-
1
-
-
0027412196
-
ALSCRIPT: A tool to format multiple sequence alignments
-
Barton, G.J. 1993. ALSCRIPT: A tool to format multiple sequence alignments. Protein Eng. 6: 37-40.
-
(1993)
Protein Eng.
, vol.6
, pp. 37-40
-
-
Barton, G.J.1
-
2
-
-
0029149907
-
Protein secondary structure prediction
-
-. 1995. Protein secondary structure prediction. Curr. Opin. Struct. Biol. 5: 372-376.
-
(1995)
Curr. Opin. Struct. Biol.
, vol.5
, pp. 372-376
-
-
-
3
-
-
0011542799
-
The Pfam protein families database
-
Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M., and Sonnhammer, E.L. 2002. The Pfam protein families database. Nucleic Acids Res. 30: 276-280.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 276-280
-
-
Bateman, A.1
Birney, E.2
Cerruti, L.3
Durbin, R.4
Etwiller, L.5
Eddy, S.R.6
Griffiths-Jones, S.7
Howe, K.L.8
Marshall, M.9
Sonnhammer, E.L.10
-
4
-
-
0037314068
-
TopDraw: A sketchpad for protein structure topology cartoons
-
Bond, C.S. 2003. TopDraw: A sketchpad for protein structure topology cartoons. Bioinformatics 19: 311-312.
-
(2003)
Bioinformatics
, vol.19
, pp. 311-312
-
-
Bond, C.S.1
-
5
-
-
0029004044
-
Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry
-
Cohen, S.L., Ferre-D'Amare, A.R., Burley, S.K., and Chait, B.T. 1995. Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry. Protein Set. 4: 1088-1099.
-
(1995)
Protein Set.
, vol.4
, pp. 1088-1099
-
-
Cohen, S.L.1
Ferre-D'Amare, A.R.2
Burley, S.K.3
Chait, B.T.4
-
6
-
-
0028103275
-
The CCP4 suite: Programs for protein crystallography, version 3.1
-
Collaborative Computational Project Number 4. 1994. The CCP4 suite: Programs for protein crystallography, version 3.1. Acta Crystallogr. D Biol. Crystallogr. 50: 760-763.
-
(1994)
Acta Crystallogr. D Biol. Crystallogr.
, vol.50
, pp. 760-763
-
-
-
7
-
-
0038810081
-
Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry
-
Englander, J.J., DelMar, C., Li, W., Englander, S.W., Kim, S.S., Stranz, D.D., Hamuro, Y., and Woods Jr., V.L. 2003. Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry. Prac. Natl. Acad. Sci. 100: 7057-7062.
-
(2003)
Prac. Natl. Acad. Sci.
, vol.100
, pp. 7057-7062
-
-
Englander, J.J.1
DelMar, C.2
Li, W.3
Englander, S.W.4
Kim, S.S.5
Stranz, D.D.6
Hamuro, Y.7
Woods Jr., V.L.8
-
8
-
-
0030729838
-
An extensively modified version of Molscript which includes greatly enhanced colouring capabilities
-
Esnouf, R.M. 1997. An extensively modified version of Molscript which includes greatly enhanced colouring capabilities. J. Mol. Graph. 15: 132-134.
-
(1997)
J. Mol. Graph.
, vol.15
, pp. 132-134
-
-
Esnouf, R.M.1
-
9
-
-
0033529952
-
Functional genomics
-
Fields, S., Kohara, Y., and Lockhart, D.J. 1999. Functional genomics. Proc. Natl. Acad. Sci. 96: 8825-8826.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 8825-8826
-
-
Fields, S.1
Kohara, Y.2
Lockhart, D.J.3
-
10
-
-
0036965184
-
Domain organization of D-AKAP2 revealed by deuterium exchange-mass spectrometry (DXMS)
-
Hamuro, Y., Burns, L.L., Canaves, J.M., Hoffman, R.C., Taylor, S.S., and Woods Jr., V.L. 2002a. Domain organization of D-AKAP2 revealed by deuterium exchange-mass spectrometry (DXMS). J. Mol. Biol. 4: 703-714.
-
(2002)
J. Mol. Biol.
, vol.4
, pp. 703-714
-
-
Hamuro, Y.1
Burns, L.L.2
Canaves, J.M.3
Hoffman, R.C.4
Taylor, S.S.5
Woods Jr., V.L.6
-
11
-
-
0036428762
-
Phosphorylation-driven motion in the COOH-terminal Src Kinase, Csk, revealed through enhanced hydrogen-deuterium exchange and mass spectrometry (DXMS)
-
Hamuro, Y., Wong, L., Shaffer, J., Kim, J.S., Jennrngs, P.A., Adams, J.A., and Woods Jr., V.L. 2002b. Phosphorylation-driven motion in the COOH-terminal Src Kinase, Csk, revealed through enhanced hydrogen-deuterium exchange and mass spectrometry (DXMS). J. Mol. Biol. 323: 871-881.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 871-881
-
-
Hamuro, Y.1
Wong, L.2
Shaffer, J.3
Kim, J.S.4
Jennrngs, P.A.5
Adams, J.A.6
Woods Jr., V.L.7
-
12
-
-
0344405702
-
Dynamics of cAPK type IIb activation revealed by enhanced amide H/2H exchange mass spectrometry (DXMS)
-
Hamuro, Y., Zawadzki, K.M., Kim, J.S., Stranz, D., Taylor, S.S., and Woods Jr., V.L. 2003. Dynamics of cAPK type IIb activation revealed by enhanced amide H/2H exchange mass spectrometry (DXMS). J. Mol. Biol. 327: 1065-1076.
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 1065-1076
-
-
Hamuro, Y.1
Zawadzki, K.M.2
Kim, J.S.3
Stranz, D.4
Taylor, S.S.5
Woods Jr., V.L.6
-
13
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
Holm, L. and Sander, C. 1993. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233: 123-138.
-
(1993)
J. Mol. Biol.
, vol.233
, pp. 123-138
-
-
Holm, L.1
Sander, C.2
-
14
-
-
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
-
15
-
-
84889120137
-
Improved methods for building protein models in electron density maps and the location of errors in these models
-
Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard, M. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47: 110-119.
-
(1991)
Acta Crystallogr. A
, vol.47
, pp. 110-119
-
-
Jones, T.A.1
Zou, J.Y.2
Cowan, S.W.3
Kjeldgaard, M.4
-
16
-
-
0033613813
-
Recognition of spatial motifs in protein structures
-
Kleywegt, G.J. 1999. Recognition of spatial motifs in protein structures. J. Mol. Biol. 285: 1887-1897.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1887-1897
-
-
Kleywegt, G.J.1
-
17
-
-
0026244229
-
MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
-
Kraulis, P.J. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24: 946-950.
-
(1991)
J. Appl. Crystallogr.
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
19
-
-
0037015054
-
Structural genomics of the Thermatoga maritima proteome implemented in a high-throughput structure determination pipeline
-
Lesley, S.A., Kuhn, P., Godzik, A., Deacon, A.M., Mathews, I., Kreusch, A., Spraggon, G., Klock, H.E., McMullan, D., Shin, T., et al. 2002. Structural genomics of the Thermatoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc. Natl. Acad. Sci. 99: 11664-11669.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 11664-11669
-
-
Lesley, S.A.1
Kuhn, P.2
Godzik, A.3
Deacon, A.M.4
Mathews, I.5
Kreusch, A.6
Spraggon, G.7
Klock, H.E.8
McMullan, D.9
Shin, T.10
-
20
-
-
0037162464
-
Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds
-
Mallick, P., Boutz, D.R., Eisenberg, D., and Yeates, T.O. 2002. Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proc. Natl. Acad. Sci. 99: 9679-9684.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 9679-9684
-
-
Mallick, P.1
Boutz, D.R.2
Eisenberg, D.3
Yeates, T.O.4
-
21
-
-
0142103146
-
Functional analysis of substrate and cofactor complex structures of a thymidylate synthetase complementing protein
-
Mathews, I.I., Deacon, A.M., Canaves, J.M., McMullan, D., Lesley, S.A., Agarwalla, S., and Kuhn, P. 2003. Functional analysis of substrate and cofactor complex structures of a thymidylate synthetase complementing protein. Structure 11: 677-690.
-
(2003)
Structure
, vol.11
, pp. 677-690
-
-
Mathews, I.I.1
Deacon, A.M.2
Canaves, J.M.3
McMullan, D.4
Lesley, S.A.5
Agarwalla, S.6
Kuhn, P.7
-
22
-
-
0028057108
-
Raster3D version 2.0: A program for photorealistic molecular graphics
-
Meritt, E.A. 1994. Raster3D version 2.0: A program for photorealistic molecular graphics. Acta. Crystallogr. D Biol. Crystallogr. 50: 869-873.
-
(1994)
Acta. Crystallogr. D Biol. Crystallogr.
, vol.50
, pp. 869-873
-
-
Meritt, E.A.1
-
23
-
-
0030924992
-
Refinement of macromolecular structures by the maximum-likelihood method
-
Murshudov, G.N. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53: 240-255.
-
(1997)
Acta Crystallogr. D Biol. Crystallogr.
, vol.53
, pp. 240-255
-
-
Murshudov, G.N.1
-
24
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
25
-
-
0033609333
-
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
-
Nelson, K.E., Clayton, R.A., Gill, S.R., Gwinn, M.L., Dodson, R.J., Haft, D.H., Hickey, E.K., Peterson, J.D., Nelson, W.C., Ketchum, K.A., et al. 1999. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399: 323-329.
-
(1999)
Nature
, vol.399
, pp. 323-329
-
-
Nelson, K.E.1
Clayton, R.A.2
Gill, S.R.3
Gwinn, M.L.4
Dodson, R.J.5
Haft, D.H.6
Hickey, E.K.7
Peterson, J.D.8
Nelson, W.C.9
Ketchum, K.A.10
-
26
-
-
0034623005
-
T-Coffee: A novel method for multiple sequence alignments
-
Notredame, C., Higgins, D., and Heringa, J. 2000. T-Coffee: A novel method for multiple sequence alignments. J. Mol. Biol. 302: 205-217.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.2
Heringa, J.3
-
27
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Otwinowski, Z. and Minor, W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307-326.
-
(1997)
Methods Enzymol.
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
28
-
-
1642514905
-
Rapid refinement of crystallographic protein construct definition employing enhanced hydrogren/deuterium exchange mass spectrometry
-
Pantazatos, D., Kim, J.S., Klock, H.E., Stevens, R.C., Wilson, I.A., Lesley, S.A., and Woods Jr., V.L. 2004. Rapid refinement of crystallographic protein construct definition employing enhanced hydrogren/deuterium exchange mass spectrometry. Proc. Natl. Acad. Sci. 101: 751-756.
-
(2004)
Proc. Natl. Acad. Sci.
, vol.101
, pp. 751-756
-
-
Pantazatos, D.1
Kim, J.S.2
Klock, H.E.3
Stevens, R.C.4
Wilson, I.A.5
Lesley, S.A.6
Woods Jr., V.L.7
-
29
-
-
0029740167
-
Aromatic hydrogen bond in sequence-specific protein DNA recognition
-
Parkinson, G., Gunasekera, A., Vojtechovsky, J., Zhang, X., Kunkel, T.A., Berman, H., and Ebright, R.H. 1996. Aromatic hydrogen bond in sequence-specific protein DNA recognition. Nat. Struct. Biol. 3: 837-841.
-
(1996)
Nat. Struct. Biol.
, vol.3
, pp. 837-841
-
-
Parkinson, G.1
Gunasekera, A.2
Vojtechovsky, J.3
Zhang, X.4
Kunkel, T.A.5
Berman, H.6
Ebright, R.H.7
-
30
-
-
0017429069
-
Areas, volumes, packing and protein structure
-
Richards, P.M. 1977. Areas, volumes, packing and protein structure. Annu. Rev. Biophys. Bioeng. 6: 151-176.
-
(1977)
Annu. Rev. Biophys. Bioeng.
, vol.6
, pp. 151-176
-
-
Richards, P.M.1
-
31
-
-
0026743174
-
Multiple protein sequence alignment from tertiary structure comparison
-
Russell, R.B. and Barton, G.J. 1992. Multiple protein sequence alignment from tertiary structure comparison. Proteins 14: 309-323.
-
(1992)
Proteins
, vol.14
, pp. 309-323
-
-
Russell, R.B.1
Barton, G.J.2
-
32
-
-
18344375268
-
An approach to rapid protein crystallization using nanodroplets
-
Santarsiero, B.D., Yegian, D.T., Lee, C.C., Spraggon, G., Gu, J., Scheibe, D., Uber, D.C., Cornell, E.W., Nordmeyer, R.A., Kolbe, W.F., et al. 2002. An approach to rapid protein crystallization using nanodroplets. J. Appl. Cryst. 35: 278-281.
-
(2002)
J. Appl. Cryst.
, vol.35
, pp. 278-281
-
-
Santarsiero, B.D.1
Yegian, D.T.2
Lee, C.C.3
Spraggon, G.4
Gu, J.5
Scheibe, D.6
Uber, D.C.7
Cornell, E.W.8
Nordmeyer, R.A.9
Kolbe, W.F.10
-
33
-
-
0037424601
-
A model for statistical significance of local similarities in structure
-
Stark, A., Sunyaev, S., and Russell, R.B. 2003. A model for statistical significance of local similarities in structure. J. Mol. Biol. 326: 1307-1316.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 1307-1316
-
-
Stark, A.1
Sunyaev, S.2
Russell, R.B.3
-
35
-
-
0035207615
-
Map-likelihood phasing
-
-. 2001a. Map-likelihood phasing. Acta Crystallogr. D Biol. Crystallogr. 57: 1763-1775.
-
(2001)
Acta Crystallogr. D Biol. Crystallogr.
, vol.57
, pp. 1763-1775
-
-
-
36
-
-
0035210945
-
Maximum-likelihood density modification using pattern recognition of structural motifs
-
-. 2001b. Maximum-likelihood density modification using pattern recognition of structural motifs. Acta Crystallogr. D Biol. Crystallogr. 57: 1755-1762.
-
(2001)
Acta Crystallogr. D Biol. Crystallogr.
, vol.57
, pp. 1755-1762
-
-
-
38
-
-
0032031476
-
Error estimates of protein structure coordinates and deviations from standard geometry by full-matrix refinement of γB- and βB2-crystallin
-
Tickle, I.J., Laskowski, R.A., and Moss, D.S. 1998. Error estimates of protein structure coordinates and deviations from standard geometry by full-matrix refinement of γB- and βB2-crystallin. Acta Crystallogr. D Biol. Crystallogr. 54: 243-252.
-
(1998)
Acta Crystallogr. D Biol. Crystallogr.
, vol.54
, pp. 243-252
-
-
Tickle, I.J.1
Laskowski, R.A.2
Moss, D.S.3
-
39
-
-
0034760077
-
Dynamic activation of protein function: A view emerging from NMR spectroscopy
-
Wand, A.J. 2001. Dynamic activation of protein function: A view emerging from NMR spectroscopy. Nat. Struct. Biol. 8: 926-931.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 926-931
-
-
Wand, A.J.1
-
40
-
-
0032917069
-
Protein structural topology: Automated analysis, diagrammatic representation and database searching
-
Westhead, D.R., Slidel, T.W.F., Flores, T.P.J., and Thornton, J.M. 1999. Protein structural topology: Automated analysis, diagrammatic representation and database searching. Protein Sci. 8: 897-904.
-
(1999)
Protein Sci.
, vol.8
, pp. 897-904
-
-
Westhead, D.R.1
Slidel, T.W.F.2
Flores, T.P.J.3
Thornton, J.M.4
-
41
-
-
85081440924
-
-
2001. Method for characterization of the fine structure of protein binding sites using amide hydrogen exchange. US patent no. 6,331,400
-
Woods Jr., V.L. 2001. Method for characterization of the fine structure of protein binding sites using amide hydrogen exchange. US patent no. 6,331,400.
-
-
-
Woods Jr., V.L.1
-
42
-
-
0035753065
-
High resolution, high-throughput amide deuterium exchange-mass spectrometry (DXMS) determination of protein binding site structure and dynamics: Utility in pharmaceutical design
-
Woods Jr., V.L. and Hamuro, Y. 2001. High resolution, high-throughput amide deuterium exchange-mass spectrometry (DXMS) determination of protein binding site structure and dynamics: Utility in pharmaceutical design. J. Cell. Biochem. Suppl. 37: 89-98.
-
(2001)
J. Cell. Biochem. Suppl.
, vol.37
, pp. 89-98
-
-
Woods Jr., V.L.1
Hamuro, Y.2
-
43
-
-
0001514262
-
Statistics of local complexity in amino acid sequences and sequence databases
-
Wootton, J.C. and Federhen, S. 1993. Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem. 17: 149-163.
-
(1993)
Comput. Chem.
, vol.17
, pp. 149-163
-
-
Wootton, J.C.1
Federhen, S.2
|