-
1
-
-
33644876507
-
The tmRDB and SRPDB resources
-
Andersen E.S., Rosenblad M.A., Larsen N., Westergaard J.C., Burks J., Wower I.K., Wower J., Gorodkin J., Samuelsson T., Zwieb C. The tmRDB and SRPDB resources. Nucleic Acids Research 2006, 34:D163-D168.
-
(2006)
Nucleic Acids Research
, vol.34
-
-
Andersen, E.S.1
Rosenblad, M.A.2
Larsen, N.3
Westergaard, J.C.4
Burks, J.5
Wower, I.K.6
Wower, J.7
Gorodkin, J.8
Samuelsson, T.9
Zwieb, C.10
-
2
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges - the resp model
-
Bayly C.I., Cieplak P., Cornell W.D., Kollman P.A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges - the resp model. Journal of Physical Chemistry 1993, 97:10269-10280.
-
(1993)
Journal of Physical Chemistry
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
3
-
-
33750587438
-
Molecular-dynamics with coupling to an external bath
-
Berendsen H.J.C., Postma J.P.M., Vangunsteren W.F., Dinola A., Haak J.R. Molecular-dynamics with coupling to an external bath. Journal of Chemical Physics 1984, 81:3684-3690.
-
(1984)
Journal of Chemical Physics
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Vangunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
4
-
-
34347399347
-
The signal recognition particle (SRP) RNA links conformational changes in the SRP to protein targeting
-
Bradshaw N., Walter P. The signal recognition particle (SRP) RNA links conformational changes in the SRP to protein targeting. Molecular Biology of the Cell 2007, 18:2728-2734.
-
(2007)
Molecular Biology of the Cell
, vol.18
, pp. 2728-2734
-
-
Bradshaw, N.1
Walter, P.2
-
5
-
-
58149264965
-
Signal sequences activate the catalytic switch of SRP RNA
-
Bradshaw N., Neher S.B., Booth D.S., Walter P. Signal sequences activate the catalytic switch of SRP RNA. Science 2009, 323:127-130.
-
(2009)
Science
, vol.323
, pp. 127-130
-
-
Bradshaw, N.1
Neher, S.B.2
Booth, D.S.3
Walter, P.4
-
6
-
-
58049201323
-
-
University of California, San Francisco
-
Case D.A., Darden T.A., Cheatham T.E., Simmerling C.L., Wang J., Duke R.E., Luo R., Crowley M., Walker R.C., Zhang W., Merz K.M., Wang B., Hayik S., Roitberg A., Seabra G., Kolossváry I., Wong K.F., Paesani F., Vanicek J., Wu X., Brozell S.R., Steinbrecher T., Gohlke H., Yang L., Tan C., Mongan J., Hornak V., Cui G., Mathews D.H., Seetin M.G., Sagui C., Babin V., Kollman P.A. AMBER 10 2008, University of California, San Francisco.
-
(2008)
AMBER 10
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
Merz, K.M.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossváry, I.16
Wong, K.F.17
Paesani, F.18
Vanicek, J.19
Wu, X.20
Brozell, S.R.21
Steinbrecher, T.22
Gohlke, H.23
Yang, L.24
Tan, C.25
Mongan, J.26
Hornak, V.27
Cui, G.28
Mathews, D.H.29
Seetin, M.G.30
Sagui, C.31
Babin, V.32
Kollman, P.A.33
more..
-
7
-
-
36549025508
-
Structure of the chloroplast signal recognition particle (SRP) receptor: domain arrangement modulates SRP-receptor interaction
-
Chandrasekar S., Chartron J., Jaru-Ampornpan P., Shan S.O. Structure of the chloroplast signal recognition particle (SRP) receptor: domain arrangement modulates SRP-receptor interaction. Journal of Molecular Biology 2008, 375:425-436.
-
(2008)
Journal of Molecular Biology
, vol.375
, pp. 425-436
-
-
Chandrasekar, S.1
Chartron, J.2
Jaru-Ampornpan, P.3
Shan, S.O.4
-
8
-
-
84986516411
-
Application of the multimolecule and multiconformational RESP methodology to biopolymers - charge derivation for DNA, RNA, and proteins
-
Cieplak P., Cornell W.D., Bayly C., Kollman P.A. Application of the multimolecule and multiconformational RESP methodology to biopolymers - charge derivation for DNA, RNA, and proteins. Journal of Computational Chemistry 1995, 16:1357-1377.
-
(1995)
Journal of Computational Chemistry
, vol.16
, pp. 1357-1377
-
-
Cieplak, P.1
Cornell, W.D.2
Bayly, C.3
Kollman, P.A.4
-
9
-
-
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. Journal of Chemical Physics 1993, 98:10089-10092.
-
(1993)
Journal of Chemical Physics
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
10
-
-
78649904193
-
-
The PyMOL Molecular Graphics system. Available on the World Wide Web
-
DeLano, W.L., 2002. The PyMOL Molecular Graphics system. Available on the World Wide Web http://www.pymol.org.
-
(2002)
-
-
DeLano, W.L.1
-
11
-
-
3242886771
-
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
-
Dolinsky T.J., Nielsen J.E., McCammon J.A., Baker N.A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research 2004, 32:W665-W667.
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
-
12
-
-
38549152775
-
REDDB: a database for RESP and ESP atomic charges, and force field libraries
-
Dupradeau F.Y., Cezard C., Lelong R., Stanislawiak E., Pecher J., Delepine J.C., Cieplak P. REDDB: a database for RESP and ESP atomic charges, and force field libraries. Nucleic Acids Research 2008, 36:D360-D367.
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Dupradeau, F.Y.1
Cezard, C.2
Lelong, R.3
Stanislawiak, E.4
Pecher, J.5
Delepine, J.C.6
Cieplak, P.7
-
13
-
-
0347584006
-
Substrate twinning activates the signal recognition particle and its receptor
-
Egea P.F., Shan S.O., Napetschnig J., Savage D.F., Walter P., Stroud R.M. Substrate twinning activates the signal recognition particle and its receptor. Nature 2004, 427:215-221.
-
(2004)
Nature
, vol.427
, pp. 215-221
-
-
Egea, P.F.1
Shan, S.O.2
Napetschnig, J.3
Savage, D.F.4
Walter, P.5
Stroud, R.M.6
-
14
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G. A smooth particle mesh Ewald method. Journal of Chemical Physics 1995, 103:8577-8593.
-
(1995)
Journal of Chemical Physics
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
15
-
-
0346373753
-
Heterodimeric GTPase core of the SRP targeting complex
-
Focia P.J., Shepotinovskaya I.V., Seidler J.A., Freymann D.M. Heterodimeric GTPase core of the SRP targeting complex. Science 2004, 303:373-377.
-
(2004)
Science
, vol.303
, pp. 373-377
-
-
Focia, P.J.1
Shepotinovskaya, I.V.2
Seidler, J.A.3
Freymann, D.M.4
-
16
-
-
0031017523
-
Structure of the conserved GTPase domain of the signal recognition particle
-
Freymann D.M., Keenan R.J., Stroud R.M., Walter P. Structure of the conserved GTPase domain of the signal recognition particle. Nature 1997, 385:361-364.
-
(1997)
Nature
, vol.385
, pp. 361-364
-
-
Freymann, D.M.1
Keenan, R.J.2
Stroud, R.M.3
Walter, P.4
-
17
-
-
33947320768
-
Structure of the GMPPNP-stabilized NG domain complex of the SRP GTPases Ffh and FtsY
-
Gawronski-Salerno J., Freymann D.M. Structure of the GMPPNP-stabilized NG domain complex of the SRP GTPases Ffh and FtsY. Journal of Structural Biology 2007, 158:122-128.
-
(2007)
Journal of Structural Biology
, vol.158
, pp. 122-128
-
-
Gawronski-Salerno, J.1
Freymann, D.M.2
-
18
-
-
0043245780
-
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RaIGDS complexes
-
Gohlke H., Kiel C., Case D.A. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RaIGDS complexes. Journal of Molecular Biology 2003, 330:891-913.
-
(2003)
Journal of Molecular Biology
, vol.330
, pp. 891-913
-
-
Gohlke, H.1
Kiel, C.2
Case, D.A.3
-
19
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
Hornak V., Abel R., Okur A., Strockbine B., Roitberg A., Simmerling C. Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins - Structure Function and Bioinformatics 2006, 65:712-725.
-
(2006)
Proteins - Structure Function and Bioinformatics
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
20
-
-
34347374732
-
Efficient interaction between two GTPases allows the chloroplast SRP pathway to bypass the requirement for an SRP RNA
-
Jaru-Ampornpan P., Chandrasekar S., Shan S.O. Efficient interaction between two GTPases allows the chloroplast SRP pathway to bypass the requirement for an SRP RNA. Molecular Biology of the Cell 2007, 18:2636-2645.
-
(2007)
Molecular Biology of the Cell
, vol.18
, pp. 2636-2645
-
-
Jaru-Ampornpan, P.1
Chandrasekar, S.2
Shan, S.O.3
-
21
-
-
73649093135
-
Quantum mechanical effect in protein-ligand interaction
-
Jing Y.Q., Han K.L. Quantum mechanical effect in protein-ligand interaction. Expert Opinion on Drug Discovery 2010, 5:33-49.
-
(2010)
Expert Opinion on Drug Discovery
, vol.5
, pp. 33-49
-
-
Jing, Y.Q.1
Han, K.L.2
-
22
-
-
0020997912
-
Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features
-
Kabsch W., Sander C. Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
23
-
-
0029041304
-
A chloroplast homolog of the signal recognition particle subunit SRP54 is involved in the posttranslational integration of a protein into thylakoid membranes
-
Li X.X., Henry R., Yuan J.G., Cline K., Hoffman N.E. A chloroplast homolog of the signal recognition particle subunit SRP54 is involved in the posttranslational integration of a protein into thylakoid membranes. Proceedings of the National Academy of Sciences of the United States of America 1995, 92:3789-3793.
-
(1995)
Proceedings of the National Academy of Sciences of the United States of America
, vol.92
, pp. 3789-3793
-
-
Li, X.X.1
Henry, R.2
Yuan, J.G.3
Cline, K.4
Hoffman, N.E.5
-
25
-
-
0032824805
-
Folding funnels and binding mechanisms
-
Ma B.Y., Kumar S., Tsai C.J., Nussinov R. Folding funnels and binding mechanisms. Protein Engineering 1999, 12:713-720.
-
(1999)
Protein Engineering
, vol.12
, pp. 713-720
-
-
Ma, B.Y.1
Kumar, S.2
Tsai, C.J.3
Nussinov, R.4
-
26
-
-
0031030085
-
Crystal structure of the NG domain from the signal-recognition particle receptor FtsY
-
Montoya G., Svensson C., Luirink J., Sinning I. Crystal structure of the NG domain from the signal-recognition particle receptor FtsY. Nature 1997, 385:365-368.
-
(1997)
Nature
, vol.385
, pp. 365-368
-
-
Montoya, G.1
Svensson, C.2
Luirink, J.3
Sinning, I.4
-
27
-
-
51349165658
-
SRP RNA controls a conformational switch regulating the SRP-SRP receptor interaction
-
Neher S.B., Bradshaw N., Floor S.N., Gross J.D., Walter P. SRP RNA controls a conformational switch regulating the SRP-SRP receptor interaction. Nature Structural and Molecular Biology 2008, 15:916-923.
-
(2008)
Nature Structural and Molecular Biology
, vol.15
, pp. 916-923
-
-
Neher, S.B.1
Bradshaw, N.2
Floor, S.N.3
Gross, J.D.4
Walter, P.5
-
28
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified generalized Born model
-
Onufriev A., Bashford D., Case D.A. Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins - Structure Function and Bioinformatics 2004, 55:383-394.
-
(2004)
Proteins - Structure Function and Bioinformatics
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
29
-
-
84952104504
-
An analysis of the accuracy of Langevin and molecular-dynamics algorithms
-
Pastor R.W., Brooks B.R., Szabo A. An analysis of the accuracy of Langevin and molecular-dynamics algorithms. Molecular Physics 1988, 65:1409-1419.
-
(1988)
Molecular Physics
, vol.65
, pp. 1409-1419
-
-
Pastor, R.W.1
Brooks, B.R.2
Szabo, A.3
-
30
-
-
0035909810
-
Role of SRP RNA in the GTPase cycles of ffh and FtsY
-
Peluso P., Shan S.O., Nock S., Herschlag D., Walter P. Role of SRP RNA in the GTPase cycles of ffh and FtsY. Biochemistry 2001, 40:15224-15233.
-
(2001)
Biochemistry
, vol.40
, pp. 15224-15233
-
-
Peluso, P.1
Shan, S.O.2
Nock, S.3
Herschlag, D.4
Walter, P.5
-
31
-
-
18844387083
-
Signal recognition particles in chloroplasts, bacteria, yeast and mammals (Review)
-
Pool M.R. Signal recognition particles in chloroplasts, bacteria, yeast and mammals (Review). Molecular Membrane Biology 2005, 22:3-15.
-
(2005)
Molecular Membrane Biology
, vol.22
, pp. 3-15
-
-
Pool, M.R.1
-
32
-
-
36749001066
-
Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes
-
Rapoport T.A. Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes. Nature 2007, 450:663-669.
-
(2007)
Nature
, vol.450
, pp. 663-669
-
-
Rapoport, T.A.1
-
33
-
-
36148931107
-
X-ray structures of the signal recognition particle receptor reveal targeting cycle intermediates
-
Reyes C.L., Rutenber E., Walter P., Stroud R.M. X-ray structures of the signal recognition particle receptor reveal targeting cycle intermediates. PLOS ONE 2007, 2(e607):1-10.
-
(2007)
PLOS ONE
, vol.2 e
, Issue.607
, pp. 1-10
-
-
Reyes, C.L.1
Rutenber, E.2
Walter, P.3
Stroud, R.M.4
-
34
-
-
33646940952
-
Numerical-integration of Cartesian equations of motion of a system with constraints - molecular-dynamics of n-alkanes
-
Ryckaert J.P., Ciccotti G., Berendsen H.J.C. Numerical-integration of Cartesian equations of motion of a system with constraints - molecular-dynamics of n-alkanes. Journal of Computational Physics 1977, 23:327-341.
-
(1977)
Journal of Computational Physics
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
35
-
-
0032544070
-
A novel signal recognition particle targets light-harvesting proteins to the thylakoid membranes
-
Schuenemann D., Gupta S., Persello-Cartieaux F., Klimyuk V.I., Jones J.D.G., Nussaume L., Hoffman N.E. A novel signal recognition particle targets light-harvesting proteins to the thylakoid membranes. Proceedings of the National Academy of Sciences of the United States of America 1998, 95:10312-10316.
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, pp. 10312-10316
-
-
Schuenemann, D.1
Gupta, S.2
Persello-Cartieaux, F.3
Klimyuk, V.I.4
Jones, J.D.G.5
Nussaume, L.6
Hoffman, N.E.7
-
36
-
-
34547924871
-
Mechanisms of protein import into thylakoids of chloroplasts
-
Schunemann D. Mechanisms of protein import into thylakoids of chloroplasts. Biological Chemistry 2007, 388:907-915.
-
(2007)
Biological Chemistry
, vol.388
, pp. 907-915
-
-
Schunemann, D.1
-
38
-
-
14544302354
-
Co-translational protein targeting by the signal recognition particle
-
Shan S.O., Walter P. Co-translational protein targeting by the signal recognition particle. FEBS Letters 2005, 579:921-926.
-
(2005)
FEBS Letters
, vol.579
, pp. 921-926
-
-
Shan, S.O.1
Walter, P.2
-
39
-
-
8844253060
-
Mechanism of association and reciprocal activation of two GTPases
-
Shan S.O., Stroud R.M., Walter P. Mechanism of association and reciprocal activation of two GTPases. PLOS Biology 2004, 2:1572-1581.
-
(2004)
PLOS Biology
, vol.2
, pp. 1572-1581
-
-
Shan, S.O.1
Stroud, R.M.2
Walter, P.3
-
40
-
-
67651230544
-
Signal recognition particle (SRP) and SRP receptor: a new paradigm for multistate regulatory GTPases
-
Shan S.O., Schmid S.L., Zhang X. Signal recognition particle (SRP) and SRP receptor: a new paradigm for multistate regulatory GTPases. Biochemistry 2009, 48:6696-6704.
-
(2009)
Biochemistry
, vol.48
, pp. 6696-6704
-
-
Shan, S.O.1
Schmid, S.L.2
Zhang, X.3
-
41
-
-
33846456974
-
SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting
-
Siu F.Y., Spanggord R.J., Doudna J.A. SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting. RNA - A Publication of the RNA Society 2007, 13:240-250.
-
(2007)
RNA - A Publication of the RNA Society
, vol.13
, pp. 240-250
-
-
Siu, F.Y.1
Spanggord, R.J.2
Doudna, J.A.3
-
42
-
-
36549073183
-
The structure of the chloroplast signal recognition particle (SRP) receptor reveals mechanistic details of SRP GTPase activation and a conserved membrane targeting site
-
Stengel K.F., Holdermann I., Wild K., Sinning I. The structure of the chloroplast signal recognition particle (SRP) receptor reveals mechanistic details of SRP GTPase activation and a conserved membrane targeting site. FEBS Letters 2007, 581:5671-5676.
-
(2007)
FEBS Letters
, vol.581
, pp. 5671-5676
-
-
Stengel, K.F.1
Holdermann, I.2
Wild, K.3
Sinning, I.4
-
43
-
-
0027968068
-
CLUSTAL-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 1994, 22:4673-4680.
-
(1994)
Nucleic Acids Research
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
45
-
-
0000580602
-
The L18 domain of light-harvesting chlorophyll proteins binds to chloroplast signal recognition particle 43
-
Tu C.J., Peterson E.C., Henry R., Hoffman N.E. The L18 domain of light-harvesting chlorophyll proteins binds to chloroplast signal recognition particle 43. Journal of Biological Chemistry 2000, 275:13187-13190.
-
(2000)
Journal of Biological Chemistry
, vol.275
, pp. 13187-13190
-
-
Tu, C.J.1
Peterson, E.C.2
Henry, R.3
Hoffman, N.E.4
-
46
-
-
0028170807
-
Signal sequence recognition and protein targeting to the endoplasmic-reticulum membrane
-
Walter P., Johnson A.E. Signal sequence recognition and protein targeting to the endoplasmic-reticulum membrane. Annual Review of Cell Biology 1994, 10:87-119.
-
(1994)
Annual Review of Cell Biology
, vol.10
, pp. 87-119
-
-
Walter, P.1
Johnson, A.E.2
-
47
-
-
53849113368
-
Selectivity of neutral/weakly basic P1 group inhibitors of thrombin and trypsin by a molecular dynamics study
-
Wu E.L., Han K.L., Zhang J.Z.H. Selectivity of neutral/weakly basic P1 group inhibitors of thrombin and trypsin by a molecular dynamics study. Chemistry - A European Journal 2008, 14:8704-8714.
-
(2008)
Chemistry - A European Journal
, vol.14
, pp. 8704-8714
-
-
Wu, E.L.1
Han, K.L.2
Zhang, J.Z.H.3
-
48
-
-
77955839666
-
Molecular dynamics simulation of SRP GTPases: towards an understanding of the complex formation from equilibrium fluctuations
-
Yang M.J., Zhang X., Han K.L. Molecular dynamics simulation of SRP GTPases: towards an understanding of the complex formation from equilibrium fluctuations. Proteins - Structure Function and Genetics 2010, 78:2222-2237.
-
(2010)
Proteins - Structure Function and Genetics
, vol.78
, pp. 2222-2237
-
-
Yang, M.J.1
Zhang, X.2
Han, K.L.3
-
49
-
-
47849117948
-
Demonstration of a multistep mechanism for assembly of the SRP·SRP receptor complex: implications for the catalytic role of SRP RNA
-
Zhang X., Kung S., Shan S.O. Demonstration of a multistep mechanism for assembly of the SRP·SRP receptor complex: implications for the catalytic role of SRP RNA. Journal of Molecular Biology 2008, 381:581-593.
-
(2008)
Journal of Molecular Biology
, vol.381
, pp. 581-593
-
-
Zhang, X.1
Kung, S.2
Shan, S.O.3
-
50
-
-
60549083291
-
Multiple conformational switches in a GTPase complex control co-translational protein targeting
-
Zhang X., Schaffitzel C., Ban N., Shan S.O. Multiple conformational switches in a GTPase complex control co-translational protein targeting. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:1754-1759.
-
(2009)
Proceedings of the National Academy of Sciences of the United States of America
, vol.106
, pp. 1754-1759
-
-
Zhang, X.1
Schaffitzel, C.2
Ban, N.3
Shan, S.O.4
|