-
1
-
-
0022798602
-
Atomic size packing defects in proteins
-
Connolly,M.L. (1986) Atomic size packing defects in proteins. Int. J. Pept. Protein Res., 28, 360-363.
-
(1986)
Int. J. Pept. Protein Res
, vol.28
, pp. 360-363
-
-
Connolly, M.L.1
-
2
-
-
0028274954
-
Intramolecular cavities in globular proteins
-
Hubbard,S.J., Gross,K.H. and Argos,P. (1994) Intramolecular cavities in globular proteins. Prot. Eng., 7, 613-626.
-
(1994)
Prot. Eng
, vol.7
, pp. 613-626
-
-
Hubbard, S.J.1
Gross, K.H.2
Argos, P.3
-
3
-
-
0015977588
-
The interpretation of protein structures: Total volume, group volume distributions and packing density
-
Richards,F.M. (1974) The interpretation of protein structures: Total volume, group volume distributions and packing density. J. Mol. Biol. 82, 1-14.
-
(1974)
J. Mol. Biol
, vol.82
, pp. 1-14
-
-
Richards, F.M.1
-
4
-
-
0017429069
-
Areas, volumes, packing and protein structure
-
Richards,F.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, F.M.1
-
5
-
-
0033516705
-
The packing density in proteins: Standard radii and volumes
-
Tsai,J., Taylor,R., Chothia,C. and Gerstein,M. (1999) The packing density in proteins: Standard radii and volumes. J. Mol. Biol., 290, 253-266.
-
(1999)
J. Mol. Biol
, vol.290
, pp. 253-266
-
-
Tsai, J.1
Taylor, R.2
Chothia, C.3
Gerstein, M.4
-
6
-
-
0023051843
-
Internal cavities and buried waters in globular proteins
-
Rashin,A.A., Iofin,M. and Honig,B. (1986) Internal cavities and buried waters in globular proteins. Biochemistry, 25, 3619-3625.
-
(1986)
Biochemistry
, vol.25
, pp. 3619-3625
-
-
Rashin, A.A.1
Iofin, M.2
Honig, B.3
-
7
-
-
0028095182
-
Buried waters and internal cavities in monomeric proteins
-
Williams,M.A., Goodfellow,J.M. and Thornton,J.M. (1994) Buried waters and internal cavities in monomeric proteins. Protein Sci., 3 1224-1235.
-
(1994)
Protein Sci
, vol.3
, pp. 1224-1235
-
-
Williams, M.A.1
Goodfellow, J.M.2
Thornton, J.M.3
-
8
-
-
0037246110
-
Buried water molecules contribute to the conformational stability of a protein
-
Takano,K., Yamagata,Y. and Yutani,K. (2003) Buried water molecules contribute to the conformational stability of a protein. Protein Eng. 16, 5-9.
-
(2003)
Protein Eng
, vol.16
, pp. 5-9
-
-
Takano, K.1
Yamagata, Y.2
Yutani, K.3
-
9
-
-
0028607523
-
Cavities and packing at protein interfaces
-
Hubbard,S.J. and Argos,P. (1994) Cavities and packing at protein interfaces. Protein Sci., 3, 2194-2206.
-
(1994)
Protein Sci
, vol.3
, pp. 2194-2206
-
-
Hubbard, S.J.1
Argos, P.2
-
10
-
-
52949132638
-
-
Sonavane,S. and Chakrabarti,P. (2008) Cavities and atomic packing in protein structures and interfaces. PLoS Comput. Biol., 4, e1000188.
-
Sonavane,S. and Chakrabarti,P. (2008) Cavities and atomic packing in protein structures and interfaces. PLoS Comput. Biol., 4, e1000188.
-
-
-
-
11
-
-
0033573827
-
Structural features of protein-nucleic acid recognition sites
-
Nadassy,K., Wodak,S.J. and Janin,J. (1999) Structural features of protein-nucleic acid recognition sites. Biochemistry, 38, 1999-2017.
-
(1999)
Biochemistry
, vol.38
, pp. 1999-2017
-
-
Nadassy, K.1
Wodak, S.J.2
Janin, J.3
-
12
-
-
0033574510
-
Protein-DNA interactions: A structural analysis
-
Jones,S., van Heyningen,P., Berman,H.M. and Thornton,J.M. (1999) Protein-DNA interactions: A structural analysis. J. Mol. Biol., 287, 877-896.
-
(1999)
J. Mol. Biol
, vol.287
, pp. 877-896
-
-
Jones, S.1
van Heyningen, P.2
Berman, H.M.3
Thornton, J.M.4
-
13
-
-
1442351139
-
Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching
-
Tolstorukov,M.Y., Jernigan,R.L. and Zhurkin,V.B. (2004) Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. J. Mol. Biol., 337, 65-76.
-
(2004)
J. Mol. Biol
, vol.337
, pp. 65-76
-
-
Tolstorukov, M.Y.1
Jernigan, R.L.2
Zhurkin, V.B.3
-
14
-
-
26444598454
-
Protein-nucleic acid recognition: Statistical analysis of atomic interactions and influence of DNA structure
-
Lejeune,D., Delsaux,N., Charloteaux,B., Thomas,A. and Brasseur,R. (2005) Protein-nucleic acid recognition: Statistical analysis of atomic interactions and influence of DNA structure. Proteins, 61, 258-271.
-
(2005)
Proteins
, vol.61
, pp. 258-271
-
-
Lejeune, D.1
Delsaux, N.2
Charloteaux, B.3
Thomas, A.4
Brasseur, R.5
-
15
-
-
20544460658
-
Protein-DNA recognition patterns and predictions
-
Sarai,A. and Kono,H. (2005) Protein-DNA recognition patterns and predictions. Annu. Rev. Biophys. Biomol. Struct., 34, 379-398.
-
(2005)
Annu. Rev. Biophys. Biomol. Struct
, vol.34
, pp. 379-398
-
-
Sarai, A.1
Kono, H.2
-
16
-
-
52949123643
-
-
Sathyapriya,R., Vijayabaskar,M.S. and Saraswathi,V. (2008) Insights into protein-DNA interactions through structure network analysis. PLoS Comput. Biol., 4, e1000170.
-
Sathyapriya,R., Vijayabaskar,M.S. and Saraswathi,V. (2008) Insights into protein-DNA interactions through structure network analysis. PLoS Comput. Biol., 4, e1000170.
-
-
-
-
17
-
-
1642452665
-
Analyzing protein-DNA recognition mechanisms
-
Paillard,G. and Lavery,R. (2004) Analyzing protein-DNA recognition mechanisms. Structure, 12, 113-122.
-
(2004)
Structure
, vol.12
, pp. 113-122
-
-
Paillard, G.1
Lavery, R.2
-
18
-
-
59849107303
-
Dissection, residue conservation, and structural classification of protein-DNA interfaces
-
Biswas,S., Guharoy,M. and Chakrabarti,P. (2009) Dissection, residue conservation, and structural classification of protein-DNA interfaces. Proteins, 74, 643-654.
-
(2009)
Proteins
, vol.74
, pp. 643-654
-
-
Biswas, S.1
Guharoy, M.2
Chakrabarti, P.3
-
19
-
-
0035865891
-
Protein-RNA interactions: A structural analysis
-
Jones,S., Daley,D.T., Luscombe,N.M., Berman,H.M. and Thornton,J.M. (2001) Protein-RNA interactions: A structural analysis. Nucleic Acids Res., 29, 943-954.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 943-954
-
-
Jones, S.1
Daley, D.T.2
Luscombe, N.M.3
Berman, H.M.4
Thornton, J.M.5
-
20
-
-
0034823943
-
Statistical analysis of atomic contacts at RNA-protein interfaces
-
Treger,M. and Westhof,E. (2001) Statistical analysis of atomic contacts at RNA-protein interfaces. J. Mol. Recognit., 14, 199-214.
-
(2001)
J. Mol. Recognit
, vol.14
, pp. 199-214
-
-
Treger, M.1
Westhof, E.2
-
21
-
-
26444619105
-
Discovering the interaction propensities of amino acids and nucleotides from protein-RNA complexes
-
Jeong,E., Kim,H., Lee,S.W. and Han,K. (2003) Discovering the interaction propensities of amino acids and nucleotides from protein-RNA complexes. Mol. Cells, 16, 161-167.
-
(2003)
Mol. Cells
, vol.16
, pp. 161-167
-
-
Jeong, E.1
Kim, H.2
Lee, S.W.3
Han, K.4
-
23
-
-
0035800599
-
Structure-based analysis of protein-RNA interactions using the program ENTANGLE
-
Allers,J. and Shamoo,Y. (2001) Structure-based analysis of protein-RNA interactions using the program ENTANGLE. J. Mol. Biol., 311, 75-86.
-
(2001)
J. Mol. Biol
, vol.311
, pp. 75-86
-
-
Allers, J.1
Shamoo, Y.2
-
24
-
-
33750997616
-
Protein-RNA interactions: Exploring binding patterns with a three-dimensional superposition analysis of high resolution structures
-
Morozova,N., Allers,J., Myers,J. and Shamoo,Y. (2006) Protein-RNA interactions: Exploring binding patterns with a three-dimensional superposition analysis of high resolution structures. Bioinformatics 22, 2746-2752.
-
(2006)
Bioinformatics
, vol.22
, pp. 2746-2752
-
-
Morozova, N.1
Allers, J.2
Myers, J.3
Shamoo, Y.4
-
25
-
-
43349105225
-
Dissecting protein-RNA recognition sites
-
Bahadur,R.P., Zacharias,M. and Janin,J. (2008) Dissecting protein-RNA recognition sites. Nucleic Acids Res., 36, 2705-2716.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 2705-2716
-
-
Bahadur, R.P.1
Zacharias, M.2
Janin, J.3
-
26
-
-
33847042739
-
Protein-RNA interactions: Structural analysis and functional classes
-
Ellis,J.J., Broom,M. and Jones,S. (2007) Protein-RNA interactions: structural analysis and functional classes. Proteins, 66, 903-911.
-
(2007)
Proteins
, vol.66
, pp. 903-911
-
-
Ellis, J.J.1
Broom, M.2
Jones, S.3
-
27
-
-
69049084284
-
Structural segments and residue propensities in protein-RNA interfaces: Comparison with protein-protein and protein-DNA complexes
-
Biswas,S., Guharoy,M. and Chakrabarti,P. (2008) Structural segments and residue propensities in protein-RNA interfaces: Comparison with protein-protein and protein-DNA complexes. Bioinformation, 2 422-427.
-
(2008)
Bioinformation
, vol.2
, pp. 422-427
-
-
Biswas, S.1
Guharoy, M.2
Chakrabarti, P.3
-
28
-
-
52649130704
-
Protein-protein interaction and quaternary structure
-
Janin,J., Bahadur,R.P. and Chakrabarti,P. (2008) Protein-protein interaction and quaternary structure. Q. Rev. Biophys., 41, 133-180.
-
(2008)
Q. Rev. Biophys
, vol.41
, pp. 133-180
-
-
Janin, J.1
Bahadur, R.P.2
Chakrabarti, P.3
-
29
-
-
0035880916
-
Standard atomic volumes in double-stranded DNA and packing in protein-DNA interfaces
-
Nadassy,K., Tomas-Oliveira,I., Alberts,I., Janin,J. and Wodak,S.J. (2001) Standard atomic volumes in double-stranded DNA and packing in protein-DNA interfaces. Nucleic Acids Res., 29, 3362-3376.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 3362-3376
-
-
Nadassy, K.1
Tomas-Oliveira, I.2
Alberts, I.3
Janin, J.4
Wodak, S.J.5
-
30
-
-
0033954256
-
The Protein Data Bank
-
Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
31
-
-
0037093645
-
Dissecting protein-protein recognition sites
-
Chakrabarti,P. and Janin,J. (2002) Dissecting protein-protein recognition sites. Proteins, 47, 334-343.
-
(2002)
Proteins
, vol.47
, pp. 334-343
-
-
Chakrabarti, P.1
Janin, J.2
-
32
-
-
0242299201
-
Dissecting subunit interfaces in homodimeric proteins
-
Bahadur,R.P., Chakrabarti,P., Rodier,F. and Janin,J. (2003) Dissecting subunit interfaces in homodimeric proteins. Proteins, 53, 708-719.
-
(2003)
Proteins
, vol.53
, pp. 708-719
-
-
Bahadur, R.P.1
Chakrabarti, P.2
Rodier, F.3
Janin, J.4
-
33
-
-
0041989751
-
CASTp: Computed atlas of surface topography of proteins
-
Binkowski,T.A., Naghibzadeh,S. and Liang,J. (2003) CASTp: Computed atlas of surface topography of proteins. Nucleic Acids Res., 31, 3352-3355.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3352-3355
-
-
Binkowski, T.A.1
Naghibzadeh, S.2
Liang, J.3
-
34
-
-
0028304962
-
Satisfying hydrogen bonding potential in proteins
-
McDonald,I.K. and Thornton,J.M. (1994) Satisfying hydrogen bonding potential in proteins. J. Mol. Biol., 238, 777-793.
-
(1994)
J. Mol. Biol
, vol.238
, pp. 777-793
-
-
McDonald, I.K.1
Thornton, J.M.2
-
35
-
-
0030040323
-
Reduced surface: An efficient way to compute molecular surfaces
-
Sanner,M.F., Olson,A.J. and Spehner,J.C. (1996) Reduced surface: An efficient way to compute molecular surfaces. Biopolymers, 38 305-320.
-
(1996)
Biopolymers
, vol.38
, pp. 305-320
-
-
Sanner, M.F.1
Olson, A.J.2
Spehner, J.C.3
-
36
-
-
0029878720
-
VMD: Visual molecular dynamics
-
33-38
-
Humphrey,W., Dalke,A. and Schulten,K. (1996) VMD: Visual molecular dynamics. J. Mol. Graph, 14, 33-38, 27-38.
-
(1996)
J. Mol. Graph
, vol.14
, pp. 27-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
37
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
38
-
-
0027066845
-
Differences in the amino acid distributions of 3(10)-helices and alpha-helices
-
Karpen,M.E., de Haseth,P.L. and Neet,K.E. (1992) Differences in the amino acid distributions of 3(10)-helices and alpha-helices. Protein Sci., 1, 1333-1342.
-
(1992)
Protein Sci
, vol.1
, pp. 1333-1342
-
-
Karpen, M.E.1
de Haseth, P.L.2
Neet, K.E.3
-
39
-
-
0035976713
-
Do water molecules mediate protein-DNA recognition?
-
Reddy,C.K., Das,A. and Jayaram,B. (2001) Do water molecules mediate protein-DNA recognition? J. Mol. Biol., 314, 619-632.
-
(2001)
J. Mol. Biol
, vol.314
, pp. 619-632
-
-
Reddy, C.K.1
Das, A.2
Jayaram, B.3
-
40
-
-
0028881975
-
SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
-
Laskowski,R.A. (1995) SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph 13, 323-330, 307-308.
-
(1995)
J. Mol. Graph
, vol.13
, Issue.323-330
, pp. 307-308
-
-
Laskowski, R.A.1
-
41
-
-
1042275583
-
A dissection of specific and non-specific protein-protein interfaces
-
Bahadur,R.P., Chakrabarti,P., Rodier,F. and Janin,J. (2004) A dissection of specific and non-specific protein-protein interfaces. J. Mol. Biol., 336, 943-955.
-
(2004)
J. Mol. Biol
, vol.336
, pp. 943-955
-
-
Bahadur, R.P.1
Chakrabarti, P.2
Rodier, F.3
Janin, J.4
-
42
-
-
19544372768
-
Hydration of protein-protein interfaces
-
Rodier,F., Bahadur,R.P., Chakrabarti,P. and Janin,J. (2005) Hydration of protein-protein interfaces. Proteins, 60, 36-45.
-
(2005)
Proteins
, vol.60
, pp. 36-45
-
-
Rodier, F.1
Bahadur, R.P.2
Chakrabarti, P.3
Janin, J.4
-
43
-
-
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
|