-
MacKerell, A.D.1
Nilsson, L.2
-
18
-
-
64349100572
-
-
Case, D. A., Darden, T. A., Cheatham Iii, T. E., Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Merz, K. M., Pearlman, D. A., Crowley, M., Walker, R. C., Zhang, W., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Wong, K. F., Paesani, F., Wu, X., Brozell, S., Tsui, V., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Beroza, P., Mathews, D. H., Schafmeister, C., Ross, W. S., Kollman, P. A. (2006) Amber 9.
-
Case, D. A., Darden, T. A., Cheatham Iii, T. E., Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Merz, K. M., Pearlman, D. A., Crowley, M., Walker, R. C., Zhang, W., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Wong, K. F., Paesani, F., Wu, X., Brozell, S., Tsui, V., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Beroza, P., Mathews, D. H., Schafmeister, C., Ross, W. S., Kollman, P. A. (2006) Amber 9.
-
-
-
-
19
-
-
33644990075
-
Molecular architecture and ligand recognition determinants for T4 RNA ligase
-
El Omari, K., Ren, J., Bird, L. E., Bona, M. K., Klarmann, G., LeGrice, S. F., and Stammers, D. K (2006) Molecular architecture and ligand recognition determinants for T4 RNA ligase. J. Biol. Chem. 281, 1573-1579.
-
(2006)
J. Biol. Chem
, vol.281
, pp. 1573-1579
-
-
El Omari, K.1
Ren, J.2
Bird, L.E.3
Bona, M.K.4
Klarmann, G.5
LeGrice, S.F.6
Stammers, D.K.7
-
20
-
-
0025398721
-
WHAT IF: A molecular modeling and drug design program
-
Vriend, G (1990) WHAT IF: A molecular modeling and drug design program. J. Mol. Graphics 8, 52-56.
-
(1990)
J. Mol. Graphics
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
21
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., and Simmerling, C. (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65, 712-725.
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
22
-
-
0037495965
-
Development of polyphosphate parameters for use with the AMBER force field
-
Meagher, K. L., Redman, L. T., and Carlson, H. A. (2003) Development of polyphosphate parameters for use with the AMBER force field. J. Comput. Chem. 24, 1016-1025.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 1016-1025
-
-
Meagher, K.L.1
Redman, L.T.2
Carlson, H.A.3
-
23
-
-
2942532422
-
Development and testing of a general amber force field
-
Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., and Case, D. A. (2004) Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
24
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
25
-
-
36449007836
-
Constant pressure molecular dynamics simulation: The Langevin piston method
-
Feller, S. E., Zhang, Y., Pastor, R. W., and Brooks, B. R. (1995) Constant pressure molecular dynamics simulation: The Langevin piston method. J. Chem. Phys. 103, 4613.
-
(1995)
J. Chem. Phys
, vol.103
, pp. 4613
-
-
Feller, S.E.1
Zhang, Y.2
Pastor, R.W.3
Brooks, B.R.4
-
26
-
-
33846823909
-
Particle mesh Ewald: An N,ãOlog(N) method for Ewald sums in large systems
-
Darden, T., York, D., and Pedersen, L. (1993) Particle mesh Ewald: An N,ãOlog(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089.
-
(1993)
J. Chem. Phys
, vol.98
, pp. 10089
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
27
-
-
0042415783
-
NAMD2: Greater scalability for parallel molecular dynamics
-
Kale, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K., and Schulten, K. (1999) NAMD2: Greater scalability for parallel molecular dynamics. J. Comput. Phys. 151, 283-312.
-
(1999)
J. Comput. Phys
, vol.151
, pp. 283-312
-
-
Kale, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
Krawetz, N.6
Phillips, J.7
Shinozaki, A.8
Varadarajan, K.9
Schulten, K.10
-
28
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kale, L., and Schulten, K (2005) Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781-1802.
-
(2005)
J. Comput. 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
-
29
-
-
67249159461
-
Exact method for the calculation of pseudorotation parameters Ptm and their errors. A comparison of the Altona-Sundaralingam and Cremer-Pople treatment of puckering of five-membered rings
-
Rao, S. T., Westhof, E., and Sundaralingam, M. (1981) Exact method for the calculation of pseudorotation parameters Ptm and their errors. A comparison of the Altona-Sundaralingam and Cremer-Pople treatment of puckering of five-membered rings. Acta Crystallogr. A37, 421-425.
-
(1981)
Acta Crystallogr
, vol.A37
, pp. 421-425
-
-
Rao, S.T.1
Westhof, E.2
Sundaralingam, M.3
-
30
-
-
0141451738
-
Deoxyadenosine sugar puckering pathway simulated by the stochastic difference equation algorithm
-
Arora, K, and Schlick, T. (2003) Deoxyadenosine sugar puckering pathway simulated by the stochastic difference equation algorithm. Chem. Phys. Lett. 378, 1-8.
-
(2003)
Chem. Phys. Lett
, vol.378
, pp. 1-8
-
-
Arora, K.1
Schlick, T.2
-
31
-
-
0027441950
-
Essential dynamics of proteins
-
Amadei, A., Linssen, A., and Berendsen, H. (1993) Essential dynamics of proteins. Proteins: Struct, Funct., Genet. 17, 412-425.
-
(1993)
Proteins: Struct, Funct., Genet
, vol.17
, pp. 412-425
-
-
Amadei, A.1
Linssen, A.2
Berendsen, H.3
-
32
-
-
0000577041
-
Large-amplitude nonlinear motions in proteins
-
Garcia, A. E. (1992) Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68, 2696-2699.
-
(1992)
Phys. Rev. Lett
, vol.68
, pp. 2696-2699
-
-
Garcia, A.E.1
-
33
-
-
0038043264
-
Structure-function analysis of T4 RNA ligase 2
-
Yin, S., Ho, C. K, and Shuman, S. (2003) Structure-function analysis of T4 RNA ligase 2. J. Biol. Chem. 278, 17601-17608.
-
(2003)
J. Biol. Chem
, vol.278
, pp. 17601-17608
-
-
Yin, S.1
Ho, C.K.2
Shuman, S.3
-
34
-
-
6344289396
-
How an RNA ligase discriminates RNA versus DNA damage
-
Nandakumar, J., and Shuman, S. (2004) How an RNA ligase discriminates RNA versus DNA damage. Mol. Cell 16, 211-221.
-
(2004)
Mol. Cell
, vol.16
, pp. 211-221
-
-
Nandakumar, J.1
Shuman, S.2
-
35
-
-
0037417236
-
Kinetoplastid RNA editing ligases: Complex association, characterization, and substrate requirements
-
Palazzo, S. S., Panigrahi, A. K, Igo, R. P., Salavati, R., and Stuart, K (2003) Kinetoplastid RNA editing ligases: Complex association, characterization, and substrate requirements. Mol. Biochem. Parasitai. 127, 161-167.
-
(2003)
Mol. Biochem. Parasitai
, vol.127
, pp. 161-167
-
-
Palazzo, S.S.1
Panigrahi, A.K.2
Igo, R.P.3
Salavati, R.4
Stuart, K.5
-
36
-
-
0032539677
-
Structure of a complex between a cap analogue and mRNA guanylyl transferase demonstrates the structural chemistry of RNA capping
-
Håkansson, K., and Wigley, D. B. (1998) Structure of a complex between a cap analogue and mRNA guanylyl transferase demonstrates the structural chemistry of RNA capping. Proc. Natl. Acad. Sci. U.S.A. 95, 1505-1510.
-
(1998)
Proc. Natl. Acad. Sci. U.S.A
, vol.95
, pp. 1505-1510
-
-
Håkansson, K.1
Wigley, D.B.2
-
37
-
-
4344585269
-
Phosphoryl group transfer: Evolution of a catalytic scaffold
-
Allen, K. N., and Dunaway-Mariano, D. (2004) Phosphoryl group transfer: Evolution of a catalytic scaffold. Trends Biochem. Sci. 29, 495-503.
-
(2004)
Trends Biochem. Sci
, vol.29
, pp. 495-503
-
-
Allen, K.N.1
Dunaway-Mariano, D.2
-
39
-
-
0033963089
-
The ENZYME database in 2000
-
Bairoch, A. (2000) The ENZYME database in 2000. Nucleic Acids Res. 28, 304-305.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 304-305
-
-
Bairoch, A.1
|