-
2
-
-
0036108484
-
3D domain swapping: As domains continue to swap
-
Liu Y, Eisenberg D (2002) 3D domain swapping: as domains continue to swap. Protein Sci 11: 1285-1299.
-
(2002)
Protein Sci
, vol.11
, pp. 1285-1299
-
-
Liu, Y.1
Eisenberg, D.2
-
3
-
-
4143058003
-
The evolving role of 3D domain swapping in proteins
-
Bennett MJ, Eisenberg D (2004) The evolving role of 3D domain swapping in proteins. Structure 12: 1339-1341.
-
(2004)
Structure
, vol.12
, pp. 1339-1341
-
-
Bennett, M.J.1
Eisenberg, D.2
-
5
-
-
0028077637
-
Refined structure of dimeric diphtheria toxin at 2.0 A resolution
-
Bennett MJ, Choe S, Eisenberg D (1994) Refined structure of dimeric diphtheria toxin at 2.0 A resolution. Protein Sci 3: 1444-1463.
-
(1994)
Protein Sci
, vol.3
, pp. 1444-1463
-
-
Bennett, M.J.1
Choe, S.2
Eisenberg, D.3
-
6
-
-
0035127031
-
A domain-swapped RNase A dimer with implications for amyloid formation
-
Liu Y, Gotte G, Libonati M, Eisenberg D (2001) A domain-swapped RNase A dimer with implications for amyloid formation. Nat Struct Biol 8: 211-214.
-
(2001)
Nat Struct Biol
, vol.8
, pp. 211-214
-
-
Liu, Y.1
Gotte, G.2
Libonati, M.3
Eisenberg, D.4
-
7
-
-
0032584210
-
The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution
-
Liu Y, Hart PJ, Schlunegger MP, Eisenberg D (1998) The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution. Proc Natl Acad Sci U S A 95: 3437-3442.
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, pp. 3437-3442
-
-
Liu, Y.1
Hart, P.J.2
Schlunegger, M.P.3
Eisenberg, D.4
-
9
-
-
0035069135
-
Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping
-
Janowski R, Kozak M, Jankowska E, Grzonka Z, Grubb A, et al. (2001) Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping. Nat Struct Biol 8: 316-320.
-
(2001)
Nat Struct Biol
, vol.8
, pp. 316-320
-
-
Janowski, R.1
Kozak, M.2
Jankowska, E.3
Grzonka, Z.4
Grubb, A.5
-
11
-
-
0035801540
-
Three-dimensional domain swapping in the folded and molten-globule states of cystatins, an amyloid-forming structural superfamily
-
Staniforth RA, Giannini S, Higgins LD, Conroy MJ, Hounslow AM, et al. (2001) Three-dimensional domain swapping in the folded and molten-globule states of cystatins, an amyloid-forming structural superfamily. Embo J 20: 4774-4781.
-
(2001)
Embo J
, vol.20
, pp. 4774-4781
-
-
Staniforth, R.A.1
Giannini, S.2
Higgins, L.D.3
Conroy, M.J.4
Hounslow, A.M.5
-
12
-
-
0034619431
-
Dimer formation through domain swapping in the crystal structure of the Grb2-SH2- Ac-pYVNV complex
-
Schiering N, Casale E, Caccia P, Giordano P, Battistini C (2000) Dimer formation through domain swapping in the crystal structure of the Grb2-SH2- Ac-pYVNV complex. Biochemistry 39: 13376-13382.
-
(2000)
Biochemistry
, vol.39
, pp. 13376-13382
-
-
Schiering, N.1
Casale, E.2
Caccia, P.3
Giordano, P.4
Battistini, C.5
-
13
-
-
0035697173
-
Structure of the SH3-guanylate kinase module from PSD-95 suggests a mechanism for regulated assembly of MAGUK scaffolding proteins
-
McGee AW, Dakoji SR, Olsen O, Bredt DS, Lim WA, et al. (2001) Structure of the SH3-guanylate kinase module from PSD-95 suggests a mechanism for regulated assembly of MAGUK scaffolding proteins. Mol Cell 8: 1291-1301.
-
(2001)
Mol Cell
, vol.8
, pp. 1291-1301
-
-
McGee, A.W.1
Dakoji, S.R.2
Olsen, O.3
Bredt, D.S.4
Lim, W.A.5
-
14
-
-
0037133242
-
Mechanism of action and NAD+-binding mode revealed by the crystal structure of Lhistidinol dehydrogenase
-
Barbosa JA, Sivaraman J, Li Y, Larocque R, Matte A, et al. (2002) Mechanism of action and NAD+-binding mode revealed by the crystal structure of Lhistidinol dehydrogenase. Proc Natl Acad Sci U S A 99: 1859-1864.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 1859-1864
-
-
Barbosa, J.A.1
Sivaraman, J.2
Li, Y.3
Larocque, R.4
Matte, A.5
-
15
-
-
0030927104
-
Crystal structure of human glyoxalase I-evidence for gene duplication and 3D domain swapping
-
Cameron AD, Olin B, Ridderstrom M, Mannervik B, Jones TA (1997) Crystal structure of human glyoxalase I-evidence for gene duplication and 3D domain swapping. Embo J 16: 3386-3395.
-
(1997)
Embo J
, vol.16
, pp. 3386-3395
-
-
Cameron, A.D.1
Olin, B.2
Ridderstrom, M.3
Mannervik, B.4
Jones, T.A.5
-
16
-
-
0033571222
-
Nterminal domain swapping and metal ion binding in nitric oxide synthase dimerization
-
Crane BR, Rosenfeld RJ, Arvai AS, Ghosh DK, Ghosh S, et al. (1999) Nterminal domain swapping and metal ion binding in nitric oxide synthase dimerization. Embo J 18: 6271-6281.
-
(1999)
Embo J
, vol.18
, pp. 6271-6281
-
-
Crane, B.R.1
Rosenfeld, R.J.2
Arvai, A.S.3
Ghosh, D.K.4
Ghosh, S.5
-
17
-
-
0034809928
-
Observation of signal transduction in three-dimensional domain swapping
-
Schymkowitz JW, Rousseau F, Wilkinson HR, Friedler A, Itzhaki LS (2001) Observation of signal transduction in three-dimensional domain swapping. Nat Struct Biol 8: 888-892.
-
(2001)
Nat Struct Biol
, vol.8
, pp. 888-892
-
-
Schymkowitz, J.W.1
Rousseau, F.2
Wilkinson, H.R.3
Friedler, A.4
Itzhaki, L.S.5
-
18
-
-
0035826713
-
Threedimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues
-
Rousseau F, Schymkowitz JW, Wilkinson HR, Itzhaki LS (2001) Threedimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues. Proc Natl Acad Sci U S A 98: 5596-5601.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 5596-5601
-
-
Rousseau, F.1
Schymkowitz, J.W.2
Wilkinson, H.R.3
Itzhaki, L.S.4
-
19
-
-
0034869693
-
Crystal structure of the human prion protein reveals a mechanism for oligomerization
-
Knaus KJ, Morillas M, Swietnicki W, Malone M, Surewicz WK, et al. (2001) Crystal structure of the human prion protein reveals a mechanism for oligomerization. Nat Struct Biol 8: 770-774.
-
(2001)
Nat Struct Biol
, vol.8
, pp. 770-774
-
-
Knaus, K.J.1
Morillas, M.2
Swietnicki, W.3
Malone, M.4
Surewicz, W.K.5
-
20
-
-
0035852764
-
Design of three-dimensional domain-swapped dimers and fibrous oligomers
-
Ogihara NL, Ghirlanda G, Bryson JW, Gingery M, DeGrado WF, et al. (2001) Design of three-dimensional domain-swapped dimers and fibrous oligomers. Proc Natl Acad Sci U S A 98: 1404-1409.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 1404-1409
-
-
Ogihara, N.L.1
Ghirlanda, G.2
Bryson, J.W.3
Gingery, M.4
DeGrado, W.F.5
-
21
-
-
0035757051
-
3D domain swapping, protein oligomerization, and amyloid formation
-
Jaskolski M (2001) 3D domain swapping, protein oligomerization, and amyloid formation. Acta Biochim Pol 48: 807-827.
-
(2001)
Acta Biochim Pol
, vol.48
, pp. 807-827
-
-
Jaskolski, M.1
-
23
-
-
4644301408
-
Domain swapping is a consequence of minimal frustration
-
Yang S, Cho SS, Levy Y, Cheung MS, Levine H, et al. (2004) Domain swapping is a consequence of minimal frustration. Proc Natl Acad Sci U S A 101: 13786-13791.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 13786-13791
-
-
Yang, S.1
Cho, S.S.2
Levy, Y.3
Cheung, M.S.4
Levine, H.5
-
25
-
-
0028843420
-
Single-chain Fvs
-
Raag R, Whitlow M (1995) Single-chain Fvs. FASEB J 9: 73-80.
-
(1995)
FASEB J
, vol.9
, pp. 73-80
-
-
Raag, R.1
Whitlow, M.2
-
26
-
-
0026354773
-
High resolution structure of an oligomeric eye lens beta-crystallin. Loops, arches, linkers and interfaces in beta B2 dimer compared to a monomeric gammacrystallin
-
Lapatto R, Nalini V, Bax B, Driessen H, Lindley PF, et al. (1991) High resolution structure of an oligomeric eye lens beta-crystallin. Loops, arches, linkers and interfaces in beta B2 dimer compared to a monomeric gammacrystallin. J Mol Biol 222: 1067-1083.
-
(1991)
J Mol Biol
, vol.222
, pp. 1067-1083
-
-
Lapatto, R.1
Nalini, V.2
Bax, B.3
Driessen, H.4
Lindley, P.F.5
-
27
-
-
0028171466
-
Dimerization of beta B2-crystallin: The role of the linker peptide and the N- and C-terminal extensions
-
Trinkl S, Glockshuber R, Jaenicke R (1994) Dimerization of beta B2-crystallin: the role of the linker peptide and the N- and C-terminal extensions. Protein Sci 3: 1392-1400.
-
(1994)
Protein Sci
, vol.3
, pp. 1392-1400
-
-
Trinkl, S.1
Glockshuber, R.2
Jaenicke, R.3
-
28
-
-
0038013591
-
Sequencestructure signals of 3D domain swapping in proteins
-
Dehouck Y, Biot C, Gilis D, Kwasigroch JM, Rooman M (2003) Sequencestructure signals of 3D domain swapping in proteins. J Mol Biol 330: 1215-1225.
-
(2003)
J Mol Biol
, vol.330
, pp. 1215-1225
-
-
Dehouck, Y.1
Biot, C.2
Gilis, D.3
Kwasigroch, J.M.4
Rooman, M.5
-
29
-
-
3042581007
-
Flexible structure alignment by chaining aligned fragment pairs allowing twists
-
Ye Y, Godzik A (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19 Suppl 2: ii246-255.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL 2
-
-
Ye, Y.1
Godzik, A.2
-
30
-
-
12944271968
-
FAST: A novel protein structure alignment algorithm
-
Zhu J, Weng Z (2005) FAST: a novel protein structure alignment algorithm. Proteins 58: 618-627.
-
(2005)
Proteins
, vol.58
, pp. 618-627
-
-
Zhu, J.1
Weng, Z.2
-
31
-
-
17644392830
-
TM-align: A protein structure alignment algorithm based on the TM-score
-
Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33: 2302-2309.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
32
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
Holm L, 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
-
33
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11: 739-747.
-
(1998)
Protein Eng
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
35
-
-
0036888353
-
Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50
-
Hayward S, Lee RA (2002) Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J Mol Graph Model 21: 181-183.
-
(2002)
J Mol Graph Model
, vol.21
, pp. 181-183
-
-
Hayward, S.1
Lee, R.A.2
-
38
-
-
56749132934
-
Angle-distance image matching techniques for protein structure comparison
-
Chu CH, Tang CY, Tang CY, Pai TW (2008) Angle-distance image matching techniques for protein structure comparison. J Mol Recognit 21: 442-452.
-
(2008)
J Mol Recognit
, vol.21
, pp. 442-452
-
-
Chu, C.H.1
Tang, C.Y.2
Tang, C.Y.3
Pai, T.W.4
-
39
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (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
-
40
-
-
0032169688
-
PQS: A protein quaternary structure file server
-
Henrick K, Thornton JM (1998) PQS: a protein quaternary structure file server. Trends Biochem Sci 23: 358-361.
-
(1998)
Trends Biochem Sci
, vol.23
, pp. 358-361
-
-
Henrick, K.1
Thornton, J.M.2
-
41
-
-
0034479757
-
TOP: A new method for protein structure comparisons and similarity searches
-
Lu GG (2000) TOP: a new method for protein structure comparisons and similarity searches. Journal of Applied Crystallography 33: 176-183.
-
(2000)
Journal of Applied Crystallography
, vol.33
, pp. 176-183
-
-
Lu, G.G.1
-
42
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
43
-
-
13444307044
-
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
-
Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60: 2256-2268.
-
(2004)
Acta Crystallogr D Biol Crystallogr
, vol.60
, pp. 2256-2268
-
-
Krissinel, E.1
Henrick, K.2
-
44
-
-
0030017889
-
Analysis of topological and nontopological structural similarities in the PDB: New examples with old structures
-
Alexandrov NN, Fischer D (1996) Analysis of topological and nontopological structural similarities in the PDB: new examples with old structures. Proteins 25: 354-365.
-
(1996)
Proteins
, vol.25
, pp. 354-365
-
-
Alexandrov, N.N.1
Fischer, D.2
-
45
-
-
0034237578
-
Large-scale comparison of protein sequence alignment algorithms with structure alignments
-
Sauder JM, Arthur JW, Dunbrack RL, Jr. (2000) Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins 40: 6-22.
-
(2000)
Proteins
, vol.40
, pp. 6-22
-
-
Sauder, J.M.1
Arthur, J.W.2
Dunbrack Jr., R.L.3
-
49
-
-
84858617091
-
-
Java OpenGL [http://jogamp.org/].
-
Java OpenGL
-
-
-
50
-
-
67849101183
-
iSARST: An integrated SARST web server for rapid protein structural similarity searches
-
Lo WC, Lee CY, Lee CC, Lyu PC (2009) iSARST: an integrated SARST web server for rapid protein structural similarity searches. Nucleic Acids Res 37: W545-551.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Lo, W.C.1
Lee, C.Y.2
Lee, C.C.3
Lyu, P.C.4
-
51
-
-
46249109058
-
CPSARST: An efficient circular permutation search tool applied to the detection of novel protein structural relationships
-
Lo WC, Lyu PC (2008) CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships. Genome Biol 9: R11.
-
(2008)
Genome Biol
, vol.9
-
-
Lo, W.C.1
Lyu, P.C.2
-
53
-
-
3142745171
-
Alternative alignments from comparison of protein structures
-
Shih ES, Hwang MJ (2004) Alternative alignments from comparison of protein structures. Proteins 56: 519-527.
-
(2004)
Proteins
, vol.56
, pp. 519-527
-
-
Shih, E.S.1
Hwang, M.J.2
-
55
-
-
84893482610
-
A solution for the best rotation to relate two sets of vectors
-
Kabsch W (1976) A solution for the best rotation to relate two sets of vectors. Acta Crystallographica Section A 32: 922-923.
-
(1976)
Acta Crystallographica Section A
, vol.32
, pp. 922-923
-
-
Kabsch, W.1
-
56
-
-
66549119395
-
Advances and pitfalls of protein structural alignment
-
Hasegawa H, Holm L (2009) Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol 19: 341-348.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 341-348
-
-
Hasegawa, H.1
Holm, L.2
-
57
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 89: 10915-10919.
-
(1992)
Proc Natl Acad Sci U S A
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
58
-
-
33644869455
-
Flexible secondary structure based protein structure comparison applied to the detection of circular permutation
-
Vesterstrom J, Taylor WR (2006) Flexible secondary structure based protein structure comparison applied to the detection of circular permutation. J Comput Biol 13: 43-63.
-
(2006)
J Comput Biol
, vol.13
, pp. 43-63
-
-
Vesterstrom, J.1
Taylor, W.R.2
-
59
-
-
0033833116
-
Protein structure alignment using environmental profiles
-
Jung J, Lee B (2000) Protein structure alignment using environmental profiles. Protein Eng 13: 535-543.
-
(2000)
Protein Eng
, vol.13
, pp. 535-543
-
-
Jung, J.1
Lee, B.2
-
61
-
-
13444279981
-
Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures
-
Kolodny R, Koehl P, Levitt M (2005) Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J Mol Biol 346: 1173-1188.
-
(2005)
J Mol Biol
, vol.346
, pp. 1173-1188
-
-
Kolodny, R.1
Koehl, P.2
Levitt, M.3
|