메뉴 건너뛰기




Volumn 107, Issue 18, 2010, Pages 8177-8182

Semiautomated model building for RNA crystallography using a directed rotameric approach

Author keywords

Backbone conformers; Pseudotorsions; Reduced representation; RNA conformation; RNA structure

Indexed keywords

BASE; PHOSPHATE; RNA;

EID: 77952352777     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0911888107     Document Type: Article
Times cited : (49)

References (26)
  • 1
    • 9244225713 scopus 로고    scopus 로고
    • Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
    • Batey RT, Gilbert SD, Montange RK (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432:411-415.
    • (2004) Nature , vol.432 , pp. 411-415
    • Batey, R.T.1    Gilbert, S.D.2    Montange, R.K.3
  • 2
    • 3042848954 scopus 로고    scopus 로고
    • Crystal structure of a self-splicing group I intron with both exons
    • DOI 10.1038/nature02642
    • Adams PL, Stahley MR, Kosek AB, Wang J, Strobel SA (2004) Crystal structure of a self-splicing group I intron with both exons. Nature 430:45-50. (Pubitemid 38915218)
    • (2004) Nature , vol.430 , Issue.6995 , pp. 45-50
    • Adams, P.L.1    Stahley, M.R.2    Kosek, A.B.3    Wang, J.4    Strobel, S.A.5
  • 3
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
    • DOI 10.1126/science.289.5481.905
    • Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289:905-920. (Pubitemid 30659939)
    • (2000) Science , vol.289 , Issue.5481 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 4
    • 41749109563 scopus 로고    scopus 로고
    • Crystal structure of a self-spliced group II intron
    • DOI 10.1126/science.1153803
    • Toor N, Keating KS, Taylor SD, Pyle AM (2008) Crystal structure of a self-spliced group II intron. Science 320:77-82. (Pubitemid 351490756)
    • (2008) Science , vol.320 , Issue.5872 , pp. 77-82
    • Toor, N.1    Keating, K.S.2    Taylor, S.D.3    Pyle, A.M.4
  • 7
    • 0027184481 scopus 로고
    • A general two-metal-ion mechanism for catalytic RNA
    • Steitz TA, Steitz JA (1993) A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 90:6498-6502.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 6498-6502
    • Steitz, T.A.1    Steitz, J.A.2
  • 8
    • 0032727991 scopus 로고    scopus 로고
    • Themes in RNA-protein recognition
    • Draper DE (1999) Themes in RNA-protein recognition. J Mol Biol 293:255-270.
    • (1999) J Mol Biol , vol.293 , pp. 255-270
    • Draper, D.E.1
  • 9
    • 0035367070 scopus 로고    scopus 로고
    • Structure and function of the small ribozymes
    • Butcher SE (2001) Structure and function of the small ribozymes. Curr Opin Struc Biol 11:315-320.
    • (2001) Curr Opin Struc Biol , vol.11 , pp. 315-320
    • Butcher, S.E.1
  • 10
    • 34547592557 scopus 로고    scopus 로고
    • MolProbity: All-atom contacts and structure validation for proteins and nucleic acids
    • Davis IW, et al. (2007) MolProbity: All-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375-W383.
    • (2007) Nucleic Acids Res , vol.35
    • Davis, I.W.1
  • 11
    • 33748337934 scopus 로고    scopus 로고
    • The Buccaneer software for automated model building. 1. Tracing protein chains
    • Cowtan K (2006) The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr D 62:1002-1011.
    • (2006) Acta Crystallogr D , vol.62 , pp. 1002-1011
    • Cowtan, K.1
  • 12
    • 0037237545 scopus 로고    scopus 로고
    • Automated main-chain model building by template matching and iterative fragment extension
    • Terwilliger TC (2002) Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr D 59:38-44.
    • (2002) Acta Crystallogr D , vol.59 , pp. 38-44
    • Terwilliger, T.C.1
  • 13
    • 50249136103 scopus 로고    scopus 로고
    • Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7
    • Langer G, Cohen SX, Lamzin VS, Perrakis A (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3:1171-1179.
    • (2008) Nat Protoc , vol.3 , pp. 1171-1179
    • Langer, G.1    Cohen, S.X.2    Lamzin, V.S.3    Perrakis, A.4
  • 14
    • 0032545158 scopus 로고    scopus 로고
    • Stepping through an RNA structure: A novel approach to conformational analysis
    • Duarte CM, Pyle AM (1998) Stepping through an RNA structure: A novel approach to conformational analysis. J Mol Biol 284:1465-1478.
    • (1998) J Mol Biol , vol.284 , pp. 1465-1478
    • Duarte, C.M.1    Pyle, A.M.2
  • 15
    • 40449091092 scopus 로고    scopus 로고
    • RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)
    • Richardson JS, et al. (2008) RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA 14:465-481.
    • (2008) RNA , vol.14 , pp. 465-481
    • Richardson, J.S.1
  • 16
    • 34548401692 scopus 로고    scopus 로고
    • Evaluating and learning from RNA pseudotorsional space: Quantitative validation of a reduced representation for RNA structure
    • Wadley LM, Keating KS, Duarte CM, Pyle AM(2007) Evaluating and learning from RNA pseudotorsional space: Quantitative validation of a reduced representation for RNA structure. J Mol Biol 372:942-957.
    • (2007) J Mol Biol , vol.372 , pp. 942-957
    • Wadley, L.M.1    Keating, K.S.2    Duarte, C.M.3    Pyle, A.M.4
  • 17
    • 36448943965 scopus 로고    scopus 로고
    • RNABC: Forward kinematics to reduce all-atom steric clashes in RNA backbone
    • DOI 10.1007/s00285-007-0082-x, RNA: Advances in algorithms and mathematics related to the structural biology of RNA
    • Wang X, et al. (2008) RNABC: Forward kinematics to reduce all-atom steric clashes in RNA backbone. J Math Biol 56:253-278. (Pubitemid 350172193)
    • (2008) Journal of Mathematical Biology , vol.56 , Issue.1-2 , pp. 253-278
    • Wang, X.1    Kapral, G.2    Murray, L.3    Richardson, D.4    Richardson, J.5    Snoeyink, J.6
  • 18
    • 40849129173 scopus 로고
    • A novel virtual bond scheme to probe ordered and random coil conformations of nucleic acids: Configurational stastistics of polynucleotie chains
    • Malathi R, Yathindra N (1980) A novel virtual bond scheme to probe ordered and random coil conformations of nucleic acids: Configurational stastistics of polynucleotie chains. Curr Sci India 49:803-808.
    • (1980) Curr Sci India , vol.49 , pp. 803-808
    • Malathi, R.1    Yathindra, N.2
  • 19
    • 0038359471 scopus 로고
    • Configurational statistics of polynucleotide chains. An updated virtual bond model to treat effects of base stacking
    • Olson WK (1980) Configurational statistics of polynucleotide chains. An updated virtual bond model to treat effects of base stacking. Macromolecules 13:721-728.
    • (1980) Macromolecules , vol.13 , pp. 721-728
    • Olson, W.K.1
  • 22
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • Fawcett T (2006) An introduction to ROC analysis. Pattern Recogn Lett 27:861-874.
    • (2006) Pattern Recogn Lett , vol.27 , pp. 861-874
    • Fawcett, T.1
  • 23
    • 0345531092 scopus 로고    scopus 로고
    • The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure
    • DOI 10.1093/nar/gkg908
    • Correll CC, Beneken J, Plantinga MJ, Lubbers M, Chan Y (2003) The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure. Nucleic Acids Res 31:6806-6818. (Pubitemid 37508788)
    • (2003) Nucleic Acids Research , vol.31 , Issue.23 , pp. 6806-6818
    • Correll, C.C.1    Beneken, J.2    Plantinga, M.J.3    Lubbers, M.4    Chan, Y.-L.5
  • 24
    • 36248982074 scopus 로고    scopus 로고
    • Mutational analysis of the purine riboswitch aptamer domain
    • Gilbert SD, Love CE, Edwards AL, Batey RT (2007) Mutational analysis of the purine riboswitch aptamer domain. Biochemistry 46:13297-13309.
    • (2007) Biochemistry , vol.46 , pp. 13297-13309
    • Gilbert, S.D.1    Love, C.E.2    Edwards, A.L.3    Batey, R.T.4
  • 26
    • 0026742978 scopus 로고
    • The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids
    • Berman H, et al. (1992) The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J 63:751-759.
    • (1992) Biophys J , vol.63 , pp. 751-759
    • Berman, H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.