메뉴 건너뛰기




Volumn , Issue , 2008, Pages 61-87

Scoring functions for protein structure prediction

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN STRUCTURE PREDICTION; SCORING FUNCTIONS;

EID: 84969131681     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/9789812778789_0003     Document Type: Chapter
Times cited : (5)

References (34)
  • 1
    • 0027490731 scopus 로고
    • Recognition of errors in three-dimensional structures of proteins
    • Sippl MJ. (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17: 355-362.
    • (1993) Proteins , vol.17 , pp. 355-362
    • Sippl, M.J.1
  • 2
    • 0037197857 scopus 로고    scopus 로고
    • Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium genome
    • Kihara D, Zhang Y, Lu H, Kolinski A, Skolnick J. (2002) Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proc Natl Acad Sci USA 99: 5993-5998.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 5993-5998
    • Kihara, D.1    Zhang, Y.2    Lu, H.3    Kolinski, A.4    Skolnick, J.5
  • 3
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM. (1992) A new approach to protein fold recognition. Nature 358: 86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 4
    • 0026539511 scopus 로고
    • Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native proteins
    • Casari G, Sippl MJ. (1992) Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native proteins. J Mol Biol 224: 725-732.
    • (1992) J Mol Biol , vol.224 , pp. 725-732
    • Casari, G.1    Sippl, M.J.2
  • 5
    • 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
  • 6
    • 0027650879 scopus 로고
    • Boltzmann principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
    • Sippl MJ. (1993) Boltzmann principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J Comput Aid Mol Des 7: 473-501.
    • (1993) J Comput Aid Mol Des , vol.7 , pp. 473-501
    • Sippl, M.J.1
  • 7
    • 33644842005 scopus 로고    scopus 로고
    • Improvement of statistical potentials and threading score functions using information maximization
    • Solis AD, Rackovsky S. (2006) Improvement of statistical potentials and threading score functions using information maximization. Proteins 62: 892-908.
    • (2006) Proteins , vol.62 , pp. 892-908
    • Solis, A.D.1    Rackovsky, S.2
  • 8
    • 33646808944 scopus 로고    scopus 로고
    • Accuracy of sequence allignment and fold assessment using reduced amino acid alphabets
    • Melo F, Marti-Renom M. (2004) Accuracy of sequence allignment and fold assessment using reduced amino acid alphabets. Proteins 63: 986-995.
    • (2004) Proteins , vol.63 , pp. 986-995
    • Melo, F.1    Marti-Renom, M.2
  • 9
    • 0036145846 scopus 로고    scopus 로고
    • Statistical potentials for fold assessment
    • Melo F, Sanchez R, Sali A. (2002) Statistical potentials for fold assessment. Protein Sci 11: 430-448.
    • (2002) Protein Sci , vol.11 , pp. 430-448
    • Melo, F.1    Sanchez, R.2    Sali, A.3
  • 10
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa S, Jernigan RL. (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
  • 11
    • 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 MJ. (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.
    • (1990) J Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 12
    • 0032540222 scopus 로고    scopus 로고
    • Assessing protein structures with a non-local atomic interaction energy
    • Melo F, Feytmans E. (1998) Assessing protein structures with a non-local atomic interaction energy. J Mol Biol 277: 1141-1152.
    • (1998) J Mol Biol , vol.277 , pp. 1141-1152
    • Melo, F.1    Feytmans, E.2
  • 13
    • 0031582083 scopus 로고    scopus 로고
    • Novel knowledge-based mean force potential at atomic level
    • Melo F, Feytmans E. (1997) Novel knowledge-based mean force potential at atomic level. J Mol Biol 267: 207-222.
    • (1997) J Mol Biol , vol.267 , pp. 207-222
    • Melo, F.1    Feytmans, E.2
  • 15
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C, Lesk AM. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5: 823-826.
    • (1986) EMBO J , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 16
    • 0027057526 scopus 로고
    • A database of protein structure families with common folding motifs
    • Holm L, Ouzounis C, Sander C, Tuparev G, Vriend G. (1992) A database of protein structure families with common folding motifs. Protein Sci 1:1691-1698.
    • (1992) Protein Sci , vol.1 , pp. 1691-1698
    • Holm, L.1    Ouzounis, C.2    Sander, C.3    Tuparev, G.4    Vriend, G.5
  • 17
    • 0034853119 scopus 로고    scopus 로고
    • DBAli: A database of protein structure alignments
    • Marti-Renom MA, Ilyin VA, Sali A. (2001) DBAli: a database of protein structure alignments. Bioinformatics 17: 746-747.
    • (2001) Bioinformatics , vol.17 , pp. 746-747
    • Marti-Renom, M.A.1    Ilyin, V.A.2    Sali, A.3
  • 18
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • Samudrala R, Moult J. (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 275: 895-916.
    • (1998) J Mol Biol , vol.275 , pp. 895-916
    • Samudrala, R.1    Moult, J.2
  • 19
    • 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 44: 223-232.
    • (2001) Proteins , vol.44 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 20
    • 34250886494 scopus 로고    scopus 로고
    • Non-bonded terms extrapolated from non-local knowledge based energy functions improve error detection in near native protein structure models
    • Ferrada E, Melo F. (2007) Non-bonded terms extrapolated from non-local knowledge based energy functions improve error detection in near native protein structure models. Protein Sci 16: 1410-1421.
    • (2007) Protein Sci , vol.16 , pp. 1410-1421
    • Ferrada, E.1    Melo, F.2
  • 21
    • 35348892593 scopus 로고    scopus 로고
    • A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations
    • Ferrada E, Vergara IA, Melo F. (2007) A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations. Cell Biochem Biophys 49: 111-124.
    • (2007) Cell Biochem Biophys , vol.49 , pp. 111-124
    • Ferrada, E.1    Vergara, I.A.2    Melo, F.3
  • 22
    • 84969129749 scopus 로고    scopus 로고
    • Knowledge-based energy functions and effective atomic interactions
    • submitted
    • Ferrada E, Melo F. (2007) Knowledge-based energy functions and effective atomic interactions. Protein Sci, submitted.
    • (2007) Protein Sci
    • Ferrada, E.1    Melo, F.2
  • 24
    • 0033853177 scopus 로고    scopus 로고
    • Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction
    • Samudrala R, Levitt M. (2000) Decoys ‘R’ Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 9: 1399-1401.
    • (2000) Protein Sci , vol.9 , pp. 1399-1401
    • Samudrala, R.1    Levitt, M.2
  • 25
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser A, Do RK, Sali A. (2000) Modeling of loops in protein structures. Protein Sci 9: 1753-1773.
    • (2000) Protein Sci , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 26
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy, minimizations and dynamic calculations
    • Brooks B, Bruccoleri R, Olafsonand B, et al. (1983) CHARMM: a program for macromolecular energy, minimizations and dynamic calculations. J Comput Chem 4: 187-217.
    • (1983) J Comput Chem , vol.4 , pp. 187-217
    • Brooks, B.1    Bruccoleri, R.2    Olafsonand, B.3
  • 27
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell AD, Jr., Bashford D, Bellott M, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586-3616.
    • (1998) J Phys Chem B , vol.102 , pp. 3586-3616
    • MacKerell, A.D.1    Bashford, D.2    Bellott, M.3
  • 28
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL. (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 29
    • 84969156186 scopus 로고    scopus 로고
    • Evolutionary potentials: Structure specific potentials exploiting the evolutionary record of sequence homologs
    • Panjkovich A, Melo F, Marti-Renom MA. (2007) Evolutionary potentials:structure specific potentials exploiting the evolutionary record of sequence homologs. Protein Sci.
    • (2007) Protein Sci
    • Panjkovich, A.1    Melo, F.2    Marti-Renom, M.A.3
  • 30
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker D, Sali A. (2001) Protein structure prediction and structural genomics. Science 294: 93-96.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 31
    • 35648999092 scopus 로고    scopus 로고
    • Fold assessment for comparative protein structure modeling
    • Melo F, Sali A. (2007) Fold assessment for comparative protein structure modeling. Protein Sci 16: 2142-2426.
    • (2007) Protein Sci , vol.16 , pp. 2142-2426
    • Melo, F.1    Sali, A.2
  • 32
    • 33644874394 scopus 로고    scopus 로고
    • MODBASE, a database of annotated comparative protein structure models, and associated resources
    • Pieper U, Eswar N, Braberg H, et al. (2006) MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucl Acids Res 33: 291-295.
    • (2006) Nucl Acids Res , vol.33 , pp. 291-295
    • Pieper, U.1    Eswar, N.2    Braberg, H.3
  • 33
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones DT. (1999) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 287: 797-815.
    • (1999) J Mol Biol , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 34
    • 0038634975 scopus 로고    scopus 로고
    • Improvement of the GenTHREADER method for genomic fold recognition
    • McGuffin LJ, Jones DT. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19: 874-881.
    • (2003) Bioinformatics , vol.19 , pp. 874-881
    • McGuffin, L.J.1    Jones, D.T.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.