-
1
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan, A.R., Durell, S.R., Jernigan, R.L., Demirel, M.C., Keskin, O., and Bahar, I. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80: 505-515.
-
(2001)
Biophys J
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Jernigan, R.L.3
Demirel, M.C.4
Keskin, O.5
Bahar, I.6
-
2
-
-
0037031128
-
The sequence of the major gas vesicle protein, GvpA, influences width and strength of halobacterial gas vesicles
-
Beard, S., Hayes, P., Pfeifer, F., and Walsby, A.E. (2002) The sequence of the major gas vesicle protein, GvpA, influences width and strength of halobacterial gas vesicles. FEMS Microbiol Lett 213: 149-157.
-
(2002)
FEMS Microbiol Lett
, vol.213
, pp. 149-157
-
-
Beard, S.1
Hayes, P.2
Pfeifer, F.3
Walsby, A.E.4
-
3
-
-
0346057921
-
Subunit structure of gas vesicles: a MALDI-TOF mass spectrometry study
-
Belenky, M., Meyers, R., and Herzfeld, J. (2004) Subunit structure of gas vesicles: a MALDI-TOF mass spectrometry study. Biophys J 86: 499-505.
-
(2004)
Biophys J
, vol.86
, pp. 499-505
-
-
Belenky, M.1
Meyers, R.2
Herzfeld, J.3
-
4
-
-
79959553743
-
Crystalline structure of gas vesicle wall from Anabaena flos-aquae
-
Blaurock, A., and Walsby, A.E. (1976) Crystalline structure of gas vesicle wall from Anabaena flos-aquae. J Mol Biol 16: 871-888.
-
(1976)
J Mol Biol
, vol.16
, pp. 871-888
-
-
Blaurock, A.1
Walsby, A.E.2
-
5
-
-
0017142818
-
Structure of the wall of Halobacterium halobium gas vesicles
-
Blaurock, A., and Wober, W. (1976) Structure of the wall of Halobacterium halobium gas vesicles. J Mol Biol 106: 871-888.
-
(1976)
J Mol Biol
, vol.106
, pp. 871-888
-
-
Blaurock, A.1
Wober, W.2
-
6
-
-
0036968925
-
De novo prediction of three-dimensional structures for major protein families
-
Bonneau, R., Strauss, C.E.M., Rohl, C.A., Chivian, D., Bradley, P., Malmström, L., etal. (2002) De novo prediction of three-dimensional structures for major protein families. J Mol Biol 322: 65-78.
-
(2002)
J Mol Biol
, vol.322
, pp. 65-78
-
-
Bonneau, R.1
Strauss, C.E.M.2
Rohl, C.A.3
Chivian, D.4
Bradley, P.5
Malmström, L.6
-
7
-
-
23144444979
-
Protein structure prediction servers at University College London
-
Bryson, K., McGuffin, L.J., Marsden, R.L., Ward, J.J., Sodhi, J.S., and Jones, D.T. (2005) Protein structure prediction servers at University College London. Nucleic Acids Res 33: W36-W38.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Bryson, K.1
McGuffin, L.J.2
Marsden, R.L.3
Ward, J.J.4
Sodhi, J.S.5
Jones, D.T.6
-
8
-
-
0027155201
-
Analysis of gas vesicle gene expression in Haloferax mediterranei reveals that GvpA and GvpC are both gas vesicle structural proteins
-
Englert, C., and Pfeifer, F. (1993) Analysis of gas vesicle gene expression in Haloferax mediterranei reveals that GvpA and GvpC are both gas vesicle structural proteins. J Biol Chem 268: 9329-9336.
-
(1993)
J Biol Chem
, vol.268
, pp. 9329-9336
-
-
Englert, C.1
Pfeifer, F.2
-
9
-
-
0026714661
-
Three different but related gene clusters encoding gas vesicles in halophilic Archaea
-
Englert, C., Krüger, K., Offner, S., and Pfeifer, F. (1992a) Three different but related gene clusters encoding gas vesicles in halophilic Archaea. J Mol Biol 227: 586-592.
-
(1992)
J Mol Biol
, vol.227
, pp. 586-592
-
-
Englert, C.1
Krüger, K.2
Offner, S.3
Pfeifer, F.4
-
10
-
-
0026677546
-
Functional analysis of the gas vesicle gene cluster of the halophilic archaeon Haloferax mediterranei defines the vac-region boundary and suggests a regulatory role for the gvpD gene or its product
-
Englert, C., Wanner, G., and Pfeifer, F. (1992b) Functional analysis of the gas vesicle gene cluster of the halophilic archaeon Haloferax mediterranei defines the vac-region boundary and suggests a regulatory role for the gvpD gene or its product. Mol Microbiol 6: 3543-3550.
-
(1992)
Mol Microbiol
, vol.6
, pp. 3543-3550
-
-
Englert, C.1
Wanner, G.2
Pfeifer, F.3
-
11
-
-
0038386050
-
3D-Jury: a simple approach to improve protein structure predictions
-
Ginalski, K., Elofsson, A., Fischer, D., and Rychlewski, L. (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19: 1015-1018.
-
(2003)
Bioinformatics
, vol.19
, pp. 1015-1018
-
-
Ginalski, K.1
Elofsson, A.2
Fischer, D.3
Rychlewski, L.4
-
12
-
-
33646196840
-
Evaluation of the information content in infrared spectra for protein secondary structure determination
-
Goormaghtigh, E., Ruysschaert, J.M., and Raussens, V. (2006) Evaluation of the information content in infrared spectra for protein secondary structure determination. Biophys J 90: 2946-2957.
-
(2006)
Biophys J
, vol.90
, pp. 2946-2957
-
-
Goormaghtigh, E.1
Ruysschaert, J.M.2
Raussens, V.3
-
13
-
-
70349472977
-
Template-free protein structure prediction and quality assessment with an all-atom free-energy model
-
Gopal, S.M., Verma, A., and Wenzel, W. (2009) Template-free protein structure prediction and quality assessment with an all-atom free-energy model. Proteins 77: 330-341.
-
(2009)
Proteins
, vol.77
, pp. 330-341
-
-
Gopal, S.M.1
Verma, A.2
Wenzel, W.3
-
14
-
-
49049087284
-
Relating sequence evolution of HIV1-protease to its underlying molecular mechanics
-
Hamacher, K. (2008) Relating sequence evolution of HIV1-protease to its underlying molecular mechanics. Gene 422: 30-36.
-
(2008)
Gene
, vol.422
, pp. 30-36
-
-
Hamacher, K.1
-
15
-
-
33846247964
-
Computing the amino acid specificity of fluctuations in biomolecular systems
-
Hamacher, K., and McCammon, J.A. (2006) Computing the amino acid specificity of fluctuations in biomolecular systems. J Chem Theor Comput 2: 873.
-
(2006)
J Chem Theor Comput
, vol.2
, pp. 873
-
-
Hamacher, K.1
McCammon, J.A.2
-
16
-
-
0023049694
-
Complete amino acid sequence of cyanobacterial gas-vesicle protein indicates a 70-residue molecule that corresponds in size to the crystallographic unit cell
-
Hayes, P., Walsby, A., and Walker, J. (1986) Complete amino acid sequence of cyanobacterial gas-vesicle protein indicates a 70-residue molecule that corresponds in size to the crystallographic unit cell. Biochem J 236: 31-36.
-
(1986)
Biochem J
, vol.236
, pp. 31-36
-
-
Hayes, P.1
Walsby, A.2
Walker, J.3
-
17
-
-
58149125398
-
Anaerobiosis inhibits gas vesicle formation in halophilic Archaea
-
Hechler, T., and Pfeifer, F. (2009) Anaerobiosis inhibits gas vesicle formation in halophilic Archaea. Mol Microbiol 71: 132-145.
-
(2009)
Mol Microbiol
, vol.71
, pp. 132-145
-
-
Hechler, T.1
Pfeifer, F.2
-
18
-
-
3142767630
-
GvpE- and GvpD-mediated transcription regulation of the p-gvp genes encoding gas vesicles in Halobacterium salinarum
-
Hofacker, A., Schmitz, K., Cichonczyk, A., Sartorius-Neef, S., and Pfeifer, F. (2004) GvpE- and GvpD-mediated transcription regulation of the p-gvp genes encoding gas vesicles in Halobacterium salinarum. Microbiology 150: 1829-1838.
-
(2004)
Microbiology
, vol.150
, pp. 1829-1838
-
-
Hofacker, A.1
Schmitz, K.2
Cichonczyk, A.3
Sartorius-Neef, S.4
Pfeifer, F.5
-
19
-
-
77951065786
-
BioPhysConnectoR: connecting sequence information and biophysical models
-
Hoffgaard, F., Weil, P., and Hamacher, K. (2010) BioPhysConnectoR: connecting sequence information and biophysical models. BMC Bioinformatics 11: 199.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 199
-
-
Hoffgaard, F.1
Weil, P.2
Hamacher, K.3
-
20
-
-
0029878720
-
VMD - visual molecular dynamics
-
Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD - visual molecular dynamics. J Mol Graph 14: 33-38.
-
(1996)
J Mol Graph
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
21
-
-
0029018548
-
The use and misuse of FTIR spectroscopy in the determination of protein structure
-
Jackson, M., and Mantsch, H.H. (1995) The use and misuse of FTIR spectroscopy in the determination of protein structure. Crit Rev Biochem Mol Biol 30: 95-120.
-
(1995)
Crit Rev Biochem Mol Biol
, vol.30
, pp. 95-120
-
-
Jackson, M.1
Mantsch, H.H.2
-
22
-
-
0242362161
-
Combining local-structure, fold-recognition, and new fold methods for protein structure prediction
-
Karplus, K., Karchin, R., Draper, J., Casper, J., Mandel-Gutfreund, Y., Diekhans, M., and Hughey, R. (2003) Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins 53 (Suppl. 6): 491-496.
-
(2003)
Proteins
, vol.53
, Issue.6 SUPPL.
, pp. 491-496
-
-
Karplus, K.1
Karchin, R.2
Draper, J.3
Casper, J.4
Mandel-Gutfreund, Y.5
Diekhans, M.6
Hughey, R.7
-
23
-
-
54949103617
-
PREDICT-2ND: a tool for generalized protein local structure prediction
-
Katzman, S., Barrett, C., Thiltgen, G., Karchin, R., and Karplus, K. (2008) PREDICT-2ND: a tool for generalized protein local structure prediction. Bioinformatics 24: 2453-2459.
-
(2008)
Bioinformatics
, vol.24
, pp. 2453-2459
-
-
Katzman, S.1
Barrett, C.2
Thiltgen, G.3
Karchin, R.4
Karplus, K.5
-
24
-
-
63849246525
-
Protein structure prediction on the Web: a case study using the PHYRE server
-
Kelley, L.A., and Sternberg, M.J.E. (2009) Protein structure prediction on the Web: a case study using the PHYRE server. Nat Protoc 4: 363-371.
-
(2009)
Nat Protoc
, vol.4
, pp. 363-371
-
-
Kelley, L.A.1
Sternberg, M.J.E.2
-
25
-
-
0029042511
-
Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4Å resolution
-
Löwe, J., Stock, D., Jap, B., Zwickl, P., Baumeister, W., and Huber, R. (1995) Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4Å resolution. Science 268: 533-539.
-
(1995)
Science
, vol.268
, pp. 533-539
-
-
Löwe, J.1
Stock, D.2
Jap, B.3
Zwickl, P.4
Baumeister, W.5
Huber, R.6
-
26
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
MacKerell, A.D., Feig, M., and Brooks, C.L., III (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 25: 1400-1415.
-
(2004)
J Comput Chem
, vol.25
, pp. 1400-1415
-
-
MacKerell, A.D.1
Feig, M.2
Brooks III, C.L.3
-
27
-
-
0029862834
-
Direct observation of protein secondary structure in gas vesicles by atomic force microscopy
-
McMaster, T., Niles, M., and Walsby, A.E. (1996) Direct observation of protein secondary structure in gas vesicles by atomic force microscopy. Biophys J 70: 2431-2436.
-
(1996)
Biophys J
, vol.70
, pp. 2431-2436
-
-
McMaster, T.1
Niles, M.2
Walsby, A.E.3
-
28
-
-
0033623952
-
Eight of fourteen gvp genes are sufficient for formation of gas vesicles in halophilic archaea
-
Offner, S., Hofacker, A., Wanner, G., and Pfeifer, F. (2000) Eight of fourteen gvp genes are sufficient for formation of gas vesicles in halophilic archaea. J Bacteriol 182: 4328-4336.
-
(2000)
J Bacteriol
, vol.182
, pp. 4328-4336
-
-
Offner, S.1
Hofacker, A.2
Wanner, G.3
Pfeifer, F.4
-
29
-
-
0027207837
-
Plasmid pHH1 of Halobacterium salinarum: characterization of the replicon region, the gas vesicle gene cluster and insertion elements
-
Pfeifer, F., and Ghahraman, P. (1993) Plasmid pHH1 of Halobacterium salinarum: characterization of the replicon region, the gas vesicle gene cluster and insertion elements. Mol Gen Genet 238: 193-200.
-
(1993)
Mol Gen Genet
, vol.238
, pp. 193-200
-
-
Pfeifer, F.1
Ghahraman, P.2
-
30
-
-
0035157178
-
A p-loop motif and two basic regions in the regulatory protein GvpD are important for the repression of gas vesicle formation in the archaeon Haloferax mediterranei
-
Pfeifer, F., Zotzel, J., Kurenbach, B., Röder, R., and Zimmermann, P. (2001) A p-loop motif and two basic regions in the regulatory protein GvpD are important for the repression of gas vesicle formation in the archaeon Haloferax mediterranei. Microbiology 147: 63-73.
-
(2001)
Microbiology
, vol.147
, pp. 63-73
-
-
Pfeifer, F.1
Zotzel, J.2
Kurenbach, B.3
Röder, R.4
Zimmermann, P.5
-
31
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., etal. (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
-
32
-
-
1642464839
-
Protein structure prediction using Rosetta
-
Rohl, C.A., Strauss, C.E., Misura, K.M., and Baker, D. (2004) Protein structure prediction using Rosetta. Methods Enzymol 383: 66-93.
-
(2004)
Methods Enzymol
, vol.383
, pp. 66-93
-
-
Rohl, C.A.1
Strauss, C.E.2
Misura, K.M.3
Baker, D.4
-
33
-
-
49749084731
-
Regulation of gvp genes encoding gas vesicle proteins in halophilic archaea
-
Scheuch, S., Marschaus, L., Sartorius-Neef, S., and Pfeifer, F. (2008) Regulation of gvp genes encoding gas vesicle proteins in halophilic archaea. Arch Microbiol 190: 333-340.
-
(2008)
Arch Microbiol
, vol.190
, pp. 333-340
-
-
Scheuch, S.1
Marschaus, L.2
Sartorius-Neef, S.3
Pfeifer, F.4
-
34
-
-
0035967880
-
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
Shi, J., Blundell, T.L., and Mizuguchi, K. (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 310: 243-257.
-
(2001)
J Mol Biol
, vol.310
, pp. 243-257
-
-
Shi, J.1
Blundell, T.L.2
Mizuguchi, K.3
-
35
-
-
2342660728
-
Complexity of gas vesicle biogenesis in Halobacterium sp. strain NRC-1: identification of five new proteins
-
Shukla, H.D., and DasSarma, S. (2004) Complexity of gas vesicle biogenesis in Halobacterium sp. strain NRC-1: identification of five new proteins. J Bacteriol 186: 3182-3186.
-
(2004)
J Bacteriol
, vol.186
, pp. 3182-3186
-
-
Shukla, H.D.1
DasSarma, S.2
-
36
-
-
0033670439
-
MaxSub: an automated measure for the assessment of protein structure prediction quality
-
Siew, N., Elofsson, A., Rychlewski, L., and Fischer, D. (2000) MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 16: 776-785.
-
(2000)
Bioinformatics
, vol.16
, pp. 776-785
-
-
Siew, N.1
Elofsson, A.2
Rychlewski, L.3
Fischer, D.4
-
37
-
-
62649156736
-
Solid-state NMR evidence for inequal GvpA subunits in gas vesicles
-
Sivertsen, A., Bayro, M., Belenky, M., Griffin, R., and Herzfeld, J. (2009) Solid-state NMR evidence for inequal GvpA subunits in gas vesicles. J Mol Biol 387: 1032-1039.
-
(2009)
J Mol Biol
, vol.387
, pp. 1032-1039
-
-
Sivertsen, A.1
Bayro, M.2
Belenky, M.3
Griffin, R.4
Herzfeld, J.5
-
38
-
-
77957340600
-
Solid-state NMR characterization of gas vesicle structure
-
Sivertsen, A., Bayro, M., Belenky, M., Griffin, R., and Herzfeld, J. (2010) Solid-state NMR characterization of gas vesicle structure. Biophys J 99: 1932-1939.
-
(2010)
Biophys J
, vol.99
, pp. 1932-1939
-
-
Sivertsen, A.1
Bayro, M.2
Belenky, M.3
Griffin, R.4
Herzfeld, J.5
-
39
-
-
0014322650
-
Further characterization of particulate fractions from lysed cell envelopes of Halobacterium halobium and isolation of gas vacuole membranes
-
Stoeckenius, W., and Kunau, W. (1968) Further characterization of particulate fractions from lysed cell envelopes of Halobacterium halobium and isolation of gas vacuole membranes. J Cell Biol 38: 337-357.
-
(1968)
J Cell Biol
, vol.38
, pp. 337-357
-
-
Stoeckenius, W.1
Kunau, W.2
-
40
-
-
0038008976
-
An improved protein decoy set for testing energy functions for protein structure prediction
-
Tsai, J., Bonneau, R., Morozov, A.V., Kuhlman, B., Rohl, C.A., and Baker, D. (2003) An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 53: 76-87.
-
(2003)
Proteins
, vol.53
, pp. 76-87
-
-
Tsai, J.1
Bonneau, R.2
Morozov, A.V.3
Kuhlman, B.4
Rohl, C.A.5
Baker, D.6
-
41
-
-
27344454932
-
GROMACS: fast, flexible, and free
-
Van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A.E., and Berendsen, H.J. (2005) GROMACS: fast, flexible, and free. J Comput Chem 26: 1701-1718.
-
(2005)
J Comput Chem
, vol.26
, pp. 1701-1718
-
-
Van der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.6
-
42
-
-
0028514996
-
Linearly scalable computation of smooth molecular surfaces
-
Varshney, A., Brooks, F.P., and Wright, W.V. (1994) Linearly scalable computation of smooth molecular surfaces. IEEE Comput Graph Appl 14: 19-25.
-
(1994)
IEEE Comput Graph Appl
, vol.14
, pp. 19-25
-
-
Varshney, A.1
Brooks, F.P.2
Wright, W.V.3
-
43
-
-
67650354848
-
A free-energy approach for all-atom protein simulation
-
Verma, A., and Wenzel, W. (2009) A free-energy approach for all-atom protein simulation. Biophys J 96: 3483-3494.
-
(2009)
Biophys J
, vol.96
, pp. 3483-3494
-
-
Verma, A.1
Wenzel, W.2
-
44
-
-
33749665952
-
Basin hopping simulations for all-atom protein folding
-
Verma, A., Schug, A., Lee, K.H., and Wenzel, W. (2006) Basin hopping simulations for all-atom protein folding. J Chem Phys 124: 044515.
-
(2006)
J Chem Phys
, vol.124
, pp. 044515
-
-
Verma, A.1
Schug, A.2
Lee, K.H.3
Wenzel, W.4
-
45
-
-
0028261412
-
Gas vesicles
-
Walsby, A.E. (1994) Gas vesicles. Microbiol Rev 58: 94-144.
-
(1994)
Microbiol Rev
, vol.58
, pp. 94-144
-
-
Walsby, A.E.1
-
46
-
-
34548861782
-
Protein-protein docking with backbone flexibility
-
Wang, C., Bradley, P., and Baker, D. (2007) Protein-protein docking with backbone flexibility. J Mol Biol 373: 503-519.
-
(2007)
J Mol Biol
, vol.373
, pp. 503-519
-
-
Wang, C.1
Bradley, P.2
Baker, D.3
-
47
-
-
9344243513
-
FTIR reveals structural differences between native β-sheet proteins and amyloid fibrils
-
Zandomeneghi, G., Krebs, M.R.H., McCammon, M.G., and Fändrich, M. (2004) FTIR reveals structural differences between native β-sheet proteins and amyloid fibrils. Protein Sci 13: 3314-3321.
-
(2004)
Protein Sci
, vol.13
, pp. 3314-3321
-
-
Zandomeneghi, G.1
Krebs, M.R.H.2
McCammon, M.G.3
Fändrich, M.4
-
48
-
-
0032128128
-
Crystallization and preliminary X-ray crystallographic studies of the native and chemically modified anion-selective porin from Comamonas acidovorans
-
Zeth, K., Schnaible, V., Przyblyski, M., Welte, W., Diederichs, K., and Engelhardt, H. (1998) Crystallization and preliminary X-ray crystallographic studies of the native and chemically modified anion-selective porin from Comamonas acidovorans. Acta Cryst D54: 650-653.
-
(1998)
Acta Cryst
, vol.D54
, pp. 650-653
-
-
Zeth, K.1
Schnaible, V.2
Przyblyski, M.3
Welte, W.4
Diederichs, K.5
Engelhardt, H.6
-
49
-
-
39449115394
-
I-TASSER server for protein 3D structure prediction
-
Zhang, Y. (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9: 40.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 40
-
-
Zhang, Y.1
-
50
-
-
0026467097
-
Expression of functional Thermoplasma acidophilum proteasomes in Escherichia coli
-
Zwickl, P., Lottspeich, F., and Baumeister, W. (1992) Expression of functional Thermoplasma acidophilum proteasomes in Escherichia coli. FEBS Lett 312: 157-160.
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(1992)
FEBS Lett
, vol.312
, pp. 157-160
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Zwickl, P.1
Lottspeich, F.2
Baumeister, W.3
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