메뉴 건너뛰기




Volumn 29, Issue 3, 2013, Pages 322-330

A knowledge-based orientation potential for transcription factor-DNA docking

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTION FACTOR;

EID: 84873321237     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts699     Document Type: Article
Times cited : (12)

References (44)
  • 1
    • 56749102973 scopus 로고    scopus 로고
    • Prediction of TF target sites based on atomistic models of protein-DNA complexes
    • Angarica, V.E. et al. (2008) Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics, 9, 436.
    • (2008) BMC Bioinformatics , vol.9 , pp. 436
    • Angarica, V.E.1
  • 2
    • 67249103597 scopus 로고    scopus 로고
    • Assessment of the optimization of affinity and specificity at protein-DNA interfaces
    • Ashworth, J. and Baker, D. (2009) Assessment of the optimization of affinity and specificity at protein-DNA interfaces. Nucleic Acids Res., 37, e73.
    • (2009) Nucleic Acids Res , vol.37
    • Ashworth, J.1    Baker, D.2
  • 3
    • 34247098754 scopus 로고    scopus 로고
    • Multiscale modeling of biomolecular systems: in serial and in parallel
    • DOI 10.1016/j.sbi.2007.03.004, PII S0959440X07000346, Theory and Simulation / Mecromolecular Assemblages
    • Ayton, G.S. et al. (2007) Multiscale modeling of biomolecular systems: in serial and in parallel. Curr. Opin. Struct. Biol., 17, 192-198. (Pubitemid 46584804)
    • (2007) Current Opinion in Structural Biology , vol.17 , Issue.2 , pp. 192-198
    • Ayton, G.S.1    Noid, W.G.2    Voth, G.A.3
  • 7
    • 24944493938 scopus 로고    scopus 로고
    • Biochemistry: Toward high-resolution de novo structure prediction for small proteins
    • DOI 10.1126/science.1113801
    • Bradley, P. et al. (2005) Toward high-resolution de novo structure prediction for small proteins. Science, 309, 1868-1871. (Pubitemid 41325099)
    • (2005) Science , vol.309 , Issue.5742 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.S.2    Baker, D.3
  • 8
    • 33745726575 scopus 로고    scopus 로고
    • Structure prediction of helical transmembrane proteins at two length scales
    • DOI 10.1142/S0219720006001965, PII S0219720006001965
    • Chen, Z. and Xu, Y. (2006) Structure prediction of helical transmembrane proteins at two length scales. J. Bioinform. Comput. Biol., 4, 317-333. (Pubitemid 43997122)
    • (2006) Journal of Bioinformatics and Computational Biology , vol.4 , Issue.2 , pp. 317-333
    • Chen, Z.1    Xu, Y.2
  • 9
    • 77949358476 scopus 로고    scopus 로고
    • Comparison of DNA binding across protein superfamilies
    • Contreras-Moreira, B. et al. (2010) Comparison of DNA binding across protein superfamilies. Proteins, 78, 52-62.
    • (2010) Proteins , vol.78 , pp. 52-62
    • Contreras-Moreira, B.1
  • 10
    • 34047138418 scopus 로고    scopus 로고
    • Energetics of protein-DNA interactions
    • Donald, J.E. et al. (2007) Energetics of protein-DNA interactions. Nucleic Acids Res., 35, 1039-1047.
    • (2007) Nucleic Acids Res , vol.35 , pp. 1039-1047
    • Donald, J.E.1
  • 12
    • 84865078347 scopus 로고    scopus 로고
    • Multiscale modeling of macromolecular biosystems
    • Flores, S.C. et al. (2012) Multiscale modeling of macromolecular biosystems. Brief. Bioinform., 13, 395-405.
    • (2012) Brief. Bioinform , vol.13 , pp. 395-405
    • Flores, S.C.1
  • 13
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • DOI 10.1002/prot.340230412
    • Frishman, D. and Argos, P. (1995) Knowledge-based protein secondary structure assignment. Proteins, 23, 566-579. (Pubitemid 26009520)
    • (1995) Proteins: Structure, Function and Genetics , vol.23 , Issue.4 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 14
    • 47249125424 scopus 로고    scopus 로고
    • DBD-Hunter: A knowledge-based method for the prediction of DNA-protein interactions
    • DOI 10.1093/nar/gkn332
    • Gao, M. and Skolnick, J. (2008) DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Res., 36, 3978-3992. (Pubitemid 351984814)
    • (2008) Nucleic Acids Research , vol.36 , Issue.12 , pp. 3978-3992
    • Gao, M.1    Skolnick, J.2
  • 15
    • 77951212412 scopus 로고    scopus 로고
    • PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy
    • Gopal, S.M. et al. (2010) PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy. Proteins, 78, 1266-1281.
    • (2010) Proteins , vol.78 , pp. 1266-1281
    • Gopal, S.M.1
  • 16
    • 36849063165 scopus 로고    scopus 로고
    • Structure and evolution of gene regulatory networks in microbial genomes
    • DOI 10.1016/j.resmic.2007.09.001, PII S0923250807001763, Microbial Genomics
    • Janga, S.C. and Collado-Vides, J. (2007) Structure and evolution of gene regulatory networks in microbial genomes. Res. Microbiol., 158, 787-794. (Pubitemid 350235176)
    • (2007) Research in Microbiology , vol.158 , Issue.10 , pp. 787-794
    • Janga, S.C.1    Collado-Vides, J.2
  • 17
    • 29444434700 scopus 로고    scopus 로고
    • Ab initio prediction of transcription factor targets using structural knowledge
    • Kaplan, T. et al. (2005) Ab initio prediction of transcription factor targets using structural knowledge. PLoS Comput. Biol., 1, e1.
    • (2005) PLoS Comput. Biol , vol.1
    • Kaplan, T.1
  • 18
    • 67650403798 scopus 로고    scopus 로고
    • PDA: An automatic and comprehensive analysis program for protein-DNA complex structures
    • Kim, R. and Guo, J.T. (2009) PDA: an automatic and comprehensive analysis program for protein-DNA complex structures. BMC Genom., 10 (Suppl. 1), S13.
    • (2009) BMC Genom , vol.10 , Issue.SUPPL. 1
    • Kim, R.1    Guo, J.T.2
  • 19
    • 37549009571 scopus 로고    scopus 로고
    • Coarse-grained models for simulations of multiprotein complexes: Application to ubiquitin binding
    • Kim, Y.C. and Hummer, G. (2008) Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. J. Mol. Biol., 375, 1416-1433.
    • (2008) J. Mol. Biol , vol.375 , pp. 1416-1433
    • Kim, Y.C.1    Hummer, G.2
  • 20
    • 80055047271 scopus 로고    scopus 로고
    • Benchmarks for flexible and rigid transcription factor-DNA docking
    • Kim, R. et al. (2011) Benchmarks for flexible and rigid transcription factor-DNA docking. BMC Struct. Biol., 11, 45.
    • (2011) BMC Struct. Biol , vol.11 , pp. 45
    • Kim, R.1
  • 21
    • 0033120215 scopus 로고    scopus 로고
    • Structure-based prediction of DNA target sites by regulatory proteins
    • DOI 10.1002/(SICI)1097-0134(19990401)35:1<114::AID-PROT11>3.0.CO;2- T
    • Kono, H. and Sarai, A. (1999) Structure-based prediction of DNA target sites by regulatory proteins. Proteins, 35, 114-131. (Pubitemid 29128158)
    • (1999) Proteins: Structure, Function and Genetics , vol.35 , Issue.1 , pp. 114-131
    • Kono, H.1    Sarai, A.2
  • 22
    • 13744259639 scopus 로고    scopus 로고
    • Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential
    • DOI 10.1093/nar/gki204
    • Liu, Z. et al. (2005) Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential. Nucleic Acids Res., 33, 546-558. (Pubitemid 40360984)
    • (2005) Nucleic Acids Research , vol.33 , Issue.2 , pp. 546-558
    • Liu, Z.1    Mao, F.2    Guo, J.-T.3    Yan, B.4    Wang, P.5    Qu, Y.6    Xu, Y.7
  • 23
    • 51349134974 scopus 로고    scopus 로고
    • Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach
    • Liu, Z. et al. (2008) Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach. Proteins, 72, 1114-1124.
    • (2008) Proteins , vol.72 , pp. 1114-1124
    • Liu, Z.1
  • 24
    • 0036074510 scopus 로고    scopus 로고
    • Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity
    • DOI 10.1016/S0022-2836(02)00571-5
    • Luscombe, N.M. and Thornton, J.M. (2002) Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J. Mol. Biol., 320, 991-1009. (Pubitemid 34808820)
    • (2002) Journal of Molecular Biology , vol.320 , Issue.5 , pp. 991-1009
    • Luscombe, N.M.1    Thornton, J.M.2
  • 25
    • 0035393302 scopus 로고    scopus 로고
    • Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
    • Luscombe, N.M. et al. (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res., 29, 2860-2874. (Pubitemid 32685051)
    • (2001) Nucleic Acids Research , vol.29 , Issue.13 , pp. 2860-2874
    • Luscombe, N.M.1    Laskowski, R.A.2    Thornton, J.M.3
  • 26
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal-structures-quasi-chemical approximation
    • Miyazawa, S. and Jernigan, R.L. (1985) Estimation of effective interresidue contact energies from protein crystal-structures-quasi-chemical approximation. Macromolecules, 18, 534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 28
    • 80052583392 scopus 로고    scopus 로고
    • (Compressed) sensing and sensibility
    • Pande, V.S. (2011) (Compressed) sensing and sensibility. Proc. Natl Acad. Sci. USA, 108, 14713-14714.
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 14713-14714
    • Pande, V.S.1
  • 29
    • 17044403057 scopus 로고    scopus 로고
    • Type II restriction endonucleases: Structure and mechanism
    • Pingoud, A. et al. (2005) Type II restriction endonucleases: structure and mechanism. Cell. Mol. Life Sci., 62, 685-707.
    • (2005) Cell. Mol. Life Sci , vol.62 , pp. 685-707
    • Pingoud, A.1
  • 30
    • 55349123996 scopus 로고    scopus 로고
    • Insights on protein-DNA recognition by coarse grain modelling
    • Poulain, P. et al. (2008) Insights on protein-DNA recognition by coarse grain modelling. J. Comput. Chem., 29, 2582-2592.
    • (2008) J. Comput. Chem , vol.29 , pp. 2582-2592
    • Poulain, P.1
  • 31
    • 33748290192 scopus 로고    scopus 로고
    • Classification of protein-dna complexes based on structural descriptors
    • DOI 10.1016/j.str.2006.06.018, PII S0969212606003029
    • Prabakaran, P. et al. (2006) Classification of protein-DNA complexes based on structural descriptors. Structure, 14, 1355-1367. (Pubitemid 44331615)
    • (2006) Structure , vol.14 , Issue.9 , pp. 1355-1367
    • Prabakaran, P.1    Siebers, J.G.2    Ahmad, S.3    Gromiha, M.M.4    Singarayan, M.G.5    Sarai, A.6
  • 32
    • 33845976703 scopus 로고    scopus 로고
    • An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure
    • DOI 10.1002/prot.21162
    • Robertson, T.A. and Varani, G. (2007) An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure. Proteins, 66, 359-374. (Pubitemid 46053467)
    • (2007) Proteins: Structure, Function and Genetics , vol.66 , Issue.2 , pp. 359-374
    • Robertson, T.A.1    Varani, G.2
  • 33
    • 34047153962 scopus 로고    scopus 로고
    • 2 zinc-finger binding specificity: Sensitivity to docking geometry
    • DOI 10.1093/nar/gkl1155
    • Siggers, T.W. and Honig, B. (2007) Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. Nucleic Acids Res., 35, 1085-1097. (Pubitemid 46522964)
    • (2007) Nucleic Acids Research , vol.35 , Issue.4 , pp. 1085-1097
    • Siggers, T.W.1    Honig, B.2
  • 34
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl, M.J. (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol., 213, 859-883. (Pubitemid 20213222)
    • (1990) Journal of Molecular Biology , vol.213 , Issue.4 , pp. 859-883
    • Sippl, M.J.1
  • 35
    • 0029000696 scopus 로고
    • Knowledge-based potentials for proteins
    • Sippl, M.J. (1995) Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol., 5, 229-235.
    • (1995) Curr. Opin. Struct. Biol , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 36
    • 77957242417 scopus 로고    scopus 로고
    • Pushing the limits of what is achievable in protein-DNA docking: Benchmarking HADDOCK's performance
    • van Dijk, M. and Bonvin, A.M. (2010) Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance. Nucleic Acids Res., 38, 5634-5647.
    • (2010) Nucleic Acids Res , vol.38 , pp. 5634-5647
    • Van Dijk, M.1    Bonvin, A.M.2
  • 37
    • 33746285812 scopus 로고    scopus 로고
    • Information-driven protein-DNA docking using HADDOCK: It is a matter of flexibility
    • van Dijk, M. et al. (2006) Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Res., 34, 3317-3325.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3317-3325
    • Van Dijk, M.1
  • 38
    • 84860388898 scopus 로고    scopus 로고
    • Integrating atom-based and residue-based scoring functions for protein-protein docking
    • Vreven, T. et al. (2011) Integrating atom-based and residue-based scoring functions for protein-protein docking. Protein Sci., 20, 1576-1586.
    • (2011) Protein Sci , vol.20 , pp. 1576-1586
    • Vreven, T.1
  • 39
    • 0027510004 scopus 로고
    • Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds
    • DOI 10.1021/jm00053a019
    • Wade, R.C. and Goodford, P.J. (1993) Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds. J. Med. Chem., 36, 148-156. (Pubitemid 23040156)
    • (1993) Journal of Medicinal Chemistry , vol.36 , Issue.1 , pp. 148-156
    • Wade, R.C.1    Goodford, P.J.2
  • 40
    • 84962704372 scopus 로고    scopus 로고
    • High performance transcription factor-DNA docking with GPU computing
    • Wu, J. et al. (2012) High performance transcription factor-DNA docking with GPU computing. Proteome Sci., 10 (Suppl. 1), S17.
    • (2012) Proteome Sci , vol.10 , Issue.SUPPL. 1
    • Wu, J.1
  • 41
    • 68049118950 scopus 로고    scopus 로고
    • An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles
    • Xu, B. et al. (2009) An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles. Proteins, 76, 718-730.
    • (2009) Proteins , vol.76 , pp. 718-730
    • Xu, B.1
  • 42
    • 17144383951 scopus 로고    scopus 로고
    • A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
    • DOI 10.1021/jm049314d
    • Zhang, C. et al. (2005) A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J. Med. Chem., 48, 2325-2335. (Pubitemid 40516427)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.7 , pp. 2325-2335
    • Zhang, C.1    Liu, S.2    Zhu, Q.3    Zhou, Y.4
  • 43
    • 77955034560 scopus 로고    scopus 로고
    • Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function
    • Zhao, H. et al. (2010) Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinformatics, 26, 1857-1863.
    • (2010) Bioinformatics , vol.26 , pp. 1857-1863
    • Zhao, H.1
  • 44
    • 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
    • DOI 10.1110/ps.0217002
    • Zhou, H. and 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. (Pubitemid 35191145)
    • (2002) Protein Science , vol.11 , Issue.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.