메뉴 건너뛰기




Volumn 523, Issue , 2013, Pages 21-40

Mining tertiary structural motifs for assessment of designability

Author keywords

Degeneracy of protein structural universe; Designability; Protein design; Protein substructure search; Tertiary structural motifs

Indexed keywords

AMINO ACID;

EID: 84874098113     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-394292-0.00002-3     Document Type: Chapter
Times cited : (16)

References (58)
  • 2
    • 80054836686 scopus 로고    scopus 로고
    • 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
  • 4
    • 34147169516 scopus 로고    scopus 로고
    • 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
  • 8
    • 0000747247 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 20
  • 22
    • 0036296028 scopus 로고    scopus 로고
    • 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
  • 23
  • 24
    • 0027440362 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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
  • 30
    • 4043048650 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 34
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • B. Kuhlman, and D. Baker Native protein sequences are close to optimal for their structures Proceedings of the National Academy of Sciences 97 2000 10383 10388
    • (2000) Proceedings of the National Academy of Sciences , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 35
    • 0345306764 scopus 로고    scopus 로고
    • 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
  • 37
    • 0028015988 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 39
    • 75849126506 scopus 로고    scopus 로고
    • The structural basis of peptide-protein binding strategies
    • N. London, D. Movshovitz-Attias, and O. Schueler-Furman The structural basis of peptide-protein binding strategies Structure 18 2010 188 199
    • (2010) Structure , vol.18 , pp. 188-199
    • London, N.1    Movshovitz-Attias, D.2    Schueler-Furman, O.3
  • 42
  • 48
    • 0031585984 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 53
    • 68149138672 scopus 로고    scopus 로고
    • 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
  • 56
    • 0346492908 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 58
    • 12844288890 scopus 로고    scopus 로고
    • The protein structure prediction problem could be solved using the current PDB library
    • DOI 10.1073/pnas.0407152101
    • Y. Zhang, and J. Skolnick The protein structure prediction problem could be solved using the current PDB library Proceedings of the National Academy of Sciences of the United States of America 102 2005 1029 1034 (Pubitemid 40170720)
    • (2005) Proceedings of the National Academy of Sciences of the United States of America , vol.102 , Issue.4 , pp. 1029-1034
    • Zhang, Y.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.