메뉴 건너뛰기




Volumn 2, Issue , 2012, Pages

Specificity quantification of biomolecular recognition and its implication for drug discovery

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; DRUG DEVELOPMENT; VALIDATION STUDY;

EID: 84859783507     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep00309     Document Type: Article
Times cited : (50)

References (44)
  • 1
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland Jr, D. E. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. 44, 98-104 (1958).
    • (1958) Proc. Natl. Acad. Sci , vol.44 , pp. 98-104
    • Koshland Jr., D.E.1
  • 2
    • 0032054612 scopus 로고    scopus 로고
    • Theory of biomolecular recognition
    • DOI 10.1016/S0959-440X(98)80046-8
    • McCammon, J. A. Theory of biomolecular recognition. Curr. Opin. Struct. Biol. 8, 245-249 (1998). (Pubitemid 28221058)
    • (1998) Current Opinion in Structural Biology , vol.8 , Issue.2 , pp. 245-249
    • McCammon, J.A.1
  • 5
    • 33749260698 scopus 로고    scopus 로고
    • A critical assessment of docking programs and scoring functions
    • Gregory, L. et al. A Critical Assessment of Docking Programs and Scoring Functions. J. Med. Chem. 49, 5912-5931 (2006).
    • (2006) J. Med. Chem , vol.49 , pp. 5912-5931
    • Gregory, L.1
  • 6
    • 42649138533 scopus 로고    scopus 로고
    • Assessment of programs for ligand binding affinity prediction
    • DOI 10.1002/jcc.20893
    • Kim, R. & Skolnick, J. Assessment of programs for ligand binding affinity prediction. J. Comput. Chem. 29, 1316-31. (2008) (Pubitemid 351594477)
    • (2008) Journal of Computational Chemistry , vol.29 , Issue.8 , pp. 1316-1331
    • Kim, R.1    Skolnick, J.2
  • 7
    • 8844263008 scopus 로고    scopus 로고
    • Docking and scoring in virtual screening for drug discovery: Methods and applications
    • DOI 10.1038/nrd1549
    • Kitchen, D. B., Decornez, H., Furr, J. R. & Bajorath, J. Docking and scoring in virtual screening for drug discovery: methods and applicaitons. Nat. Rev. Drug Discov. 3, 935-949 (2004). (Pubitemid 39529931)
    • (2004) Nature Reviews Drug Discovery , vol.3 , Issue.11 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 8
    • 0028853544 scopus 로고
    • Principles of protein-protein recognition from structure to thermodynamics
    • Janin, J. Principles of protein-protein recognition from structure to thermodynamics. Biochimie 77, 497-505 (1995).
    • (1995) Biochimie , vol.77 , pp. 497-505
    • Janin, J.1
  • 9
    • 0037217406 scopus 로고    scopus 로고
    • Automated design of specificity in molecular recognition
    • DOI 10.1038/nsb877
    • Havranek, J. J. & Harbury, P. B. Automated design of specificity in molecular recognition. Nat. Struct. Biol. 10, 45-52 (2003). (Pubitemid 36034176)
    • (2003) Nature Structural Biology , vol.10 , Issue.1 , pp. 45-52
    • Havranek, J.J.1    Harbury, P.B.2
  • 12
    • 77957898063 scopus 로고    scopus 로고
    • Scoring functions and their evaluation methods for protein-ligand docking: Recent advances and future directions
    • Huang, S. Y., Grinter, S. Z. & Zou, X. Q. Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. Phys. Chem. Chem. Phys. 12, 12899-12908 (2010).
    • (2010) Phys. Chem. Chem. Phys , vol.12 , pp. 12899-12908
    • Huang, S.Y.1    Grinter, S.Z.2    Zou, X.Q.3
  • 13
    • 0038266221 scopus 로고    scopus 로고
    • Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding
    • Wang, J. & Verkhivker, G. M. Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding. Phys. Rev. Lett. 90, 188101-188104 (2003).
    • (2003) Phys. Rev. Lett , vol.90 , pp. 188101-188104
    • Wang, J.1    Verkhivker, G.M.2
  • 14
    • 35948986361 scopus 로고    scopus 로고
    • Quantifying intrinsic specificity: A potential complement to affinity in drug screening
    • Wang, J. et al. Quantifying intrinsic specificity: A potential complement to affinity in drug screening. Phys. Rev. Lett. 99, 198101-198104 (2007).
    • (2007) Phys. Rev. Lett , vol.99 , pp. 198101-198104
    • Wang, J.1
  • 15
    • 79959275847 scopus 로고    scopus 로고
    • How does a drug molecule find its target binding site?
    • Shan, Y. et al. How does a drug molecule find its target binding site? J. Am. Chem. Soc. 133, 9181-9183 (2011).
    • (2011) J. Am. Chem. Soc , vol.133 , pp. 9181-9183
    • Shan, Y.1
  • 16
    • 0023449962 scopus 로고
    • Spin-glasses and the statistical-mechanics of protein folding
    • Bryngelson, J. D. & Wolynes, P. G. Spin-glasses and the statistical-mechanics of protein folding. Proc. Natl. Acad. Sci. USA 84, 7524-7528 (1987).
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 7524-7528
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 18
    • 0029794940 scopus 로고    scopus 로고
    • Quantifying biological specificity: The statistical mechanics of molecular recognition
    • DOI 10.1002/(SICI)1097-0134(199608)25:4<438::AID-PROT4>3.0.CO;2-9
    • Janin, J. Quantifying biological specificity: the statistical mechanics of molecular recognition. Proteins: Struct. Funct. Bioinf. 25, 438-445 (1996). (Pubitemid 26277721)
    • (1996) Proteins: Structure, Function and Genetics , vol.25 , Issue.4 , pp. 438-445
    • Janin, J.1
  • 20
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • Tsai, C. J., Kumar, S., Ma, B. & Nussinov. R. Folding funnels, binding funnels, and protein function. Protein Sci. 8, 1181-1190 (1999). (Pubitemid 29264948)
    • (1999) Protein Science , vol.8 , Issue.6 , pp. 1181-1190
    • Tsai, C.-J.1    Kumar, S.2    Ma, B.3    Nussinov, R.4
  • 21
    • 4143082530 scopus 로고    scopus 로고
    • Native atom types for knowledge-based potential: Applications to binding energy prediction
    • Dominy, B. N. & Shakhnovich, E. I. Native atom types for knowledge-based potential: Applications to binding energy prediction. J. Med. Chem. 47, 4838-4558 (2004).
    • (2004) J. Med. Chem , vol.47 , pp. 4838-4558
    • Dominy, B.N.1    Shakhnovich, E.I.2
  • 22
    • 3142745414 scopus 로고    scopus 로고
    • Structural mining: Self-consistent design on flexible protein-peptide docking and transferable binding affinity potential
    • DOI 10.1021/ja032018q
    • Liu, Z., Dominy, B. N. & Shakhnovich, E. I. Structural mining: Self-consistent design on flexible protein-peptide docking and transferable binding affinity potential. J. Am. Chem. Soc. 126, 8515-8528 (2004). (Pubitemid 38917975)
    • (2004) Journal of the American Chemical Society , vol.126 , Issue.27 , pp. 8515-8528
    • Liu, Z.1    Dominy, B.N.2    Shakhnovich, E.I.3
  • 24
    • 66149103553 scopus 로고    scopus 로고
    • Comparative assessment of scoring functions on a diverse test set
    • Cheng, T. J., Li, X., Li, Y., Liu, Z. H. & Wang, R. X. Comparative assessment of scoring functions on a diverse test set. J. Chem. Inf. Model. 49, 1079-1093 (2009).
    • (2009) J. Chem. Inf. Model , vol.49 , pp. 1079-1093
    • Cheng, T.J.1    Li, X.2    Li, Y.3    Liu, Z.H.4    Wang, R.X.5
  • 25
    • 17144414125 scopus 로고    scopus 로고
    • Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA
    • DOI 10.1021/jm049606e
    • Wang, J., Kang, K., Kuntz, I. D. & Kollman, P. A. Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA. J. Med. Chem. 48, 2432-2444 (2005). (Pubitemid 40516435)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.7 , pp. 2432-2444
    • Wang, J.1    Kang, X.2    Kuntz, I.D.3    Kollman, P.A.4
  • 27
    • 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. & Zhou, Y. 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). (Pubitemid 35191145)
    • (2002) Protein Science , vol.11 , Issue.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2
  • 28
    • 33750555073 scopus 로고    scopus 로고
    • An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials
    • DOI 10.1002/jcc.20504
    • Huang, S. Y. & Zou, X. An Iterative knowledge-based scoring function to predict proteinligand interactions: I. Derivation of interaction potentials. J. Comput. Chem. 27, 1866-1875 (2006). (Pubitemid 44672568)
    • (2006) Journal of Computational Chemistry , vol.27 , Issue.15 , pp. 1866-1875
    • Huang, S.-Y.1    Zou, X.2
  • 29
    • 2542530042 scopus 로고    scopus 로고
    • The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
    • DOI 10.1021/jm030580l
    • Wang, R., Fang, X., Lu, S. & Wang, Y. The pdbbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J. Med. Chem. 47, 2977-2980 (2004). (Pubitemid 38702694)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.12 , pp. 2977-2980
    • Wang, R.1    Fang, X.2    Lu, Y.3    Wang, S.4
  • 30
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical libraries
    • DOI 10.1038/nature03197
    • Shoichet, B. K. Virtual screening of chemical libraries. Nature 432, 862-865 (2004). (Pubitemid 40037142)
    • (2004) Nature , vol.432 , Issue.7019 , pp. 862-865
    • Shoichet, B.K.1
  • 31
    • 34250829219 scopus 로고    scopus 로고
    • OPUS-Ca: A knowledge-based potential function requiring only Cα positions
    • DOI 10.1110/ps.072796107
    • Wu, Y., Lu, M., Chen, M. Li, J. & Ma, J. OPUS-Ca: A knowledge-based potential function requiring study only Ca positions. Protein Sci. 16, 1449-1463 (2007). (Pubitemid 46984879)
    • (2007) Protein Science , vol.16 , Issue.7 , pp. 1449-1463
    • Wu, Y.1    Lu, M.2    Chen, M.3    Li, J.4    Ma, J.5
  • 32
    • 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. 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 (1990). (Pubitemid 20213222)
    • (1990) Journal of Molecular Biology , vol.213 , Issue.4 , pp. 859-883
    • Sippl, M.J.1
  • 33
    • 84859746909 scopus 로고    scopus 로고
    • PDBbind Database website: http://www. pdbbind-cn. org/
    • PDBbind Database
  • 34
    • 84988115618 scopus 로고
    • Validation of the general purpose tripos 5. 2 force field
    • Clark, M., Cramer III, R. D. & Opdenbosch, N. V. Validation of the general purpose tripos 5. 2 force field. J. Comput. Chem. 10, 982-1012 (1989).
    • (1989) J. Comput. Chem , vol.10 , pp. 982-1012
    • Clark, M.1    Cramer Iii, R.D.2    Opdenbosch, N.V.3
  • 35
    • 33745359822 scopus 로고    scopus 로고
    • The blue obelisk-interoperability in chemical informatics
    • Guha, T. et al. The blue obelisk-interoperability in chemical informatics. J. Chem. Inf. Model 46, 991-998 (2006).
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 991-998
    • Guha, T.1
  • 37
    • 0030596063 scopus 로고    scopus 로고
    • How to derive a protein folding potential? A new approach to an old problem
    • DOI 10.1006/jmbi.1996.0704
    • Leonid, A. M. & Shakhnovich, E. I. How to derive a protein folding potential? A new approach to an old problem. J. Mol. Biol. 264, 1164-1179 (1996). (Pubitemid 27019500)
    • (1996) Journal of Molecular Biology , vol.264 , Issue.5 , pp. 1164-1179
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 40
    • 84859759879 scopus 로고    scopus 로고
    • NCI Website: http://dtp. nci. nih. gov/branches/dscb/diversity- explanation. html.
    • NCI
  • 41
    • 0030461132 scopus 로고    scopus 로고
    • Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents
    • Kurumbail, R. G. et al. Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents. Nature 384, 644-648 (1996).
    • (1996) Nature , vol.384 , pp. 644-648
    • Kurumbail, R.G.1
  • 42
    • 0032916736 scopus 로고    scopus 로고
    • Cox-2-selective inhibitors: The new super aspirins
    • Dewitt, D. L. Cox-2-selective inhibitors: The new super aspirins. Mol. Pharmacol. 55, 625-631 (1999).
    • (1999) Mol. Pharmacol , vol.55 , pp. 625-631
    • Dewitt, D.L.1
  • 43
    • 77958565592 scopus 로고    scopus 로고
    • Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening
    • Wei, D., Zheng, H., Su, N., Deng, M. & Lai, L. Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening. J. Chem. Inf. Model. 50, 1855-1864 (2010).
    • (2010) J. Chem. Inf. Model , vol.50 , pp. 1855-1864
    • Wei, D.1    Zheng, H.2    Su, N.3    Deng, M.4    Lai, L.5
  • 44
    • 41349106585 scopus 로고    scopus 로고
    • Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes?
    • DOI 10.1007/s10822-007-9163-6
    • Kirchmair, J., Markt, P., Distinto, S., Wolber, G. & Langer, T. Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection-what can we learn from earlier mistakes. J. Comput. Aided. Mol. Des. 22, 213-228 (2008). (Pubitemid 351447959)
    • (2008) Journal of Computer-Aided Molecular Design , vol.22 , Issue.3-4 , pp. 213-228
    • Kirchmair, J.1    Markt, P.2    Distinto, S.3    Wolber, G.4    Langer, T.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.