-
1
-
-
38549153238
-
Data growth and its impact on the SCOP database: New developments
-
A. Andreeva, D. Howorth, J.M. Chandonia, S.E. Brenner, T.J. Hubbard, and C. Chothia Data growth and its impact on the SCOP database: New developments Nucleic Acids Research 36 2008 D419 D425
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Andreeva, A.1
Howorth, D.2
Chandonia, J.M.3
Brenner, S.E.4
Hubbard, T.J.5
Chothia, C.6
-
2
-
-
80054836686
-
Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold
-
M.L. Azoitei, B.E. Correia, Y.E. Ban, C. Carrico, O. Kalyuzhniy, and L. Chen Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold Science 334 2011 373 376
-
(2011)
Science
, vol.334
, pp. 373-376
-
-
Azoitei, M.L.1
Correia, B.E.2
Ban, Y.E.3
Carrico, C.4
Kalyuzhniy, O.5
Chen, L.6
-
3
-
-
45149114391
-
Reconstruction of protein backbones from the BriX collection of canonical protein fragments
-
L. Baeten, J. Reumers, V. Tur, F. Stricher, T. Lenaerts, and L. Serrano Reconstruction of protein backbones from the BriX collection of canonical protein fragments PLoS Computational Biology 4 2008 e1000083
-
(2008)
PLoS Computational Biology
, vol.4
, pp. 1000083
-
-
Baeten, L.1
Reumers, J.2
Tur, V.3
Stricher, F.4
Lenaerts, T.5
Serrano, L.6
-
4
-
-
34147169516
-
Potential energy functions for protein design
-
DOI 10.1016/j.sbi.2007.03.006, PII S0959440X0700036X, Theory and Simulation / Mecromolecular Assemblages
-
F.E. Boas, and P.B. Harbury Potential energy functions for protein design Current Opinion in Structural Biology 17 2007 199 204 (Pubitemid 46575252)
-
(2007)
Current Opinion in Structural Biology
, vol.17
, Issue.2
, pp. 199-204
-
-
Boas, F.E.1
Harbury, P.B.2
-
5
-
-
77649240530
-
FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately
-
I. Budowski-Tal, Y. Nov, and R. Kolodny FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately Proceedings of the National Academy of Sciences of the United States of America 107 2010 3481 3486
-
(2010)
Proceedings of the National Academy of Sciences of the United States of America
, vol.107
, pp. 3481-3486
-
-
Budowski-Tal, I.1
Nov, Y.2
Kolodny, R.3
-
6
-
-
74049108922
-
BLAST +: Architecture and applications
-
C. Camacho, G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos, and K. Bealer BLAST +: Architecture and applications BMC Bioinformatics 10 2009 421
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
-
8
-
-
0000747247
-
The Fourier transform of a coiled-coil
-
F.H.C. Crick The Fourier transform of a coiled-coil Acta Crystallographica 6 1953 685
-
(1953)
Acta Crystallographica
, vol.6
, pp. 685
-
-
Crick, F.H.C.1
-
9
-
-
2142738304
-
WebLogo: A sequence logo generator
-
DOI 10.1101/gr.849004
-
G.E. Crooks, G. Hon, J.M. Chandonia, and S.E. Brenner WebLogo: A sequence logo generator Genome Research 14 2004 1188 1190 (Pubitemid 38811555)
-
(2004)
Genome Research
, vol.14
, Issue.6
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.-M.3
Brenner, S.E.4
-
14
-
-
77955823082
-
Structural comparison and classification of alpha-helical transmembrane domains based on helix interaction patterns
-
A. Fuchs, and D. Frishman Structural comparison and classification of alpha-helical transmembrane domains based on helix interaction patterns Proteins 78 2010 2587 2599
-
(2010)
Proteins
, vol.78
, pp. 2587-2599
-
-
Fuchs, A.1
Frishman, D.2
-
16
-
-
33846033844
-
The CATH domain structure database: New protocols and classification levels give a more comprehensive resource for exploring evolution
-
L.H. Greene, T.E. Lewis, S. Addou, A. Cuff, T. Dallman, and M. Dibley The CATH domain structure database: New protocols and classification levels give a more comprehensive resource for exploring evolution Nucleic Acids Research 35 2007 D291 D297
-
(2007)
Nucleic Acids Research
, vol.35
-
-
Greene, L.H.1
Lewis, T.E.2
Addou, S.3
Cuff, A.4
Dallman, T.5
Dibley, M.6
-
17
-
-
79251600167
-
Probing designability via a generalized model of helical bundle geometry
-
G. Grigoryan, and W.F. Degrado Probing designability via a generalized model of helical bundle geometry Journal of Molecular Biology 405 2011 1079 1100
-
(2011)
Journal of Molecular Biology
, vol.405
, pp. 1079-1100
-
-
Grigoryan, G.1
Degrado, W.F.2
-
18
-
-
79957589641
-
Computational design of virus-like protein assemblies on carbon nanotube surfaces
-
G. Grigoryan, Y.H. Kim, R. Acharya, K. Axelrod, R.M. Jain, and L. Willis Computational design of virus-like protein assemblies on carbon nanotube surfaces Science 332 2011 1071 1076
-
(2011)
Science
, vol.332
, pp. 1071-1076
-
-
Grigoryan, G.1
Kim, Y.H.2
Acharya, R.3
Axelrod, K.4
Jain, R.M.5
Willis, L.6
-
19
-
-
34249821932
-
Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates
-
DOI 10.1002/jcc.20624
-
D. Gront, S. Kmiecik, and A. Kolinski Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates Journal of Computational Chemistry 28 2007 1593 1597 (Pubitemid 46853797)
-
(2007)
Journal of Computational Chemistry
, vol.28
, Issue.9
, pp. 1593-1597
-
-
Gront, D.1
Kmiecik, S.2
Kolinski, A.3
-
21
-
-
0035005949
-
The designability of protein structures
-
DOI 10.1016/S1093-3263(00)00137-6, PII S1093326300001376
-
R. Helling, H. Li, R. Melin, J. Miller, N. Wingreen, and C. Zeng The designability of protein structures Journal of Molecular Graphics & Modelling 19 2001 157 167 (Pubitemid 32411513)
-
(2001)
Journal of Molecular Graphics and Modelling
, vol.19
, Issue.1
, pp. 157-167
-
-
Helling, R.1
Li, H.2
Melin, R.3
Miller, J.4
Wingreen, N.5
Zeng, C.6
Tang, C.7
-
22
-
-
0036296028
-
Twist and shear in beta-sheets and beta-ribbons
-
B.K. Ho, and P.M. Curmi Twist and shear in beta-sheets and beta-ribbons Journal of Molecular Biology 317 2002 291 308
-
(2002)
Journal of Molecular Biology
, vol.317
, pp. 291-308
-
-
Ho, B.K.1
Curmi, P.M.2
-
24
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
DOI 10.1006/jmbi.1993.1489
-
L. Holm, and C. Sander Protein structure comparison by alignment of distance matrices Journal of Molecular Biology 233 1993 123 138 (Pubitemid 23288916)
-
(1993)
Journal of Molecular Biology
, vol.233
, Issue.1
, pp. 123-138
-
-
Holm, L.1
Sander, C.2
-
26
-
-
0029785147
-
Mapping the protein universe
-
L. Holm, and C. Sander Mapping the protein universe Science 273 1996 595 603
-
(1996)
Science
, vol.273
, pp. 595-603
-
-
Holm, L.1
Sander, C.2
-
27
-
-
77951245613
-
Helix-sheet packing in proteins
-
C. Hu, and P. Koehl Helix-sheet packing in proteins Proteins 78 2010 1736 1747
-
(2010)
Proteins
, vol.78
, pp. 1736-1747
-
-
Hu, C.1
Koehl, P.2
-
28
-
-
0028566270
-
A revised set of potentials for beta-turn formation in proteins
-
E.G. Hutchinson, and J.M. Thornton A revised set of potentials for beta-turn formation in proteins Protein Science 3 1994 2207 2216
-
(1994)
Protein Science
, vol.3
, pp. 2207-2216
-
-
Hutchinson, E.G.1
Thornton, J.M.2
-
29
-
-
78651277458
-
A series of PDB related databases for everyday needs
-
R.P. Joosten, T.A. te Beek, E. Krieger, M.L. Hekkelman, R.W. Hooft, and R. Schneider A series of PDB related databases for everyday needs Nucleic Acids Research 39 2011 D411 D419
-
(2011)
Nucleic Acids Research
, vol.39
-
-
Joosten, R.P.1
Te Beek, T.A.2
Krieger, E.3
Hekkelman, M.L.4
Hooft, R.W.5
Schneider, R.6
-
30
-
-
4043048650
-
Backbone-backbone geometry of tertiary contacts between α-helices
-
DOI 10.1002/prot.20201
-
P. Kallblad, and P.M. Dean Backbone-backbone geometry of tertiary contacts between alpha-helices Proteins 56 2004 693 703 (Pubitemid 39063313)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.56
, Issue.4
, pp. 693-703
-
-
Kallblad, P.1
Dean, P.M.2
-
32
-
-
13444279981
-
Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures
-
DOI 10.1016/j.jmb.2004.12.032
-
R. Kolodny, P. Koehl, and M. Levitt Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures Journal of Molecular Biology 346 2005 1173 1188 (Pubitemid 40215537)
-
(2005)
Journal of Molecular Biology
, vol.346
, Issue.4
, pp. 1173-1188
-
-
Kolodny, R.1
Koehl, P.2
Levitt, M.3
-
33
-
-
1842577654
-
Computational redesign of protein-protein interaction specificity
-
DOI 10.1038/nsmb749
-
T. Kortemme, L.A. Joachimiak, A.N. Bullock, A.D. Schuler, B.L. Stoddard, and D. Baker Computational redesign of protein-protein interaction specificity Nature Structural & Molecular Biology 11 2004 371 379 (Pubitemid 38436803)
-
(2004)
Nature Structural and Molecular Biology
, vol.11
, Issue.4
, pp. 371-379
-
-
Kortemme, T.1
Joachimiak, L.A.2
Bullock, A.N.3
Schuler, A.D.4
Stoddard, B.L.5
Baker, D.6
-
35
-
-
0345306764
-
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
-
DOI 10.1126/science.1089427
-
B. Kuhlman, G. Dantas, G.C. Ireton, G. Varani, B.L. Stoddard, and D. Baker Design of a novel globular protein fold with atomic-level accuracy Science 302 2003 1364 1368 (Pubitemid 37452172)
-
(2003)
Science
, vol.302
, Issue.5649
, pp. 1364-1368
-
-
Kuhlman, B.1
Dantas, G.2
Ireton, G.C.3
Varani, G.4
Stoddard, B.L.5
Baker, D.6
-
36
-
-
84862572941
-
Structural informatics, modeling, and design with an open-source molecular software library (MSL)
-
D.W. Kulp, S. Subramaniam, J.E. Donald, B.T. Hannigan, B.K. Mueller, and G. Grigoryan Structural informatics, modeling, and design with an open-source molecular software library (MSL) Journal of Computational Chemistry 33 2012 1645 1661
-
(2012)
Journal of Computational Chemistry
, vol.33
, pp. 1645-1661
-
-
Kulp, D.W.1
Subramaniam, S.2
Donald, J.E.3
Hannigan, B.T.4
Mueller, B.K.5
Grigoryan, G.6
-
37
-
-
0028015988
-
The protein threading problem with sequence amino acid interaction preferences is NP-complete
-
R.H. Lathrop The protein threading problem with sequence amino acid interaction preferences is NP-Complete Protein Engineering 7 1994 1059 1068 (Pubitemid 24282490)
-
(1994)
Protein Engineering
, vol.7
, Issue.9
, pp. 1059-1068
-
-
Lathrop, R.H.J.1
-
38
-
-
0029772552
-
Emergence of preferred structures in a simple model of protein folding
-
H. Li, R. Helling, C. Tang, and N. Wingreen Emergence of preferred structures in a simple model of protein folding Science 273 1996 666 669 (Pubitemid 26262124)
-
(1996)
Science
, vol.273
, Issue.5275
, pp. 666-669
-
-
Li, H.1
Helling, R.2
Tang, C.3
Wingreen, N.4
-
40
-
-
78651285748
-
CDD: A conserved domain database for the functional annotation of proteins
-
A. Marchler-Bauer, S. Lu, J.B. Anderson, F. Chitsaz, M.K. Derbyshire, and C. DeWeese-Scott CDD: A conserved domain database for the functional annotation of proteins Nucleic Acids Research 39 2011 D225 D229
-
(2011)
Nucleic Acids Research
, vol.39
-
-
Marchler-Bauer, A.1
Lu, S.2
Anderson, J.B.3
Chitsaz, F.4
Derbyshire, M.K.5
Deweese-Scott, C.6
-
41
-
-
83755178457
-
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
-
F. Morcos, A. Pagnani, B. Lunt, A. Bertolino, D.S. Marks, and C. Sander Direct-coupling analysis of residue coevolution captures native contacts across many protein families Proceedings of the National Academy of Sciences of the United States of America 108 2011 E1293 E1301
-
(2011)
Proceedings of the National Academy of Sciences of the United States of America
, vol.108
-
-
Morcos, F.1
Pagnani, A.2
Lunt, B.3
Bertolino, A.4
Marks, D.S.5
Sander, C.6
-
43
-
-
0038141205
-
Classification schemes for protein structure and function
-
DOI 10.1038/nrg1113
-
C.A. Ouzounis, R.M. Coulson, A.J. Enright, V. Kunin, and J.B. Pereira-Leal Classification schemes for protein structure and function Nature Reviews. Genetics 4 2003 508 519 (Pubitemid 36781342)
-
(2003)
Nature Reviews Genetics
, vol.4
, Issue.7
, pp. 508-519
-
-
Ouzounis, C.A.1
Coulson, R.M.R.2
Enright, A.J.3
Kunin, V.4
Pereira-Leal, J.B.5
-
45
-
-
0141815540
-
Global secondary structure packing angle bias in proteins
-
DOI 10.1002/prot.10448
-
D.E. Platt, C. Guerra, G. Zanotti, and I. Rigoutsos Global secondary structure packing angle bias in proteins Proteins 53 2003 252 261 (Pubitemid 37193820)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.53
, Issue.2
, pp. 252-261
-
-
Platt, D.E.1
Guerra, C.2
Zanotti, G.3
Rigoutsos, I.4
-
46
-
-
0036315558
-
Computer-aided design of a PDZ domain to recognize new target sequences
-
DOI 10.1038/nsb815
-
J. Reina, E. Lacroix, S.D. Hobson, G. Fernandez-Ballester, V. Rybin, and M.S. Schwab Computer-aided design of a PDZ domain to recognize new target sequences Nature Structural Biology 9 2002 621 627 (Pubitemid 34816144)
-
(2002)
Nature Structural Biology
, vol.9
, Issue.8
, pp. 621-627
-
-
Reina, J.1
Lacroix, E.2
Hobson, S.D.3
Fernandez-Ballester, G.4
Rybin, V.5
Schwab, M.S.6
Serrano, L.7
Gonzalez, C.8
-
48
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
DOI 10.1006/jmbi.1997.0959
-
K.T. Simons, C. Kooperberg, E. Huang, and D. Baker Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions Journal of Molecular Biology 268 1997 209 225 (Pubitemid 27192690)
-
(1997)
Journal of Molecular Biology
, vol.268
, Issue.1
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
49
-
-
79960609097
-
Predicting the tolerated sequences for proteins and protein interfaces using Rosettabackrub flexible backbone design
-
C.A. Smith, and T. Kortemme Predicting the tolerated sequences for proteins and protein interfaces using Rosettabackrub flexible backbone design PloS One 6 2011 e20451
-
(2011)
PloS One
, vol.6
, pp. 20451
-
-
Smith, C.A.1
Kortemme, T.2
-
50
-
-
78651344377
-
3did: Identification and classification of domain-based interactions of known three-dimensional structure
-
A. Stein, A. Ceol, and P. Aloy 3did: Identification and classification of domain-based interactions of known three-dimensional structure Nucleic Acids Research 39 2011 D718 D723
-
(2011)
Nucleic Acids Research
, vol.39
-
-
Stein, A.1
Ceol, A.2
Aloy, P.3
-
52
-
-
75549088586
-
PepX: A structural database of non-redundant protein-peptide complexes
-
P. Vanhee, J. Reumers, F. Stricher, L. Baeten, L. Serrano, and J. Schymkowitz PepX: A structural database of non-redundant protein-peptide complexes Nucleic Acids Research 38 2010 D545 D551
-
(2010)
Nucleic Acids Research
, vol.38
-
-
Vanhee, P.1
Reumers, J.2
Stricher, F.3
Baeten, L.4
Serrano, L.5
Schymkowitz, J.6
-
53
-
-
68149138672
-
Protein-peptide interactions adopt the same structural motifs as monomeric protein folds
-
P. Vanhee, F. Stricher, L. Baeten, E. Verschueren, T. Lenaerts, and L. Serrano Protein-peptide interactions adopt the same structural motifs as monomeric protein folds Structure 17 2009 1128 1136
-
(2009)
Structure
, vol.17
, pp. 1128-1136
-
-
Vanhee, P.1
Stricher, F.2
Baeten, L.3
Verschueren, E.4
Lenaerts, T.5
Serrano, L.6
-
54
-
-
80052089195
-
Protein design with fragment databases
-
E. Verschueren, P. Vanhee, A.M. van der Sloot, L. Serrano, F. Rousseau, and J. Schymkowitz Protein design with fragment databases Current Opinion in Structural Biology 21 2011 452 459
-
(2011)
Current Opinion in Structural Biology
, vol.21
, pp. 452-459
-
-
Verschueren, E.1
Vanhee, P.2
Van Der Sloot, A.M.3
Serrano, L.4
Rousseau, F.5
Schymkowitz, J.6
-
56
-
-
0346492908
-
Designability and thermal stability of protein structures
-
DOI 10.1016/j.polymer.2003.10.062
-
N.S. Wingreen, H. Li, and C. Tang Designability and thermal stability of protein structures Polymer 45 2004 699 705 (Pubitemid 38082203)
-
(2004)
Polymer
, vol.45
, Issue.2
, pp. 699-705
-
-
Wingreen, N.S.1
Li, H.2
Tang, C.3
-
57
-
-
82955239912
-
Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling
-
J. Zhang, Y. Liang, and Y. Zhang Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling Structure 19 2011 1784 1795
-
(2011)
Structure
, vol.19
, pp. 1784-1795
-
-
Zhang, J.1
Liang, Y.2
Zhang, Y.3
|