메뉴 건너뛰기




Volumn 12, Issue , 2011, Pages

DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking

Author keywords

RNAproteinRNPmacromolecular dockingcomplex modeling; structural bioinformatics

Indexed keywords

COMPUTATIONAL DOCKINGS; COMPUTATIONAL PREDICTIONS; DISCRIMINATIVE POWER; EXPERIMENTAL DETERMINATION; INDIVIDUAL STRUCTURES; PROTEIN-RNA INTERACTION; STATISTICAL POTENTIAL; STRUCTURAL BIOINFORMATICS;

EID: 80051788801     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-348     Document Type: Article
Times cited : (87)

References (33)
  • 1
    • 18444383371 scopus 로고    scopus 로고
    • Protein families and RNA recognition
    • 10.1111/j.1742-4658.2005.04650.x, 15853794
    • Chen Y, Varani G. Protein families and RNA recognition. Febs J 2005, 272(9):2088-2097. 10.1111/j.1742-4658.2005.04650.x, 15853794.
    • (2005) Febs J , vol.272 , Issue.9 , pp. 2088-2097
    • Chen, Y.1    Varani, G.2
  • 2
    • 48949115091 scopus 로고    scopus 로고
    • RNA-binding proteins in human genetic disease
    • 10.1016/j.tig.2008.05.004, 18597886
    • Lukong KE, Chang KW, Khandjian EW, Richard S. RNA-binding proteins in human genetic disease. Trends Genet 2008, 24(8):416-425. 10.1016/j.tig.2008.05.004, 18597886.
    • (2008) Trends Genet , vol.24 , Issue.8 , pp. 416-425
    • Lukong, K.E.1    Chang, K.W.2    Khandjian, E.W.3    Richard, S.4
  • 3
    • 4344596976 scopus 로고    scopus 로고
    • Crystallization of RNA and RNA-protein complexes
    • 10.1016/j.ymeth.2004.03.027, 15325657
    • Ke A, Doudna JA. Crystallization of RNA and RNA-protein complexes. Methods 2004, 34(3):408-414. 10.1016/j.ymeth.2004.03.027, 15325657.
    • (2004) Methods , vol.34 , Issue.3 , pp. 408-414
    • Ke, A.1    Doudna, J.A.2
  • 4
    • 84934438470 scopus 로고    scopus 로고
    • RNA structure determination by NMR
    • 10.1007/978-1-60327-159-2_2, 18563368
    • Scott LG, Hennig M. RNA structure determination by NMR. Methods Mol Biol 2008, 452:29-61. 10.1007/978-1-60327-159-2_2, 18563368.
    • (2008) Methods Mol Biol , vol.452 , pp. 29-61
    • Scott, L.G.1    Hennig, M.2
  • 5
    • 77953784130 scopus 로고    scopus 로고
    • Computational approaches to 3D modeling of RNA
    • 10.1088/0953-8984/22/28/283101, 21399271
    • Laing C, Schlick T. Computational approaches to 3D modeling of RNA. J Phys Condens Matter 2010, 22(28):283101. 10.1088/0953-8984/22/28/283101, 21399271.
    • (2010) J Phys Condens Matter , vol.22 , Issue.28 , pp. 283101
    • Laing, C.1    Schlick, T.2
  • 6
    • 80255140476 scopus 로고    scopus 로고
    • RNA and protein 3D structure modeling: similarities and differences
    • 10.1007/s00894-010-0951-x, 21258831
    • Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM. RNA and protein 3D structure modeling: similarities and differences. J Mol Model 2011, 17(9):2325-2336. 10.1007/s00894-010-0951-x, 21258831.
    • (2011) J Mol Model , vol.17 , Issue.9 , pp. 2325-2336
    • Rother, K.1    Rother, M.2    Boniecki, M.3    Puton, T.4    Bujnicki, J.M.5
  • 7
    • 76149086786 scopus 로고    scopus 로고
    • Protein-protein docking dealing with the unknown
    • Moreira IS, Fernandes PA, Ramos MJ. Protein-protein docking dealing with the unknown. J Comp Chem 2010, 31(2):317-342.
    • (2010) J Comp Chem , vol.31 , Issue.2 , pp. 317-342
    • Moreira, I.S.1    Fernandes, P.A.2    Ramos, M.J.3
  • 8
    • 77951297973 scopus 로고    scopus 로고
    • Accounting for conformational changes during protein-protein docking
    • 10.1016/j.sbi.2010.02.001, 20194014
    • Zacharias M. Accounting for conformational changes during protein-protein docking. Curr Opin Struct Biol 2010, 20(2):180-186. 10.1016/j.sbi.2010.02.001, 20194014.
    • (2010) Curr Opin Struct Biol , vol.20 , Issue.2 , pp. 180-186
    • Zacharias, M.1
  • 10
    • 28144444798 scopus 로고    scopus 로고
    • Fine-Tuning of RNA Functions by Modification and Editing
    • Grosjean H. Fine-Tuning of RNA Functions by Modification and Editing. 2009,
    • (2009)
    • Grosjean, H.1
  • 11
    • 0035960675 scopus 로고    scopus 로고
    • Anticodon domain methylated nucleosides of yeast tRNA(Phe) are significant recognition determinants in the binding of a phage display selected peptide
    • 10.1021/bi010978o, 11714272
    • Mucha P, Szyk A, Rekowski P, Weiss PA, Agris PF. Anticodon domain methylated nucleosides of yeast tRNA(Phe) are significant recognition determinants in the binding of a phage display selected peptide. Biochemistry 2001, 40(47):14191-14199. 10.1021/bi010978o, 11714272.
    • (2001) Biochemistry , vol.40 , Issue.47 , pp. 14191-14199
    • Mucha, P.1    Szyk, A.2    Rekowski, P.3    Weiss, P.A.4    Agris, P.F.5
  • 12
    • 10744229752 scopus 로고    scopus 로고
    • An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA
    • 10.1016/S1097-2765(03)00346-0, 14527414
    • Soma A, Ikeuchi Y, Kanemasa S, Kobayashi K, Ogasawara N, Ote T, Kato J, Watanabe K, Sekine Y, Suzuki T. An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol Cell 2003, 12(3):689-698. 10.1016/S1097-2765(03)00346-0, 14527414.
    • (2003) Mol Cell , vol.12 , Issue.3 , pp. 689-698
    • Soma, A.1    Ikeuchi, Y.2    Kanemasa, S.3    Kobayashi, K.4    Ogasawara, N.5    Ote, T.6    Kato, J.7    Watanabe, K.8    Sekine, Y.9    Suzuki, T.10
  • 13
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
    • 10.1021/ja026939x, 12580598
    • Dominguez C, Boelens R, Bonvin AM. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003, 125(7):1731-1737. 10.1021/ja026939x, 12580598.
    • (2003) J Am Chem Soc , vol.125 , Issue.7 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 14
    • 0028575449 scopus 로고
    • Hydrophobic docking: a proposed enhancement to molecular recognition techniques
    • 10.1002/prot.340200405, 7731951
    • Vakser IA, Aflalo C. Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins 1994, 20(4):320-329. 10.1002/prot.340200405, 7731951.
    • (1994) Proteins , vol.20 , Issue.4 , pp. 320-329
    • Vakser, I.A.1    Aflalo, C.2
  • 15
    • 0034193510 scopus 로고    scopus 로고
    • Protein docking using spherical polar Fourier correlations
    • 10.1002/(SICI)1097-0134(20000501)39:2<178::AID-PROT8>3.0.CO;2-6, 10737939
    • Ritchie DW, Kemp GJ. Protein docking using spherical polar Fourier correlations. Proteins 2000, 39(2):178-194. 10.1002/(SICI)1097-0134(20000501)39:2<178::AID-PROT8>3.0.CO;2-6, 10737939.
    • (2000) Proteins , vol.39 , Issue.2 , pp. 178-194
    • Ritchie, D.W.1    Kemp, G.J.2
  • 16
    • 36749008025 scopus 로고    scopus 로고
    • A knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins
    • Zheng S, Robertson TA, Varani G. A knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins. Febs J 2007, 274(24):6378-6391.
    • (2007) Febs J , vol.274 , Issue.24 , pp. 6378-6391
    • Zheng, S.1    Robertson, T.A.2    Varani, G.3
  • 17
    • 84873031500 scopus 로고    scopus 로고
    • Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials
    • Perez-Cano L, Solernou A, Pons C, Fernandez-Recio J. Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials. Pac Symp Biocomput 2010, 293-301.
    • (2010) Pac Symp Biocomput , pp. 293-301
    • Perez-Cano, L.1    Solernou, A.2    Pons, C.3    Fernandez-Recio, J.4
  • 18
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • 10.1006/jmbi.1997.1203, 9299341
    • Gabb HA, Jackson RM, Sternberg MJ. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997, 272(1):106-120. 10.1006/jmbi.1997.1203, 9299341.
    • (1997) J Mol Biol , vol.272 , Issue.1 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.3
  • 19
    • 58149152509 scopus 로고    scopus 로고
    • DARS (Decoys As the Reference State) potentials for protein-protein docking
    • 10.1529/biophysj.108.135814, 2567923, 18676649
    • Chuang GY, Kozakov D, Brenke R, Comeau SR, Vajda S. DARS (Decoys As the Reference State) potentials for protein-protein docking. Biophys J 2008, 95(9):4217-4227. 10.1529/biophysj.108.135814, 2567923, 18676649.
    • (2008) Biophys J , vol.95 , Issue.9 , pp. 4217-4227
    • Chuang, G.Y.1    Kozakov, D.2    Brenke, R.3    Comeau, S.R.4    Vajda, S.5
  • 20
    • 0026572775 scopus 로고
    • Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques
    • 10.1073/pnas.89.6.2195, 48623, 1549581
    • Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992, 89(6):2195-2199. 10.1073/pnas.89.6.2195, 48623, 1549581.
    • (1992) Proc Natl Acad Sci USA , vol.89 , Issue.6 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.A.4    Aflalo, C.5    Vakser, I.A.6
  • 21
    • 34047138418 scopus 로고    scopus 로고
    • Energetics of protein-DNA interactions
    • 10.1093/nar/gkl1103, 1851630, 17259221
    • Donald JE, Chen WW, Shakhnovich EI. Energetics of protein-DNA interactions. Nucleic Acids Res 2007, 35(4):1039-1047. 10.1093/nar/gkl1103, 1851630, 17259221.
    • (2007) Nucleic Acids Res , vol.35 , Issue.4 , pp. 1039-1047
    • Donald, J.E.1    Chen, W.W.2    Shakhnovich, E.I.3
  • 22
    • 0035010211 scopus 로고    scopus 로고
    • Geometric nomenclature and classification of RNA base pairs
    • 10.1017/S1355838201002515, 1370104, 11345429
    • Leontis NB, Westhof E. Geometric nomenclature and classification of RNA base pairs. Rna 2001, 7(4):499-512. 10.1017/S1355838201002515, 1370104, 11345429.
    • (2001) Rna , vol.7 , Issue.4 , pp. 499-512
    • Leontis, N.B.1    Westhof, E.2
  • 24
    • 20344391939 scopus 로고    scopus 로고
    • Theoretical model of prion propagation: a misfolded protein induces misfolding
    • 10.1073/pnas.0409389102, 1142357, 15911770
    • Malolepsza E, Boniecki M, Kolinski A, Piela L. Theoretical model of prion propagation: a misfolded protein induces misfolding. Proc Natl Acad Sci USA 2005, 102(22):7835-7840. 10.1073/pnas.0409389102, 1142357, 15911770.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.22 , pp. 7835-7840
    • Malolepsza, E.1    Boniecki, M.2    Kolinski, A.3    Piela, L.4
  • 26
    • 4944226552 scopus 로고    scopus 로고
    • A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys
    • 10.1093/nar/gkh785, 521638, 15459285
    • Chen Y, Kortemme T, Robertson T, Baker D, Varani G. A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Res 2004, 32(17):5147-5162. 10.1093/nar/gkh785, 521638, 15459285.
    • (2004) Nucleic Acids Res , vol.32 , Issue.17 , pp. 5147-5162
    • Chen, Y.1    Kortemme, T.2    Robertson, T.3    Baker, D.4    Varani, G.5
  • 28
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • 10.1016/S0022-2836(03)00670-3, 12875852
    • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003, 331(1):281-299. 10.1016/S0022-2836(03)00670-3, 12875852.
    • (2003) J Mol Biol , vol.331 , Issue.1 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 29
    • 0034780030 scopus 로고    scopus 로고
    • Pcons: a neural-network-based consensus predictor that improves fold recognition
    • 2374055, 11604541
    • Lundstrom J, Rychlewski L, Bujnicki J, Elofsson A. Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 2001, 10(11):2354-2362. 2374055, 11604541.
    • (2001) Protein Sci , vol.10 , Issue.11 , pp. 2354-2362
    • Lundstrom, J.1    Rychlewski, L.2    Bujnicki, J.3    Elofsson, A.4
  • 30
    • 74249102516 scopus 로고    scopus 로고
    • Evaluation of CASP8 model quality predictions
    • Cozzetto D, Kryshtafovych A, Tramontano A. Evaluation of CASP8 model quality predictions. Proteins 2009, 77(Suppl 9):157-166.
    • (2009) Proteins , vol.77 , Issue.SUPPL. 9 , pp. 157-166
    • Cozzetto, D.1    Kryshtafovych, A.2    Tramontano, A.3
  • 31
    • 0032530578 scopus 로고    scopus 로고
    • Clustering of low-energy conformations near the native structures of small proteins
    • 10.1073/pnas.95.19.11158, 21612, 9736706
    • Shortle D, Simons KT, Baker D. Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci USA 1998, 95(19):11158-11162. 10.1073/pnas.95.19.11158, 21612, 9736706.
    • (1998) Proc Natl Acad Sci USA , vol.95 , Issue.19 , pp. 11158-11162
    • Shortle, D.1    Simons, K.T.2    Baker, D.3
  • 32
    • 78449278402 scopus 로고    scopus 로고
    • FILTREST3D: discrimination of structural models using restraints from experimental data
    • 10.1093/bioinformatics/btq582, 20956242
    • Gajda MJ, Tuszynska I, Kaczor M, Bakulina AY, Bujnicki JM. FILTREST3D: discrimination of structural models using restraints from experimental data. Bioinformatics 2010, 26(23):2986-2987. 10.1093/bioinformatics/btq582, 20956242.
    • (2010) Bioinformatics , vol.26 , Issue.23 , pp. 2986-2987
    • Gajda, M.J.1    Tuszynska, I.2    Kaczor, M.3    Bakulina, A.Y.4    Bujnicki, J.M.5
  • 33
    • 79959292152 scopus 로고    scopus 로고
    • ModeRNA: a tool for comparative modeling of RNA 3D structure
    • 10.1093/nar/gkq1320, 3105415, 21300639
    • Rother M, Rother K, Puton T, Bujnicki JM. ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Res 2011, 39(10):4007-4022. 10.1093/nar/gkq1320, 3105415, 21300639.
    • (2011) Nucleic Acids Res , vol.39 , Issue.10 , pp. 4007-4022
    • Rother, M.1    Rother, K.2    Puton, T.3    Bujnicki, J.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.