-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
2
-
-
0242323637
-
Multi-domain protein families and domain pairs: Comparison with known structures and a random model of domain recombination
-
Apic,G. et al. (2003) Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. J. Struct. Funct. Genomics, 4, 67-78.
-
(2003)
J. Struct. Funct. Genomics
, vol.4
, pp. 67-78
-
-
Apic, G.1
-
3
-
-
21644483402
-
Docking to single-domain and multiple-domain proteins: Old and new challenges
-
Ben-Zeev,E. et al. (2005) Docking to single-domain and multiple-domain proteins: old and new challenges. Proteins, 60, 195-201.
-
(2005)
Proteins
, vol.60
, pp. 195-201
-
-
Ben-Zeev, E.1
-
4
-
-
0033954256
-
The protein data bank
-
Berman,H.M. 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
-
5
-
-
33748052051
-
Expansion of protein domain repeats
-
Bjorklund,A.K. et al. (2006) Expansion of protein domain repeats. PLoS Comput. Biol., 2, e114.
-
(2006)
PLoS Comput. Biol.
, vol.2
, pp. e114
-
-
Bjorklund, A.K.1
-
6
-
-
20444453307
-
Protein length in eukaryotic and prokaryotic proteomes
-
Brocchieri,L. and Karlin,S. (2005) Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Res., 33, 3390-3400.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 3390-3400
-
-
Brocchieri, L.1
Karlin, S.2
-
7
-
-
55649094201
-
Structural assembly of two-domain proteins by rigid-body docking
-
Cheng,T.M. et al. (2008) Structural assembly of two-domain proteins by rigid-body docking. BMC Bioinformatics, 9, 441.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 441
-
-
Cheng, T.M.1
-
8
-
-
0037841804
-
Evolution of the protein repertoire
-
Chothia,C. et al. (2003) Evolution of the protein repertoire. Science, 300, 1701-1703.
-
(2003)
Science
, vol.300
, pp. 1701-1703
-
-
Chothia, C.1
-
9
-
-
16244423379
-
Multi-domain proteins in the three kingdoms of life: Orphan domains and other unassigned regions
-
Ekman,D. et al. (2005) Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J. Mol. Biol., 348, 231-243.
-
(2005)
J. Mol. Biol.
, vol.348
, pp. 231-243
-
-
Ekman, D.1
-
10
-
-
33947501381
-
The folding and evolution of multidomain proteins
-
Han,J.H. et al. (2007) The folding and evolution of multidomain proteins. Nat. Rev. Mol. Cell Biol., 8, 319-330.
-
(2007)
Nat. Rev. Mol. Cell Biol.
, vol.8
, pp. 319-330
-
-
Han, J.H.1
-
11
-
-
27744576807
-
Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies
-
Inbar,Y. et al. (2005) Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies. Phys. Biol., 2, S156-S165.
-
(2005)
Phys. Biol.
, vol.2
, pp. S156-S165
-
-
Inbar, Y.1
-
12
-
-
23144463912
-
FFAS03: A server for profile-profile sequence alignments
-
Jaroszewski,L. et al. (2005) FFAS03: A server for profile-profile sequence alignments. Nucleic Acids Res., 33, W284-W288.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. W284-W288
-
-
Jaroszewski, L.1
-
13
-
-
0033578684
-
Protein secondary structure prediction based on positionspecific scoring matrices
-
Jones,D.T. (1999) Protein secondary structure prediction based on positionspecific scoring matrices. J. Mol. Biol., 292, 195-202.
-
(1999)
J. Mol. Biol.
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
14
-
-
67149143183
-
Inferring protein-protein interactions from multiple protein domain combinations
-
Kanaan,S.P. et al. (2009) Inferring protein-protein interactions from multiple protein domain combinations. Methods Mol. Biol., 541, 43-59.
-
(2009)
Methods Mol. Biol.
, vol.541
, pp. 43-59
-
-
Kanaan, S.P.1
-
15
-
-
63849246525
-
Protein structure prediction on the WEB: A case study using the Phyre server
-
Kelley,L.A. and Sternberg,M.J. (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.2
-
16
-
-
70450106216
-
Improved prediction of protein side-chain conformations with SCWRL4
-
Krivov,G.G. et al. (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins, 77, 778-795.
-
(2009)
Proteins
, vol.77
, pp. 778-795
-
-
Krivov, G.G.1
-
17
-
-
33748300623
-
Docking protein domains in contact space
-
Lise,S. et al. (2006) Docking protein domains in contact space. BMC Bioinformatics, 7, 310.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 310
-
-
Lise, S.1
-
19
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
20
-
-
0043180474
-
PISCES: A protein sequence culling server
-
Wang,G. and Dunbrack,R.L. Jr. (2003) PISCES: A protein sequence culling server. Bioinformatics, 19, 1589-1591.
-
(2003)
Bioinformatics
, vol.19
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack, R.L.2
-
21
-
-
33846471085
-
Prediction of structures of multidomain proteins from structures of the individual domains
-
Wollacott,A.M. et al. (2007) Prediction of structures of multidomain proteins from structures of the individual domains. Protein Sci., 16, 165-175.
-
(2007)
Protein Sci.
, vol.16
, pp. 165-175
-
-
Wollacott, A.M.1
-
22
-
-
84904799548
-
AIDA: Ab initio domain assembly server
-
Xu,D. et al. (2014a) AIDA: ab initio domain assembly server. Nucleic Acids Res., 42, W308-W313.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. W308-W313
-
-
Xu, D.1
-
23
-
-
84897692613
-
FFAS-3D: Improving fold recognition by including optimized structural features and template re-ranking
-
Xu,D. et al. (2014b) FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking. Bioinformatics, 30, 660-667.
-
(2014)
Bioinformatics
, vol.30
, pp. 660-667
-
-
Xu, D.1
-
24
-
-
84862225232
-
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field
-
Xu,D. and Zhang,Y. (2012) Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins, 80, 1715-1735.
-
(2012)
Proteins
, vol.80
, pp. 1715-1735
-
-
Xu, D.1
Zhang, Y.2
-
25
-
-
77951961719
-
How significant is a protein structure similarity with TM-score = 0. 5?
-
Xu,J. and Zhang,Y. (2010) How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics, 26, 889-895.
-
(2010)
Bioinformatics
, vol.26
, pp. 889-895
-
-
Xu, J.1
Zhang, Y.2
-
26
-
-
0034491038
-
Protein domain decomposition using a graph-theoretic approach
-
Xu,Y. et al. (2000) Protein domain decomposition using a graph-theoretic approach. Bioinformatics, 16, 1091-1104.
-
(2000)
Bioinformatics
, vol.16
, pp. 1091-1104
-
-
Xu, Y.1
-
27
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang,Y. and Skolnick,J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins, 57, 702-710.
-
(2004)
Proteins
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
28
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou,H. and Zhou,Y. (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci., 11, 2714-2726.
-
(2002)
Protein Sci.
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
29
-
-
84870662087
-
This Déjà Vu feeling-analysis of multidomain protein evolution in eukaryotic genomes
-
Zmasek,C.M. and Godzik,A. (2012) This Déjà Vu feeling-analysis of multidomain protein evolution in eukaryotic genomes. PLoS Comput. Biol., 8, e1002701.
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002701
-
-
Zmasek, C.M.1
Godzik, A.2
|