메뉴 건너뛰기




Volumn 18, Issue 9, 2002, Pages 1257-1263

A dissimilarity matrix between protein atom classes based on Gaussian mixtures

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

EID: 0036738899     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.9.1257     Document Type: Article
Times cited : (4)

References (32)
  • 3
    • 0026813925 scopus 로고
    • The computer program LUDI: A new method for the de novo design of enzyme inhibitors
    • Böhm,H.J. (1992a) The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J. Comput. Aided Mol. Des., 6, 61-78.
    • (1992) J. Comput. Aided Mol. Des , vol.6 , pp. 61-78
    • Böhm, H.J.1
  • 4
    • 0027027467 scopus 로고
    • LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads
    • Böhm,H.J. (1992b) LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J. Comput. Aided Mol. Des., 6, 593-606.
    • (1992) J. Comput. Aided Mol. Des , vol.6 , pp. 593-606
    • Böhm, H.J.1
  • 5
    • 0028522983 scopus 로고
    • On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure
    • Böhm,H.J. (1994) On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure. J. Comput. Aided Mol. Des., 8, 623-632.
    • (1994) J. Comput. Aided Mol. Des , vol.8 , pp. 623-632
    • Böhm, H.J.1
  • 6
    • 0024549279 scopus 로고
    • Automated site-directed drug design: A general algorithm for knowledge acquisition about hydrogen-bonding regions at protein surfaces
    • Danziger,D.J. and Dean,P.M. (1989a) Automated site-directed drug design: a general algorithm for knowledge acquisition about hydrogen-bonding regions at protein surfaces. Proc. R. Soc. Ser. B, 236, 101-113.
    • (1989) Proc. R. Soc. Ser. B , vol.236 , pp. 101-113
    • Danziger, D.J.1    Dean, P.M.2
  • 7
    • 0024498660 scopus 로고
    • Automated site-directed drug design: The prediction and observation of ligand point positions at hydrogen-bonding regions on protein surfaces
    • Danziger,D.J. and Dean,P.M. (1989b) Automated site-directed drug design: the prediction and observation of ligand point positions at hydrogen-bonding regions on protein surfaces. Proc. R. Soc. Ser. B, 236, 115-124.
    • (1989) Proc. R. Soc. Ser. B , vol.236 , pp. 115-124
    • Danziger, D.J.1    Dean, P.M.2
  • 8
    • 0035882572 scopus 로고    scopus 로고
    • Adenine recognition: A motif present in ATP-, CoA-, NAD-, NADP- and FAD-dependent proteins
    • Denessiouk,K.A., Rantanen,V.-V. and Johnson,M.S. (2001) Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP- and FAD-dependent proteins. Proteins, 44, 282-291.
    • (2001) Proteins , vol.44 , pp. 282-291
    • Denessiouk, K.A.1    Rantanen, V.-V.2    Johnson, M.S.3
  • 12
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • Felsenstein,J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 13
    • 0014211361 scopus 로고
    • Construction of phylogenetic trees
    • Fitch,W.M. and Margoliash,E. (1967) Construction of phylogenetic trees. Science, 155, 279-284.
    • (1967) Science , vol.155 , pp. 279-284
    • Fitch, W.M.1    Margoliash, E.2
  • 14
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford,P.J. (1985) A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem., 28, 849-857.
    • (1985) J. Med. Chem , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 15
    • 0026292147 scopus 로고
    • HINT: A new method of empirical hydrophobic field calculation for CoMFA
    • Kellogg,G.E., Semus,S.F. and Abraham,D.J. (1991) HINT: a new method of empirical hydrophobic field calculation for CoMFA. J. Comput. Aided. Mol. Des., 5, 545-552.
    • (1991) J. Comput. Aided Mol. Des , vol.5 , pp. 545-552
    • Kellogg, G.E.1    Semus, S.F.2    Abraham, D.J.3
  • 16
    • 0028287528 scopus 로고
    • The use of composite crystal-field environments in molecular recognition and de novo design of protein ligands
    • Klebe,G. (1994) The use of composite crystal-field environments in molecular recognition and de novo design of protein ligands. J. Mol. Biol., 237, 212-235.
    • (1994) J. Mol. Biol , vol.237 , pp. 212-235
    • Klebe, G.1
  • 18
    • 0004257990 scopus 로고    scopus 로고
    • Dover Publications, Mineola, New York, Republication of the 1968 Dover edition (1969)
    • Kullback,S. (1997) Information Theory and Statistics. Dover Publications, Mineola, New York, Republication of the 1968 Dover edition (1969).
    • (1997) Information Theory and Statistics
    • Kullback, S.1
  • 19
    • 0029895576 scopus 로고    scopus 로고
    • X-SITE: Use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins
    • Laskowski,R.A., Thornton,J.M., Humblet,C. and Singh,J. (1996) X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins. J. Mol. Biol., 259, 175-201.
    • (1996) J. Mol. Biol , vol.259 , pp. 175-201
    • Laskowski, R.A.1    Thornton, J.M.2    Humblet, C.3    Singh, J.4
  • 20
    • 0032125607 scopus 로고    scopus 로고
    • A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking
    • Li,A.-J. and Nussinov,R. (1998) A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking. Proteins: Struct. Funct. Genet., 32, 111-127.
    • (1998) Proteins: Struct. Funct. Genet , vol.32 , pp. 111-127
    • Li, A.-J.1    Nussinov, R.2
  • 21
    • 0032821685 scopus 로고    scopus 로고
    • Towards more meaningful hierarchical classification of amino acid scoring matrices
    • May,A.C.W. (1999a) Towards more meaningful hierarchical classification of amino acid scoring matrices. Protein Eng., 12, 707-712.
    • (1999) Protein Eng , vol.12 , pp. 707-712
    • May, A.C.W.1
  • 22
    • 0033214429 scopus 로고    scopus 로고
    • Towards more meaningful hierarchical classification of protein three-dimensional structures
    • May,A.C.W. (1999b) Towards more meaningful hierarchical classification of protein three-dimensional structures. Proteins, 37, 20-29.
    • (1999) Proteins , vol.37 , pp. 20-29
    • May, A.C.W.1
  • 23
    • 0033568305 scopus 로고    scopus 로고
    • A cautionary note on interpretation of hierachical classifications of protein folds
    • May,A.C.W. (1999c) A cautionary note on interpretation of hierachical classifications of protein folds. Structure, 7, R213.
    • (1999) Structure , vol.7
    • May, A.C.W.1
  • 24
    • 84948109721 scopus 로고    scopus 로고
    • John Wiley and Sons, New York, Chichester, Brisbane, Toronto, Singapore, Weinheim
    • McLachlan,G.J. and Krishnan,T. (1997) The EM Algorithm and Extensions. John Wiley and Sons, New York, Chichester, Brisbane, Toronto, Singapore, Weinheim.
    • (1997) The EM Algorithm and Extensions
    • McLachlan, G.J.1    Krishnan, T.2
  • 25
    • 0033669857 scopus 로고    scopus 로고
    • Simple knowledge-based descriptors to predict protein-ligand interactions. Methodology and validation
    • Nissink,J.W.M, Verdonk,M.L. and Klebe,G. (2000) Simple knowledge-based descriptors to predict protein-ligand interactions. Methodology and validation. J. Comput. Aided Mol. Des., 14, 787-803.
    • (2000) J. Comput. Aided Mol. Des , vol.14 , pp. 787-803
    • Nissink, J.W.M.1    Verdonk, M.L.2    Klebe, G.3
  • 26
    • 0025770179 scopus 로고
    • Modelling of solvent positions around polar groups in proteins
    • Pitt,W.R. and Goodfellow,J.M. (1991) Modelling of solvent positions around polar groups in proteins. Protein Eng., 4, 531-537.
    • (1991) Protein Eng , vol.4 , pp. 531-537
    • Pitt, W.R.1    Goodfellow, J.M.2
  • 27
    • 0035850756 scopus 로고    scopus 로고
    • A fragment library based on Gaussian mixtures predicting favorable molecular interactions
    • Rantanen,V.-V., Denessiouk,K.A., Gyllenberg,M., Koski,T. and Johnson,M.S. (2001) A fragment library based on Gaussian mixtures predicting favorable molecular interactions. J. Mol. Biol., 313, 197-214.
    • (2001) J. Mol. Biol , vol.313 , pp. 197-214
    • Rantanen, V.-V.1    Denessiouk, K.A.2    Gyllenberg, M.3    Koski, T.4    Johnson, M.S.5
  • 29
    • 0033047007 scopus 로고    scopus 로고
    • SuperStar: A knowledge-based approach for indentifying interaction sites in proteins
    • Verdonk,M.L., Cole,J.C. and Taylor,R. (1999) SuperStar: a knowledge-based approach for indentifying interaction sites in proteins. J. Mol. Biol., 289, 1093-1108.
    • (1999) J. Mol. Biol , vol.289 , pp. 1093-1108
    • Verdonk, M.L.1    Cole, J.C.2    Taylor, R.3
  • 30
    • 0035970295 scopus 로고    scopus 로고
    • SuperStar: Improved knowledge-based interaction field for protein binding sites
    • Verdonk,M.L., Cole,J.C., Watson,P., Gillet,V. and Willett,P. (2001) SuperStar: improved knowledge-based interaction field for protein binding sites. J. Mol. Biol., 307, 841-859.
    • (2001) J. Mol. Biol , vol.307 , pp. 841-859
    • Verdonk, M.L.1    Cole, J.C.2    Watson, P.3    Gillet, V.4    Willett, P.5
  • 31
    • 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
    • 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.
    • (1993) J. Med. Chem , vol.36 , pp. 148-156
    • Wade, R.C.1    Goodford, P.J.2
  • 32
    • 0027439587 scopus 로고
    • Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds
    • Wade,R.C., Clark,K.J. and Goodford,P.J. (1993) Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds. J. Med. Chem., 36, 140-147.
    • (1993) J. Med. Chem , vol.36 , pp. 140-147
    • Wade, R.C.1    Clark, K.J.2    Goodford, P.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.