메뉴 건너뛰기




Volumn 30, Issue 21, 2014, Pages 3029-3035

CCBuilder: An interactive web-based tool for building, designing and assessing coiled-coil protein assemblies

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; INTERNET; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; SOFTWARE;

EID: 84911394089     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu502     Document Type: Article
Times cited : (98)

References (46)
  • 1
    • 0033994775 scopus 로고    scopus 로고
    • HELANAL: A program to characterize helix geometry in proteins
    • Bansal, M. et al. (2000) HELANAL: a program to characterize helix geometry in proteins. J. Biomol. Struct. Dyn., 17, 811-819.
    • (2000) J. Biomol. Struct. Dyn. , vol.17 , pp. 811-819
    • Bansal, M.1
  • 2
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie, J.U. et al. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1
  • 3
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • Bradley, P. et al. (2005) Toward high-resolution de novo structure prediction for small proteins. Science, 309, 1868-1871.
    • (2005) Science , vol.309 , pp. 1868-1871
    • Bradley, P.1
  • 4
    • 84883303145 scopus 로고    scopus 로고
    • Accessibility, reactivity, and selectivity of side chains within a channel of de novo peptide assembly
    • Burton, A.J. et al. (2013) Accessibility, reactivity, and selectivity of side chains within a channel of de novo peptide assembly. J. Am. Chem. Soc., 135, 12524-12527.
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 12524-12527
    • Burton, A.J.1
  • 5
    • 0037126590 scopus 로고    scopus 로고
    • The structure of bovine IF(1), the regulatory subunit of mitochondrial F-ATPase
    • Cabezon, E. et al. (2001) The structure of bovine IF(1), the regulatory subunit of mitochondrial F-ATPase. EMBO J., 20, 6990-6996.
    • (2001) EMBO J. , vol.20 , pp. 6990-6996
    • Cabezon, E.1
  • 6
    • 0034977013 scopus 로고    scopus 로고
    • A normalized root-mean-square distance for comparing protein three-dimensional structures
    • Carugo, O. and Pongor, S. (2001) A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Sci., 10, 1470-1473.
    • (2001) Protein Sci. , vol.10 , pp. 1470-1473
    • Carugo, O.1    Pongor, S.2
  • 7
    • 77949617607 scopus 로고    scopus 로고
    • PyRosetta: A script-based interface for implementing molecular modeling algorithms using Rosetta
    • Chaudhury, S. et al. (2010) PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta. Bioinformatics, 26, 689-691.
    • (2010) Bioinformatics , vol.26 , pp. 689-691
    • Chaudhury, S.1
  • 8
    • 0019872825 scopus 로고
    • Helix to helix packing in proteins
    • Chothia, C. et al. (1981) Helix to helix packing in proteins. J. Mol. Biol., 145, 215-250.
    • (1981) J. Mol. Biol. , vol.145 , pp. 215-250
    • Chothia, C.1
  • 9
    • 0000747247 scopus 로고
    • The Fourier transform of a coiled-coil
    • Crick, F.H.C. (1953a) The Fourier transform of a coiled-coil. Acta Crystallogr., 6, 685-689.
    • (1953) Acta Crystallogr. , vol.6 , pp. 685-689
    • Crick, F.H.C.1
  • 10
    • 0000920828 scopus 로고
    • The packing of α-helices: Simple coiled-coils
    • Crick, F.H.C. (1953b) The packing of α-helices: simple coiled-coils. Acta Crystallogr., 6, 689-697.
    • (1953) Acta Crystallogr. , vol.6 , pp. 689-697
    • Crick, F.H.C.1
  • 11
    • 0035999986 scopus 로고    scopus 로고
    • An HMM model for coiled-coil domains and a comparison with PSSM-based predictions
    • Delorenzi, M. and Speed, T. (2002) An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. Bioinformatics, 18, 617-625.
    • (2002) Bioinformatics , vol.18 , pp. 617-625
    • Delorenzi, M.1    Speed, T.2
  • 12
    • 0035342435 scopus 로고    scopus 로고
    • Ab initio protein structure prediction using physicochemical potentials and a simplified off-lattice model
    • Gibbs, N. et al. (2001) Ab initio protein structure prediction using physicochemical potentials and a simplified off-lattice model. Proteins, 43, 186-202.
    • (2001) Proteins , vol.43 , pp. 186-202
    • Gibbs, N.1
  • 13
    • 16944366990 scopus 로고    scopus 로고
    • Buried polar residues and structural specificity in the GCN4 leucine zipper
    • Gonzalez, L. et al. (1996) Buried polar residues and structural specificity in the GCN4 leucine zipper. Nat. Struct. Mol. Biol., 3, 1011-1018.
    • (1996) Nat. Struct. Mol. Biol. , vol.3 , pp. 1011-1018
    • Gonzalez, L.1
  • 14
    • 79251600167 scopus 로고    scopus 로고
    • Probing designability via a generalized model of helical bundle geometry
    • Grigoryan, G. and DeGrado, W.F. (2011) Probing designability via a generalized model of helical bundle geometry. J. Mol. Biol., 405, 1079-1100.
    • (2011) J. Mol. Biol. , vol.405 , pp. 1079-1100
    • Grigoryan, G.1    Degrado, W.F.2
  • 15
    • 0027756896 scopus 로고
    • A switch between, two- , three-, and four-stranded coiled coils in GCN4 leucine zipper mutants
    • Harbury, P.B. et al. (1993) A switch between, two- , three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science, 262, 1401-1407.
    • (1993) Science , vol.262 , pp. 1401-1407
    • Harbury, P.B.1
  • 16
    • 0027934571 scopus 로고
    • Crystal structure of an isoleucine-zipper trimer
    • Harbury, P.B. et al. (1994) Crystal structure of an isoleucine-zipper trimer. Nature, 371, 80-83.
    • (1994) Nature , vol.371 , pp. 80-83
    • Harbury, P.B.1
  • 17
    • 0020997912 scopus 로고
    • 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
  • 18
    • 84868611622 scopus 로고    scopus 로고
    • Principles for designing ideal protein structures
    • Koga, N. et al. (2012) Principles for designing ideal protein structures. Nature, 491, 222-227.
    • (2012) Nature , vol.491 , pp. 222-227
    • Koga, N.1
  • 19
    • 0034702177 scopus 로고    scopus 로고
    • Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export
    • Koronakis, V. et al. (2000) Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export. Nature, 405, 914-919.
    • (2000) Nature , vol.405 , pp. 914-919
    • Koronakis, V.1
  • 20
    • 70450106216 scopus 로고    scopus 로고
    • 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
  • 21
    • 33750309175 scopus 로고    scopus 로고
    • A seven-helix coiled coil
    • Liu, J. et al. (2006) A seven-helix coiled coil. Proc. Natl Acad. Sci. USA., 103, 15457-15462.
    • (2006) Proc. Natl Acad. Sci. USA. , vol.103 , pp. 15457-15462
    • Liu, J.1
  • 22
    • 67649887151 scopus 로고    scopus 로고
    • PGenTHREADER and pDomTHREADER: New methods for improved protein fold recognition and superfamily discrimination
    • Lobley, A. et al. (2009) pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination. Bioinformatics, 25, 1761-1767.
    • (2009) Bioinformatics , vol.25 , pp. 1761-1767
    • Lobley, A.1
  • 23
    • 0026356891 scopus 로고
    • Predicting coiled coils from protein sequences
    • Lupas, A. et al. (1991) Predicting coiled coils from protein sequences. Science, 252, 1162-1164.
    • (1991) Science , vol.252 , pp. 1162-1164
    • Lupas, A.1
  • 24
    • 17444424974 scopus 로고    scopus 로고
    • The structure of α-helical coiled coils
    • Lupas, A.N. and Gruber, M. (2005) The structure of α-helical coiled coils. Adv. Protein Chem., 70, 37-78.
    • (2005) Adv. Protein Chem. , vol.70 , pp. 37-78
    • Lupas, A.N.1    Gruber, M.2
  • 25
    • 0029911261 scopus 로고    scopus 로고
    • The crystal structure of a five-stranded coiled coil in COMP: A prototype ion channel?
    • Malashkevich, V.N. et al. (1996) The crystal structure of a five-stranded coiled coil in COMP: a prototype ion channel? Science, 274, 761-765.
    • (1996) Science , vol.274 , pp. 761-765
    • Malashkevich, V.N.1
  • 26
    • 0033873929 scopus 로고    scopus 로고
    • Comparative protein structure modeling of genes and genomes
    • Mart?-Renom, M.A. et al. (2000) Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct., 29, 291-325.
    • (2000) Annu. Rev. Biophys. Biomol. Struct. , vol.29 , pp. 291-325
    • Mart-Renom, M.A.1
  • 27
    • 84856866322 scopus 로고    scopus 로고
    • Benchmarking energy efficiency, power costs and carbon emissions on heterogeneous systems
    • McIntosh-Smith, S. et al. (2011) Benchmarking energy efficiency, power costs and carbon emissions on heterogeneous systems. Comput. J., 55, 192-205.
    • (2011) Comput. J. , vol.55 , pp. 192-205
    • McIntosh-Smith, S.1
  • 28
    • 84911417989 scopus 로고    scopus 로고
    • High performance in silico virtual drug screening on many-core processors
    • Mcintosh-smith, S. et al. (2014) High performance in silico virtual drug screening on many-core processors. Int. J. High Perform. Comput. Appl. doi:101177/094342014528252.
    • (2014) Int. J. High Perform. Comput. Appl.
    • McIntosh-Smith, S.1
  • 29
    • 0000009443 scopus 로고
    • Rapid comparison of protein structures
    • McLachlan, A. (1982) Rapid comparison of protein structures. Acta Crystallogr. Sect. A, 38, 871-873.
    • (1982) Acta Crystallogr. Sect. A , vol.38 , pp. 871-873
    • McLachlan, A.1
  • 30
    • 58149119313 scopus 로고    scopus 로고
    • A periodic table of coiled-coil protein structures
    • Moutevelis, E. and Woolfson, D.N. (2009) A periodic table of coiled-coil protein structures. J. Mol. Biol., 385, 726-732.
    • (2009) J. Mol. Biol. , vol.385 , pp. 726-732
    • Moutevelis, E.1    Woolfson, D.N.2
  • 31
    • 0036444017 scopus 로고    scopus 로고
    • Generalized Crick equations for modeling noncanonical coiled coils
    • Offer, G. et al. (2002) Generalized Crick equations for modeling noncanonical coiled coils. J. Struct. Biol., 137, 41-53.
    • (2002) J. Struct. Biol. , vol.137 , pp. 41-53
    • Offer, G.1
  • 32
    • 0028978047 scopus 로고
    • Computer modelling of the a α-helical coiled coil: Packing of side-chains in the inner core
    • Offer, G. and Sessions, R.B. (1995) Computer modelling of the a α-helical coiled coil: packing of side-chains in the inner core. J. Mol. Biol., 249, 967-987.
    • (1995) J. Mol. Biol. , vol.249 , pp. 967-987
    • Offer, G.1    Sessions, R.B.2
  • 33
    • 0029063717 scopus 로고
    • The Complexity and Accuracy of Discrete State Models of Protein Structure
    • Park, B.H. and Levitt, M. (1995) The Complexity and Accuracy of Discrete State Models of Protein Structure. J. Mol. Biol., 249, 493-507.
    • (1995) J. Mol. Biol. , vol.249 , pp. 493-507
    • Park, B.H.1    Levitt, M.2
  • 34
    • 0023155210 scopus 로고
    • Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • Ponder, J.W. and Richards, F.M. (1987) Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol., 193, 775-791.
    • (1987) J. Mol. Biol. , vol.193 , pp. 775-791
    • Ponder, J.W.1    Richards, F.M.2
  • 35
    • 1642464839 scopus 로고    scopus 로고
    • Protein structure prediction using Rosetta
    • Rohl, C.A. et al. (2004) Protein structure prediction using Rosetta. Methods Enzymol., 383, 66-93.
    • (2004) Methods Enzymol. , vol.383 , pp. 66-93
    • Rohl, C.A.1
  • 36
    • 0026009212 scopus 로고
    • Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions
    • Rooman, M.J. et al. (1991) Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions. J. Mol. Biol., 221, 961-979.
    • (1991) J. Mol. Biol. , vol.221 , pp. 961-979
    • Rooman, M.J.1
  • 37
    • 0036445512 scopus 로고    scopus 로고
    • Analysis of alpha-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation
    • Strelkov, S.V. and Burkhard, P. (2002) Analysis of alpha-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation. J. Struct. Biol., 137, 54-64.
    • (2002) J. Struct. Biol. , vol.137 , pp. 54-64
    • Strelkov, S.V.1    Burkhard, P.2
  • 38
    • 84892585316 scopus 로고    scopus 로고
    • Icosahedral bacteriophage X174 forms a tail for DNA transport during infection
    • Sun, L. et al. (2014) Icosahedral bacteriophage X174 forms a tail for DNA transport during infection. Nature, 505, 432-435.
    • (2014) Nature , vol.505 , pp. 432-435
    • Sun, L.1
  • 39
    • 58149185130 scopus 로고    scopus 로고
    • CC+: A relational database of coiled-coil structures
    • Testa, O.D. et al. (2009) CC+: a relational database of coiled-coil structures. Nucleic Acids Res., 37, D315-D322.
    • (2009) Nucleic Acids Res. , vol.37 , pp. D315-D322
    • Testa, O.D.1
  • 40
    • 84871757783 scopus 로고    scopus 로고
    • LOGICOIL-multi-state prediction of coiled-coil oligomeric state
    • Vincent, T.L. et al. (2013) LOGICOIL-multi-state prediction of coiled-coil oligomeric state. Bioinformatics, 29, 69-76.
    • (2013) Bioinformatics , vol.29 , pp. 69-76
    • Vincent, T.L.1
  • 41
    • 0035853291 scopus 로고    scopus 로고
    • Socket: A program for identifying and analysing coiled-coil motifs within protein structures
    • Walshaw, J. and Woolfson, D.N. (2001) Socket: a program for identifying and analysing coiled-coil motifs within protein structures. J. Mol. Biol., 307, 1427-1450.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1427-1450
    • Walshaw, J.1    Woolfson, D.N.2
  • 42
    • 0029083811 scopus 로고
    • Predicting oligomerization states of coiled coils
    • Woolfson, D.N. and Alber, T. (1995) Predicting oligomerization states of coiled coils. Protein Sci., 4, 1596-1607.
    • (1995) Protein Sci. , vol.4 , pp. 1596-1607
    • Woolfson, D.N.1    Alber, T.2
  • 43
    • 17444433002 scopus 로고    scopus 로고
    • The design of coiled-coil structures and assemblies
    • Woolfson, D.N. (2005) The design of coiled-coil structures and assemblies. Adv. Protein Chem., 70, 79-112.
    • (2005) Adv. Protein Chem. , vol.70 , pp. 79-112
    • Woolfson, D.N.1
  • 44
    • 84865288368 scopus 로고    scopus 로고
    • New currency for old rope: From coiled-coil assemblies to α-helical barrels
    • Woolfson, D.N. et al. (2012) New currency for old rope: from coiled-coil assemblies to α-helical barrels. Curr. Opin. Struct. Biol., 22, 432-441.
    • (2012) Curr. Opin. Struct. Biol. , vol.22 , pp. 432-441
    • Woolfson, D.N.1
  • 45
    • 46449123146 scopus 로고    scopus 로고
    • MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information
    • Wu, S. and Zhang, Y. (2008) MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins, 72, 547-556.
    • (2008) Proteins , vol.72 , pp. 547-556
    • Wu, S.1    Zhang, Y.2
  • 46
    • 81355127213 scopus 로고    scopus 로고
    • A de novo peptide hexamer with a mutable channel
    • Zaccai, N.R. et al. (2011) A de novo peptide hexamer with a mutable channel. Nat. Chem. Biol., 7, 935-941.
    • (2011) Nat. Chem. Biol. , vol.7 , pp. 935-941
    • Zaccai, N.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.