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Volumn 7, Issue 11, 2012, Pages

Coarse-Grained Prediction of RNA Loop Structures

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE;

EID: 84869026752     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048460     Document Type: Article
Times cited : (10)

References (74)
  • 1
    • 44149101971 scopus 로고    scopus 로고
    • Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms
    • Ding F, Sharma S, Chalasani P, Demidov V, Broude N, et al. (2008) Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA 14: 1164-1173.
    • (2008) RNA , vol.14 , pp. 1164-1173
    • Ding, F.1    Sharma, S.2    Chalasani, P.3    Demidov, V.4    Broude, N.5
  • 2
    • 73249145274 scopus 로고    scopus 로고
    • Prediction of geometrically feasible three-dimensional structures of pseudoknotted RNA through free energy estimation
    • Zhang J, Dundas J, Lin M, Chen R, Wang W, et al. (2009) Prediction of geometrically feasible three-dimensional structures of pseudoknotted RNA through free energy estimation. RNA 15: 2248-2263.
    • (2009) RNA , vol.15 , pp. 2248-2263
    • Zhang, J.1    Dundas, J.2    Lin, M.3    Chen, R.4    Wang, W.5
  • 3
    • 67849127180 scopus 로고    scopus 로고
    • Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics
    • Gherghe C, Leonard C, Ding F, Dokholyan N, Weeks K, (2009) Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J Am Chem Soc 131: 2541-2546.
    • (2009) J Am Chem Soc , vol.131 , pp. 2541-2546
    • Gherghe, C.1    Leonard, C.2    Ding, F.3    Dokholyan, N.4    Weeks, K.5
  • 4
    • 77953648210 scopus 로고    scopus 로고
    • On the significance of an RNA tertiary structure prediction
    • Hajdin C, Ding F, Dokholyan N, Weeks K, (2010) On the significance of an RNA tertiary structure prediction. RNA 16: 1340-1349.
    • (2010) RNA , vol.16 , pp. 1340-1349
    • Hajdin, C.1    Ding, F.2    Dokholyan, N.3    Weeks, K.4
  • 5
    • 35548950310 scopus 로고    scopus 로고
    • Automated de novo prediction of native-like RNA tertiary struc22 tures
    • Das R, Baker D, (2007) Automated de novo prediction of native-like RNA tertiary struc22 tures. Proc Natl Acad Sci U S A 104: 14664.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 14664
    • Das, R.1    Baker, D.2
  • 7
    • 40449139010 scopus 로고    scopus 로고
    • The MC-fold and MC-Sym pipeline infers RNA structure from sequence data
    • Parisien M, Major F, (2008) The MC-fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452: 51-55.
    • (2008) Nature , vol.452 , pp. 51-55
    • Parisien, M.1    Major, F.2
  • 8
    • 58249111738 scopus 로고    scopus 로고
    • Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
    • Jonikas M, Radmer R, Laederach A, Das R, Pearlman S, et al. (2009) Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA 15: 189-199.
    • (2009) RNA , vol.15 , pp. 189-199
    • Jonikas, M.1    Radmer, R.2    Laederach, A.3    Das, R.4    Pearlman, S.5
  • 9
    • 77951643739 scopus 로고    scopus 로고
    • Atomic accuracy in predicting and designing noncanonical RNA structure
    • Das R, Karanicolas J, Baker D, (2010) Atomic accuracy in predicting and designing noncanonical RNA structure. Nat Methods 7: 291-294.
    • (2010) Nat Methods , vol.7 , pp. 291-294
    • Das, R.1    Karanicolas, J.2    Baker, D.3
  • 10
    • 77955336463 scopus 로고    scopus 로고
    • RNA structure determination using SAXS data
    • Yang S, Parisien M, Major F, Roux B, (2010) RNA structure determination using SAXS data. J Phys Chem B 114: 10039-10048.
    • (2010) J Phys Chem B , vol.114 , pp. 10039-10048
    • Yang, S.1    Parisien, M.2    Major, F.3    Roux, B.4
  • 11
    • 77956746033 scopus 로고    scopus 로고
    • HiRE-RNA: a high resolution coarse-grained energy model for RNA
    • Pasquali S, Derreumaux P, (2010) HiRE-RNA: a high resolution coarse-grained energy model for RNA. J Phys Chem B 114: 11957-11966.
    • (2010) J Phys Chem B , vol.114 , pp. 11957-11966
    • Pasquali, S.1    Derreumaux, P.2
  • 12
    • 77958490892 scopus 로고    scopus 로고
    • Coarse-grained model for simulation of RNA three-dimensional structures
    • Xia Z, Gardner D, Gutell R, Ren P, (2010) Coarse-grained model for simulation of RNA three-dimensional structures. J Phys Chem B 114: 13497-13506.
    • (2010) J Phys Chem B , vol.114 , pp. 13497-13506
    • Xia, Z.1    Gardner, D.2    Gutell, R.3    Ren, P.4
  • 13
    • 77956026060 scopus 로고    scopus 로고
    • Turning limited experimental information into 3D models of RNA
    • Flores S, Altman R, (2010) Turning limited experimental information into 3D models of RNA. RNA 16: 1769.
    • (2010) RNA , vol.16 , pp. 1769
    • Flores, S.1    Altman, R.2
  • 14
    • 79953795893 scopus 로고    scopus 로고
    • Physics-based de novo prediction of RNA 3D structures
    • Cao S, Chen SJ, (2011) Physics-based de novo prediction of RNA 3D structures. J Phys Chem B 115: 4216-4226.
    • (2011) J Phys Chem B , vol.115 , pp. 4216-4226
    • Cao, S.1    Chen, S.J.2
  • 15
    • 79956189724 scopus 로고    scopus 로고
    • Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation
    • Bernauer J, Huang X, Sim A, Levitt M, (2011) Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation. RNA 17: 1066-1075.
    • (2011) RNA , vol.17 , pp. 1066-1075
    • Bernauer, J.1    Huang, X.2    Sim, A.3    Levitt, M.4
  • 16
    • 84855480988 scopus 로고    scopus 로고
    • An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling
    • Sripakdeevong P, Kladwang W, Das R, (2011) An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling. Proc Natl Acad Sci U S A 108: 20573-20578.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 20573-20578
    • Sripakdeevong, P.1    Kladwang, W.2    Das, R.3
  • 17
    • 84865187135 scopus 로고    scopus 로고
    • Determining RNA three-dimensional structures using low resolution data
    • Parisien M, Major F, (2012) Determining RNA three-dimensional structures using low resolution data. J Struct Biol in press.
    • (2012) J Struct Biol
    • Parisien, M.1    Major, F.2
  • 18
    • 84857412659 scopus 로고    scopus 로고
    • Improved prediction of RNA tertiary structure with insights into native state dynamics
    • Bida J, Maher L III, (2012) Improved prediction of RNA tertiary structure with insights into native state dynamics. RNA 18: 385-393.
    • (2012) RNA , vol.18 , pp. 385-393
    • Bida, J.1    Maher III, L.2
  • 20
    • 77953784130 scopus 로고    scopus 로고
    • Computational approaches to 3D modeling of RNA
    • Laing C, Schlick T, (2010) Computational approaches to 3D modeling of RNA. J Phys: Condens Matter 22: 283101.
    • (2010) J Phys: Condens Matter , vol.22 , pp. 283101
    • Laing, C.1    Schlick, T.2
  • 21
    • 79958073354 scopus 로고    scopus 로고
    • Computational approaches to RNA structure prediction, analysis, and design
    • Laing C, Schlick T, (2011) Computational approaches to RNA structure prediction, analysis, and design. Curr Opin Struct Biol 21: 306-318.
    • (2011) Curr Opin Struct Biol , vol.21 , pp. 306-318
    • Laing, C.1    Schlick, T.2
  • 23
    • 84870556516 scopus 로고    scopus 로고
    • RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction
    • Cruz J, Blanchet M, Boniecki M, Bujnicki J, Chen S, et al. (2012) RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction. RNA 8: 1-16.
    • (2012) RNA , vol.8 , pp. 1-16
    • Cruz, J.1    Blanchet, M.2    Boniecki, M.3    Bujnicki, J.4    Chen, S.5
  • 24
  • 25
    • 14144252846 scopus 로고    scopus 로고
    • Extracting stacking interaction parameters for RNA from the data set of native structures
    • Dima R, Hyeon C, Thirumalai D, (2005) Extracting stacking interaction parameters for RNA from the data set of native structures. J Mol Biol 347: 53-69.
    • (2005) J Mol Biol , vol.347 , pp. 53-69
    • Dima, R.1    Hyeon, C.2    Thirumalai, D.3
  • 26
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure1
    • Mathews D, Sabina J, Zuker M, Turner D, (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure1. J Mol Biol 288: 911-940.
    • (1999) J Mol Biol , vol.288 , pp. 911-940
    • Mathews, D.1    Sabina, J.2    Zuker, M.3    Turner, D.4
  • 27
    • 68149132469 scopus 로고    scopus 로고
    • Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding
    • Wu J, Gardner D, Ozer S, Gutell R, Ren P, (2009) Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding. J Mol Biol 391: 769-783.
    • (2009) J Mol Biol , vol.391 , pp. 769-783
    • Wu, J.1    Gardner, D.2    Ozer, S.3    Gutell, R.4    Ren, P.5
  • 28
    • 0019082587 scopus 로고
    • Fast algorithm for predicting the secondary structure of single-stranded RNA
    • Nussinov R, Jacobson A, (1980) Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci U S A 77: 6309.
    • (1980) Proc Natl Acad Sci U S A , vol.77 , pp. 6309
    • Nussinov, R.1    Jacobson, A.2
  • 29
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker M, (1989) On finding all suboptimal foldings of an RNA molecule. Science 244: 48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1
  • 31
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker I, (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31: 3429-3431.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.1
  • 32
    • 33744790273 scopus 로고    scopus 로고
    • Prediction of RNA secondary structure by free energy minimization
    • Mathews D, Turner D, (2006) Prediction of RNA secondary structure by free energy minimization. Curr Opin Struct Biol 16: 270-278.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 270-278
    • Mathews, D.1    Turner, D.2
  • 33
    • 0030890755 scopus 로고    scopus 로고
    • Improved param eters for the prediction of RNA hairpin stability
    • Serra M, Barnes T, Betschart K, Gutierrez M, Sprouse K, et al. (1997) Improved param eters for the prediction of RNA hairpin stability. Biochemistry 36: 4844-4851.
    • (1997) Biochemistry , vol.36 , pp. 4844-4851
    • Serra, M.1    Barnes, T.2    Betschart, K.3    Gutierrez, M.4    Sprouse, K.5
  • 34
    • 0032570280 scopus 로고    scopus 로고
    • Stability of RNA hairpins closed by wobble base pairs
    • Giese M, Betschart K, Dale T, Riley C, Rowan C, et al. (1998) Stability of RNA hairpins closed by wobble base pairs. Biochemistry 37: 1094-1100.
    • (1998) Biochemistry , vol.37 , pp. 1094-1100
    • Giese, M.1    Betschart, K.2    Dale, T.3    Riley, C.4    Rowan, C.5
  • 35
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    • Mathews D, Disney M, Childs J, Schroeder S, Zuker M, et al. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A 101: 7287.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 7287
    • Mathews, D.1    Disney, M.2    Childs, J.3    Schroeder, S.4    Zuker, M.5
  • 36
    • 0034002687 scopus 로고    scopus 로고
    • A test of the model to predict unusually stable RNA hairpin loop stability
    • Dale T, Smith R, Serra M, (2000) A test of the model to predict unusually stable RNA hairpin loop stability. RNA 6: 608-615.
    • (2000) RNA , vol.6 , pp. 608-615
    • Dale, T.1    Smith, R.2    Serra, M.3
  • 38
    • 33846820159 scopus 로고    scopus 로고
    • Mechanical unfolding of RNA: from hairpins to structures with internal multiloops
    • Hyeon C, Thirumalai D, (2007) Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys J 92: 731-743.
    • (2007) Biophys J , vol.92 , pp. 731-743
    • Hyeon, C.1    Thirumalai, D.2
  • 39
    • 33846284150 scopus 로고    scopus 로고
    • What NMR relaxation can tell us about the internal motion of an RNA hairpin: a molecular dynamics simulation study
    • Villa A, Stock G, (2006) What NMR relaxation can tell us about the internal motion of an RNA hairpin: a molecular dynamics simulation study. J Chem Theory Comput 2: 1228-1236.
    • (2006) J Chem Theory Comput , vol.2 , pp. 1228-1236
    • Villa, A.1    Stock, G.2
  • 40
    • 0042845840 scopus 로고    scopus 로고
    • Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations
    • Sorin E, Rhee Y, Nakatani B, Pande V, (2003) Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations. Biophys J 85: 790-803.
    • (2003) Biophys J , vol.85 , pp. 790-803
    • Sorin, E.1    Rhee, Y.2    Nakatani, B.3    Pande, V.4
  • 41
    • 77952352777 scopus 로고    scopus 로고
    • Semiautomated model building for RNA crystallography using a directed rotameric approach
    • Keating K, Pyle A, (2010) Semiautomated model building for RNA crystallography using a directed rotameric approach. Proc Natl Acad Sci U S A 107: 8177.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 8177
    • Keating, K.1    Pyle, A.2
  • 42
    • 28344438036 scopus 로고    scopus 로고
    • Predicting RNA folding thermodynamics with a reduced chain representation model
    • Cao S, Chen SJ, (2005) Predicting RNA folding thermodynamics with a reduced chain representation model. RNA 11: 1884-1897.
    • (2005) RNA , vol.11 , pp. 1884-1897
    • Cao, S.1    Chen, S.J.2
  • 43
    • 33744547883 scopus 로고    scopus 로고
    • Predicting RNA pseudoknot folding thermodynamics
    • Cao S, Chen SJ, (2006) Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Res 34: 2634.
    • (2006) Nucleic Acids Res , vol.34 , pp. 2634
    • Cao, S.1    Chen, S.J.2
  • 44
    • 62549128665 scopus 로고    scopus 로고
    • Predicting structures and stabilities for h-type pseudoknots with interhelix loops
    • Cao S, Chen SJ, (2009) Predicting structures and stabilities for h-type pseudoknots with interhelix loops. RNA 15: 696-706.
    • (2009) RNA , vol.15 , pp. 696-706
    • Cao, S.1    Chen, S.J.2
  • 45
    • 77953852852 scopus 로고    scopus 로고
    • Computing the conformational entropy for RNA folds
    • Liu L, Chen SJ, (2010) Computing the conformational entropy for RNA folds. J Chem Phys 132: 235104.
    • (2010) J Chem Phys , vol.132 , pp. 235104
    • Liu, L.1    Chen, S.J.2
  • 46
    • 77149158794 scopus 로고    scopus 로고
    • Predicting loop-helix tertiary structural contacts in RNA pseudoknots
    • Cao S, Giedroc D, Chen SJ, (2010) Predicting loop-helix tertiary structural contacts in RNA pseudoknots. RNA 16: 538-552.
    • (2010) RNA , vol.16 , pp. 538-552
    • Cao, S.1    Giedroc, D.2    Chen, S.J.3
  • 47
    • 84861537681 scopus 로고    scopus 로고
    • Predicting kissing interactions in microRNA-target complex and assessment of microrna activity
    • Cao S, Chen SJ, (2012) Predicting kissing interactions in microRNA-target complex and assessment of microrna activity. Nucleic Acids Res 40: 4681-4690.
    • (2012) Nucleic Acids Res , vol.40 , pp. 4681-4690
    • Cao, S.1    Chen, S.J.2
  • 48
    • 42449155819 scopus 로고    scopus 로고
    • RNA folding: conformational statistics, folding kinetics, and ion electro statics
    • Chen SJ, (2008) RNA folding: conformational statistics, folding kinetics, and ion electro statics. Annu Rev Biophys 37: 197.
    • (2008) Annu Rev Biophys , vol.37 , pp. 197
    • Chen, S.J.1
  • 49
    • 32244434006 scopus 로고    scopus 로고
    • Sequence dependence of the stability of RNA hairpin molecules with six nucleotide loops
    • Vecenie C, Morrow C, Zyra A, Serra M, (2006) Sequence dependence of the stability of RNA hairpin molecules with six nucleotide loops. Biochemistry 45: 1400-1407.
    • (2006) Biochemistry , vol.45 , pp. 1400-1407
    • Vecenie, C.1    Morrow, C.2    Zyra, A.3    Serra, M.4
  • 50
    • 77950366829 scopus 로고    scopus 로고
    • Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling
    • Schudoma C, May P, Nikiforova V, Walther D, (2010) Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling. Nucleic Acids Res 38: 970-980.
    • (2010) Nucleic Acids Res , vol.38 , pp. 970-980
    • Schudoma, C.1    May, P.2    Nikiforova, V.3    Walther, D.4
  • 52
    • 79954460627 scopus 로고    scopus 로고
    • All-atom knowledge-based potential for RNA structure prediction and assessment
    • Capriotti E, Norambuena T, Marti-Renom M, Melo F, (2011) All-atom knowledge-based potential for RNA structure prediction and assessment. Bioinformatics 27: 1086.
    • (2011) Bioinformatics , vol.27 , pp. 1086
    • Capriotti, E.1    Norambuena, T.2    Marti-Renom, M.3    Melo, F.4
  • 53
    • 0017411710 scopus 로고
    • The protein data bank: A computer-based archival file for macromolecular structures
    • Bernstein F, Koetzle T, Williams G, Meyer E, Brice M, et al. (1977) The protein data bank: A computer-based archival file for macromolecular structures. J Mol Biol 112: 535-542.
    • (1977) J Mol Biol , vol.112 , pp. 535-542
    • Bernstein, F.1    Koetzle, T.2    Williams, G.3    Meyer, E.4    Brice, M.5
  • 54
    • 0026742978 scopus 로고
    • The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids
    • Berman H, Olson W, Beveridge D, Westbrook J, Gelbin A, et al. (1992) The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J 63: 751.
    • (1992) Biophys J , vol.63 , pp. 751
    • Berman, H.1    Olson, W.2    Beveridge, D.3    Westbrook, J.4    Gelbin, A.5
  • 55
    • 0032545158 scopus 로고    scopus 로고
    • Stepping through an RNA structure: a novel approach to conformational analysis1
    • Duarte C, Pyle A, (1998) Stepping through an RNA structure: a novel approach to conformational analysis1. J Mol Biol 284: 1465-1478.
    • (1998) J Mol Biol , vol.284 , pp. 1465-1478
    • Duarte, C.1    Pyle, A.2
  • 56
    • 34548401692 scopus 로고    scopus 로고
    • Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure
    • Wadley L, Keating K, Duarte C, Pyle A, (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.1    Keating, K.2    Duarte, C.3    Pyle, A.4
  • 58
    • 0015262029 scopus 로고
    • Spatial configurations of polynucleotide chains. I. steric interactions in polyribonucleotides: a virtual bond model
    • Olson W, Flory P, (1972) Spatial configurations of polynucleotide chains. I. steric interactions in polyribonucleotides: a virtual bond model. Biopolymers 11: 1-23.
    • (1972) Biopolymers , vol.11 , pp. 1-23
    • Olson, W.1    Flory, P.2
  • 59
    • 0016502853 scopus 로고
    • Configuration statistical of polynucleotide chains: A single virtual bond treatment
    • Olson WK, (1975) Configuration statistical of polynucleotide chains: A single virtual bond treatment. Macromolecules 8: 272-275.
    • (1975) Macromolecules , vol.8 , pp. 272-275
    • Olson, W.K.1
  • 60
    • 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
  • 61
    • 84856928701 scopus 로고
    • Statistical mechanics of chain molecules
    • Flory P, et al. (1969) Statistical mechanics of chain molecules. Biopolymers 8: 699-700.
    • (1969) Biopolymers , vol.8 , pp. 699-700
    • Flory, P.1
  • 63
    • 33750555073 scopus 로고    scopus 로고
    • An iterative knowledge-based scoring function to predict protein-ligand interactions: I. derivation of interaction potentials
    • Huang S, Zou X, (2006) An iterative knowledge-based scoring function to predict protein-ligand interactions: I. derivation of interaction potentials. J Comput Chem 27: 1866-1875.
    • (2006) J Comput Chem , vol.27 , pp. 1866-1875
    • Huang, S.1    Zou, X.2
  • 64
    • 0035882533 scopus 로고    scopus 로고
    • A distance-dependent atomic knowledge-based potential for improved protein structure selection
    • Lu H, Skolnick J, (2001) A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins: Struct, Funct, Bioinf 44: 223-232.
    • (2001) Proteins: Struct, Funct, Bioinf , vol.44 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 65
    • 0036838311 scopus 로고    scopus 로고
    • Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
    • Zhou H, 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
  • 66
    • 79955638463 scopus 로고    scopus 로고
    • Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets
    • Zhao H, Yang Y, Zhou Y, (2011) Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets. Nucleic Acids Res 39: 3017-3025.
    • (2011) Nucleic Acids Res , vol.39 , pp. 3017-3025
    • Zhao, H.1    Yang, Y.2    Zhou, Y.3
  • 67
    • 50549096615 scopus 로고    scopus 로고
    • iFoldRNA: three-dimensional RNA structure prediction and folding
    • Sharma S, Ding F, Dokholyan N, (2008) iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics 24: 1951-1952.
    • (2008) Bioinformatics , vol.24 , pp. 1951-1952
    • Sharma, S.1    Ding, F.2    Dokholyan, N.3
  • 68
    • 0029976427 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures: how accurate are they?
    • Thomas P, Dill K, (1996) Statistical potentials extracted from protein structures: how accurate are they? J Mol Biol 257: 457-469.
    • (1996) J Mol Biol , vol.257 , pp. 457-469
    • Thomas, P.1    Dill, K.2
  • 69
    • 0029909384 scopus 로고    scopus 로고
    • An iterative method for extracting energy-like quantities from protein structures
    • Thomas P, Dill K, (1996) An iterative method for extracting energy-like quantities from protein structures. Proc Natl Acad Sci U S A 93: 11628-11633.
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 11628-11633
    • Thomas, P.1    Dill, K.2
  • 70
    • 0033970623 scopus 로고    scopus 로고
    • Derivation of protein-specific pair potentials based on weak sequence fragment similarity
    • Skolnick J, Kolinski A, Ortiz A, (2000) Derivation of protein-specific pair potentials based on weak sequence fragment similarity. Proteins: Struct, Funct, Bioinf 38: 3-16.
    • (2000) Proteins: Struct, Funct, Bioinf , vol.38 , pp. 3-16
    • Skolnick, J.1    Kolinski, A.2    Ortiz, A.3
  • 71
    • 0035010211 scopus 로고    scopus 로고
    • Geometric nomenclature and classification of RNA base pairs
    • Leontis N, Westhof E, (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7: 499-512.
    • (2001) RNA , vol.7 , pp. 499-512
    • Leontis, N.1    Westhof, E.2
  • 72
    • 0036760665 scopus 로고    scopus 로고
    • Motif prediction in ribosomal RNAs lessons and prospects for automated motif prediction in homologous RNA molecules
    • Leontis N, Stombaugh J, Westhof E, (2002) Motif prediction in ribosomal RNAs lessons and prospects for automated motif prediction in homologous RNA molecules. Biochimie 84: 961-973.
    • (2002) Biochimie , vol.84 , pp. 961-973
    • Leontis, N.1    Stombaugh, J.2    Westhof, E.3
  • 73
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • Lu X, Olson W, (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31: 5108.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5108
    • Lu, X.1    Olson, W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.