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Volumn 34, Issue 7, 2006, Pages 2085-2097

A supersecondary structure library and search algorithm for modeling loops in protein structures

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; GEOMETRY; INTERNET; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; CHEMICAL STRUCTURE; EVALUATION; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS;

EID: 33645923385     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl156     Document Type: Article
Times cited : (65)

References (77)
  • 3
    • 0036308741 scopus 로고    scopus 로고
    • Enzyme function less conserved than anticipated
    • Rost,B. (2002) Enzyme function less conserved than anticipated. J. Mol. Biol., 318, 595.
    • (2002) J. Mol. Biol. , vol.318 , pp. 595
    • Rost, B.1
  • 4
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfamilies, from a structural perspective
    • Todd,A.E., Orengo,C.A. and Thornton,J.M. (2001) Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol., 307, 1113.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1113
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 7
    • 0027136282 scopus 로고
    • Comparative protein modeling by satisfaction of spatial restraints
    • Sali,A. and Blundell,T.L. (1993) Comparative protein modeling 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
  • 8
    • 0034615787 scopus 로고    scopus 로고
    • Structure-based evaluation of sequence comparison and fold recognition alignment accuracy
    • Domingues,F.S., Lackner,P., Andreeva,A. and Sippl,M.J. (2000) Structure-based evaluation of sequence comparison and fold recognition alignment accuracy. J. Mol. Biol., 297, 1003.
    • (2000) J. Mol. Biol. , vol.297 , pp. 1003
    • Domingues, F.S.1    Lackner, P.2    Andreeva, A.3    Sippl, M.J.4
  • 9
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons,K.T., Kooperberg,C., Huang,E. and Baker,D. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol., 268, 209-225.
    • (1997) J. Mol. Biol. , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 10
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker,D. and 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
  • 13
    • 33645734536 scopus 로고    scopus 로고
    • Protein structure modeling in the proteomics era
    • Fiser,A. (2004) Protein structure modeling in the proteomics era. Expert Rev Proteomics., 1, 97-110.
    • (2004) Expert Rev Proteomics. , vol.1 , pp. 97-110
    • Fiser, A.1
  • 14
    • 0036283048 scopus 로고    scopus 로고
    • Evolution and physics in comparative protein structure modeling
    • Fiser,A., Feig,M., Brooks,C.L.III and, Sali,A. (2002) Evolution and physics in comparative protein structure modeling. Acc. Chem. Res., 35, 413-421.
    • (2002) Acc. Chem. Res. , vol.35 , pp. 413-421
    • Fiser, A.1    Feig, M.2    Brooks III, C.L.3    Sali, A.4
  • 16
    • 0242267499 scopus 로고    scopus 로고
    • Assessment of progress over the CASP experiments
    • Venclovas,C., Zemla,A., Fidelis,K. and Moult,J. (2003) Assessment of progress over the CASP experiments. Proteins, 53, 585.
    • (2003) Proteins , vol.53 , pp. 585
    • Venclovas, C.1    Zemla, A.2    Fidelis, K.3    Moult, J.4
  • 17
    • 1342310533 scopus 로고    scopus 로고
    • Rapid evolution in conformational space: A study of loop regions in a ubiquitous GTP binding domain
    • Blouin,C., Butt,D. and Roger,A.J. (2004) Rapid evolution in conformational space: A study of loop regions in a ubiquitous GTP binding domain. Protein Sci., 13, 608-616.
    • (2004) Protein Sci. , vol.13 , pp. 608-616
    • Blouin, C.1    Butt, D.2    Roger, A.J.3
  • 18
    • 0344642583 scopus 로고    scopus 로고
    • Enhanced conformational diversity search of CDR-H3 in antibodies: Role of the first CDR-H3 residue
    • Kim,S.T., Shirai,H., Nakajima,N., Higo,J. and Nakamura,H. (1999) Enhanced conformational diversity search of CDR-H3 in antibodies: Role of the first CDR-H3 residue. Proteins, 37, 683-696.
    • (1999) Proteins , vol.37 , pp. 683-696
    • Kim, S.T.1    Shirai, H.2    Nakajima, N.3    Higo, J.4    Nakamura, H.5
  • 19
    • 0025048136 scopus 로고
    • The P-loop - A common motif in ATP- and GTP-binding proteins
    • Saraste,M., Sibbald,P.R. and Wittinghofer,A. (1990) The P-loop - a common motif in ATP- and GTP-binding proteins. Trends Biochem. Sci., 15, 430-434.
    • (1990) Trends Biochem. Sci. , vol.15 , pp. 430-434
    • Saraste, M.1    Sibbald, P.R.2    Wittinghofer, A.3
  • 20
    • 0029189946 scopus 로고
    • Calcium-binding proteins 1: EF-hands
    • Kawasaki,H. and Kretsinger,R.H. (1995) Calcium-binding proteins 1: EF-hands. Protein Profile, 2, 297-490.
    • (1995) Protein Profile , vol.2 , pp. 297-490
    • Kawasaki, H.1    Kretsinger, R.H.2
  • 21
    • 0023041821 scopus 로고
    • Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint
    • Wierenga,R.K., Terpstra,P. and Hol,W.G. (1986) Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint. J. Mol. Biol., 187, 101-107.
    • (1986) J. Mol. Biol. , vol.187 , pp. 101-107
    • Wierenga, R.K.1    Terpstra, P.2    Hol, W.G.3
  • 23
    • 0032560489 scopus 로고    scopus 로고
    • The Eleventh Datta Lecture. The structural basis for substrate recognition and control by protein kinases
    • Johnson,L.N., Lowe,E.D., Noble,M.E. and Owen,D.J. (1998) The Eleventh Datta Lecture. The structural basis for substrate recognition and control by protein kinases. FEBS Lett., 430, 1-11.
    • (1998) FEBS Lett. , vol.430 , pp. 1-11
    • Johnson, L.N.1    Lowe, E.D.2    Noble, M.E.3    Owen, D.J.4
  • 25
    • 0022842039 scopus 로고
    • Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations
    • Fine,R.M., Wang,H., Shenkin,P.S., Yarmush,D.L. and Levinthal,C. (1986) Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations. Proteins, 1, 342.
    • (1986) Proteins , vol.1 , pp. 342
    • Fine, R.M.1    Wang, H.2    Shenkin, P.S.3    Yarmush, D.L.4    Levinthal, C.5
  • 26
    • 0022788691 scopus 로고
    • An algorithm for determining the conformation of polypeptide segments in proteins by systematic search
    • Moult,J. and James,M.N. (1986) An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins, 1, 146.
    • (1986) Proteins , vol.1 , pp. 146
    • Moult, J.1    James, M.N.2
  • 27
    • 0023173201 scopus 로고
    • Prediction of the folding of short polypeptide segments by uniform conformational sampling
    • Bruccoleri,R.E. and Karplus,M. (1987) Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers., 26, 137.
    • (1987) Biopolymers , vol.26 , pp. 137
    • Bruccoleri, R.E.1    Karplus, M.2
  • 28
    • 0022701772 scopus 로고
    • Using known substructures in protein model building and crystallography
    • Jones,T.A. and Thirup,S. (1986) Using known substructures in protein model building and crystallography. EMBO J., 5, 819.
    • (1986) EMBO J. , vol.5 , pp. 819
    • Jones, T.A.1    Thirup, S.2
  • 29
    • 0023278330 scopus 로고
    • Canonical structures for the hypervariable regions of immunoglobulins
    • Chothia,C. and Lesk,A.M. (1987) Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol., 196, 901.
    • (1987) J. Mol. Biol. , vol.196 , pp. 901
    • Chothia, C.1    Lesk, A.M.2
  • 30
    • 0028066936 scopus 로고
    • Comparison of systematic search and database methods for constructing segments of protein structure
    • Fidelis,K., Stern,P.S., Bacon,D. and Moult,J. (1994) Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng., 7, 953.
    • (1994) Protein Eng. , vol.7 , pp. 953
    • Fidelis, K.1    Stern, P.S.2    Bacon, D.3    Moult, J.4
  • 31
    • 0029863769 scopus 로고    scopus 로고
    • Automatic classification and analysis of alpha alpha-turn motifs in proteins
    • Wintjens,R.T., Rooman,M.J. and Wodak,S.J. (1996) Automatic classification and analysis of alpha alpha-turn motifs in proteins. J. Mol. Biol., 255, 235-253.
    • (1996) J. Mol. Biol. , vol.255 , pp. 235-253
    • Wintjens, R.T.1    Rooman, M.J.2    Wodak, S.J.3
  • 32
    • 0035107308 scopus 로고    scopus 로고
    • CODA: A combined algorithm for predicting the structurally variable regions of protein models
    • Deane,C.M. and Blundell,T.L. (2001) CODA: A combined algorithm for predicting the structurally variable regions of protein models. Protein Sci., 10, 599.
    • (2001) Protein Sci. , vol.10 , pp. 599
    • Deane, C.M.1    Blundell, T.L.2
  • 33
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser,A., Do,R.K. and Sali,A. (2000) Modeling of loops in protein structures. Protein Sci., 9, 1753.
    • (2000) Protein Sci. , vol.9 , pp. 1753
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 34
    • 0037188507 scopus 로고    scopus 로고
    • Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction
    • Xiang,Z., Soto,C.S. and Honig,B. (2002) Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction. Proc. Natl Acad. Sci. USA, 99, 7432-7437.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 7432-7437
    • Xiang, Z.1    Soto, C.S.2    Honig, B.3
  • 35
    • 0036096608 scopus 로고    scopus 로고
    • A divide and conquer approach to fast loop modeling
    • Tosatto,S.C., Bindewald,E., Hesser,J. and Manner,R. (2002) A divide and conquer approach to fast loop modeling. Protein Eng., 15, 279-286.
    • (2002) Protein Eng. , vol.15 , pp. 279-286
    • Tosatto, S.C.1    Bindewald, E.2    Hesser, J.3    Manner, R.4
  • 36
    • 0037375615 scopus 로고    scopus 로고
    • Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model
    • de Bakker,P.I., DePristo,M.A., Burke,D.F. and Blundell,T.L. (2003) Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model. Proteins, 51, 21.
    • (2003) Proteins , vol.51 , pp. 21
    • de Bakker, P.I.1    DePristo, M.A.2    Burke, D.F.3    Blundell, T.L.4
  • 37
    • 0037941126 scopus 로고    scopus 로고
    • Generation of accurate protein loop conformations through low-barrier molecular dynamics
    • Hornak,V. and Simmerling,C. (2003) Generation of accurate protein loop conformations through low-barrier molecular dynamics. Proteins, 51, 577-590.
    • (2003) Proteins , vol.51 , pp. 577-590
    • Hornak, V.1    Simmerling, C.2
  • 39
    • 1642575364 scopus 로고    scopus 로고
    • Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential
    • Zhang,C., Liu,S. and Zhou,Y. (2004) Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. Protein Sci., 13, 391-399.
    • (2004) Protein Sci. , vol.13 , pp. 391-399
    • Zhang, C.1    Liu, S.2    Zhou, Y.3
  • 40
    • 2442449534 scopus 로고    scopus 로고
    • Modeling structurally variable regions in homologous proteins with rosetta
    • Rohl,C.A., Strauss,C.E., Chivian,D. and Baker,D. (2004) Modeling structurally variable regions in homologous proteins with rosetta. Proteins, 55, 656-677.
    • (2004) Proteins , vol.55 , pp. 656-677
    • Rohl, C.A.1    Strauss, C.E.2    Chivian, D.3    Baker, D.4
  • 41
    • 0033135619 scopus 로고    scopus 로고
    • Prediction of loop geometries using a generalized born model of solvation effects
    • Rapp,C.S. and Friesner,R.A. (1999) Prediction of loop geometries using a generalized born model of solvation effects. Proteins, 35, 173.
    • (1999) Proteins , vol.35 , pp. 173
    • Rapp, C.S.1    Friesner, R.A.2
  • 42
    • 0028040064 scopus 로고
    • Evaluation of the conformational free energies of loops in proteins
    • Smith,K.C. and Honig,B. (1994) Evaluation of the conformational free energies of loops in proteins. Proteins, 18, 119.
    • (1994) Proteins , vol.18 , pp. 119
    • Smith, K.C.1    Honig, B.2
  • 43
    • 0030833061 scopus 로고    scopus 로고
    • Does conformational free energy distinguish loop conformations in proteins?
    • Pellequer,J.L. and Chen,S.W. (1997) Does conformational free energy distinguish loop conformations in proteins? Biophys. J., 73, 2359-2375.
    • (1997) Biophys. J. , vol.73 , pp. 2359-2375
    • Pellequer, J.L.1    Chen, S.W.2
  • 44
    • 0019888748 scopus 로고
    • Comparative model-building of the mammalian serine proteases
    • Greer,J. (1981) Comparative model-building of the mammalian serine proteases. J. Mol. Biol., 153, 1027.
    • (1981) J. Mol. Biol. , vol.153 , pp. 1027
    • Greer, J.1
  • 45
    • 0033214836 scopus 로고    scopus 로고
    • Importance of anchor group positioning in protein loop prediction
    • Lessel,U. and Schomburg,D. (1999) Importance of anchor group positioning in protein loop prediction. Proteins, 37, 56.
    • (1999) Proteins , vol.37 , pp. 56
    • Lessel, U.1    Schomburg, D.2
  • 46
    • 0030449155 scopus 로고    scopus 로고
    • Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: A database for modeling and prediction
    • Donate,L.E., Rufino,S.D., Canard,L.H. and Blundell,T.L. (1996) Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: A database for modeling and prediction. Protein Sci., 5, 2600.
    • (1996) Protein Sci. , vol.5 , pp. 2600
    • Donate, L.E.1    Rufino, S.D.2    Canard, L.H.3    Blundell, T.L.4
  • 47
    • 0030309801 scopus 로고    scopus 로고
    • Analysis, clustering and prediction of the conformation of short and medium size loops connecting regular secondary structures
    • Rufino,S.D., Donate,L.E., Canard,L. and Blundell,T.L. (1996) Analysis, clustering and prediction of the conformation of short and medium size loops connecting regular secondary structures. Pac. Symp. Biocomput., 570-589.
    • (1996) Pac. Symp. Biocomput. , pp. 570-589
    • Rufino, S.D.1    Donate, L.E.2    Canard, L.3    Blundell, T.L.4
  • 50
    • 0034847744 scopus 로고    scopus 로고
    • Improved protein loop prediction from sequence alone
    • Burke,D.F. and Deane,C.M. (2001) Improved protein loop prediction from sequence alone. Protein Eng., 14, 473-478.
    • (2001) Protein Eng. , vol.14 , pp. 473-478
    • Burke, D.F.1    Deane, C.M.2
  • 51
    • 24644439203 scopus 로고    scopus 로고
    • Prediction of the conformation and geometry of loops in globular proteins: Testing ArchDB, a structural classification of loops
    • Fernandez-Fuentes,N., Querol,E., Aviles,F.X., Sternberg,M.J. and Oliva,B. (2005) Prediction of the conformation and geometry of loops in globular proteins: Testing ArchDB, a structural classification of loops. Proteins, 60, 746-757.
    • (2005) Proteins , vol.60 , pp. 746-757
    • Fernandez-Fuentes, N.1    Querol, E.2    Aviles, F.X.3    Sternberg, M.J.4    Oliva, B.5
  • 52
    • 0030589039 scopus 로고    scopus 로고
    • Structural families in loops of homologous proteins: Automatic classification, modelling and application to antibodies
    • Martin,A.C. and Thornton,J.M. (1996) Structural families in loops of homologous proteins: Automatic classification, modelling and application to antibodies. J. Mol. Biol., 263, 800.
    • (1996) J. Mol. Biol. , vol.263 , pp. 800
    • Martin, A.C.1    Thornton, J.M.2
  • 53
    • 0032568959 scopus 로고    scopus 로고
    • Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction
    • Oliva,B., Bates,P.A., Querol,E., Aviles,F.X. and Sternberg,M.J. (1998) Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction. J. Mol. Biol., 279, 1193.
    • (1998) J. Mol. Biol. , vol.279 , pp. 1193
    • Oliva, B.1    Bates, P.A.2    Querol, E.3    Aviles, F.X.4    Sternberg, M.J.5
  • 54
    • 0030767954 scopus 로고    scopus 로고
    • Creation and characterization of a new, non-redundant fragment data bank
    • Lessel,U. and Schomburg,D. (1997) Creation and characterization of a new, non-redundant fragment data bank. Protein Eng., 10, 659.
    • (1997) Protein Eng. , vol.10 , pp. 659
    • Lessel, U.1    Schomburg, D.2
  • 55
    • 0043268757 scopus 로고    scopus 로고
    • Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update
    • Du,P., Andrec,M. and Levy,R.M. (2003) Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. Protein Eng., 16, 407.
    • (2003) Protein Eng. , vol.16 , pp. 407
    • Du, P.1    Andrec, M.2    Levy, R.M.3
  • 56
    • 1442310610 scopus 로고    scopus 로고
    • Loops in proteins (LIP) - A comprehensive loop database for homology modelling
    • Michalsky,E., Goede,A. and Preissner,R. (2003) Loops in proteins (LIP) - a comprehensive loop database for homology modelling. Protein Eng., 16, 979.
    • (2003) Protein Eng. , vol.16 , pp. 979
    • Michalsky, E.1    Goede, A.2    Preissner, R.3
  • 57
    • 0024310232 scopus 로고
    • Modeling antibody hypervariable loops: A combined algorithm
    • Martin,A.C., Cheetham,J.C. and Rees,A.L. (1989) Modeling antibody hypervariable loops: A combined algorithm. PNAS., 86, 9268-9272.
    • (1989) PNAS , vol.86 , pp. 9268-9272
    • Martin, A.C.1    Cheetham, J.C.2    Rees, A.L.3
  • 59
    • 0034237227 scopus 로고    scopus 로고
    • A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins
    • Deane,C.M. and Blundell,T.L. (2000) A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins. Proteins, 40, 135-144.
    • (2000) Proteins , vol.40 , pp. 135-144
    • Deane, C.M.1    Blundell, T.L.2
  • 60
    • 0026557751 scopus 로고
    • Sequence alignment approach to pick up conformationally similar protein fragments
    • Kolaskar,A.S. and Kulkarni-Kale,U. (1992) Sequence alignment approach to pick up conformationally similar protein fragments. J. Mol. Biol., 223, 1053-1061.
    • (1992) J. Mol. Biol. , vol.223 , pp. 1053-1061
    • Kolaskar, A.S.1    Kulkarni-Kale, U.2
  • 61
    • 0036136694 scopus 로고    scopus 로고
    • Composites of local structure propensities: Evidence for local encoding of long-range structure
    • Shortle,D. (2002) Composites of local structure propensities: Evidence for local encoding of long-range structure. Protein Sci., 11, 18-26.
    • (2002) Protein Sci. , vol.11 , pp. 18-26
    • Shortle, D.1
  • 62
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 63
    • 0027207221 scopus 로고
    • Comparison of three algorithms for the assignment of secondary structure in proteins: The advantages of a consensus assignment
    • Colloc'h,N., Etchebest,C., Thoreau,E., Henrissat,B. and Mornon,J.P. (1993) Comparison of three algorithms for the assignment of secondary structure in proteins: The advantages of a consensus assignment. Protein Eng., 6, 377-382.
    • (1993) Protein Eng. , vol.6 , pp. 377-382
    • Colloc'h, N.1    Etchebest, C.2    Thoreau, E.3    Henrissat, B.4    Mornon, J.P.5
  • 64
    • 0042622443 scopus 로고    scopus 로고
    • DSSPcont: Continuous secondary structure assignments for proteins
    • Carter,P., Andersen,C.A. and Rost,B. (2003) DSSPcont: Continuous secondary structure assignments for proteins. Nucleic Acids Res., 31, 3293-3295.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3293-3295
    • Carter, P.1    Andersen, C.A.2    Rost, B.3
  • 65
    • 0033516705 scopus 로고    scopus 로고
    • The packing density in proteins: Standard radii and volumes
    • Tsai,J., Taylor,R., Chothia,C.and Gerstein,M. (1999)The packing density in proteins: Standard radii and volumes. J. Mol. Biol., 290, 253.
    • (1999) J. Mol. Biol. , vol.290 , pp. 253
    • Tsai, J.1    Taylor, R.2    Chothia, C.3    Gerstein, M.4
  • 66
    • 0025997601 scopus 로고
    • Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities
    • Luthy,R., McLachlan,A.D. and Eisenberg,D. (1991) Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins, 10, 229-239.
    • (1991) Proteins , vol.10 , pp. 229-239
    • Luthy, R.1    McLachlan, A.D.2    Eisenberg, D.3
  • 67
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA., 89, 10915-10919.
    • (1992) Proc. Natl Acad. Sci. USA. , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 68
    • 0027439391 scopus 로고
    • Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables
    • Topham,C.M., McLeod,A., Eisenmenger,F., Overington,J.P., Johnson,M.S. and Blundell,T.L. (1993) Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables. J. Mol. Biol., 229, 194.
    • (1993) J. Mol. Biol. , vol.229 , pp. 194
    • Topham, C.M.1    McLeod, A.2    Eisenmenger, F.3    Overington, J.P.4    Johnson, M.S.5    Blundell, T.L.6
  • 69
    • 0031470058 scopus 로고    scopus 로고
    • Interchanges of spatially neighbouring residues in structurally conserved environments
    • Azarya-Sprinzak,E., Naor,D., Wolfson,H.J. and Nussinov,R. (1997) Interchanges of spatially neighbouring residues in structurally conserved environments. Protein Eng., 10, 1109-1122.
    • (1997) Protein Eng. , vol.10 , pp. 1109-1122
    • Azarya-Sprinzak, E.1    Naor, D.2    Wolfson, H.J.3    Nussinov, R.4
  • 70
    • 0031564630 scopus 로고    scopus 로고
    • A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence
    • Rice,D.W. and Eisenberg,D. (1997) A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J. Mol. Biol., 267, 1026.
    • (1997) J. Mol. Biol. , vol.267 , pp. 1026
    • Rice, D.W.1    Eisenberg, D.2
  • 71
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • Shi,J., Blundell,T.L. and Mizuguchi,K. (2001) FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol., 310, 243.
    • (2001) J. Mol. Biol. , vol.310 , pp. 243
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 72
    • 0035937260 scopus 로고    scopus 로고
    • Pairwise sequence alignment below the twilight zone
    • Blake,J.D. and Cohen,F.E. (2001) Pairwise sequence alignment below the twilight zone. J. Mol. Biol., 307, 721.
    • (2001) J. Mol. Biol. , vol.307 , pp. 721
    • Blake, J.D.1    Cohen, F.E.2
  • 73
    • 0031455857 scopus 로고    scopus 로고
    • Beta-hairpins in proteins revisited: Lessons for de novo design
    • Gunasekaran,K., Ramakrishnan,C. and Balaram,P. (1997) Beta-hairpins in proteins revisited: Lessons for de novo design. Protein Eng., 10, 1131-1141.
    • (1997) Protein Eng. , vol.10 , pp. 1131-1141
    • Gunasekaran, K.1    Ramakrishnan, C.2    Balaram, P.3
  • 74
    • 0347385656 scopus 로고    scopus 로고
    • Statistical analysis of the loop-geometry on a non-redundant database of protein
    • Marti-Renom,M.A., Mas,J.M., Aloy,P., Querol,E., Aviles,F.X. and Oliva,B. (1998) Statistical analysis of the loop-geometry on a non-redundant database of protein. J. Mol. Model., 4, 347-354.
    • (1998) J. Mol. Model. , vol.4 , pp. 347-354
    • Marti-Renom, M.A.1    Mas, J.M.2    Aloy, P.3    Querol, E.4    Aviles, F.X.5    Oliva, B.6
  • 75
    • 1042279566 scopus 로고    scopus 로고
    • Efficient methods for filtering and ranking fragments for the prediction of structurally variable regions in proteins
    • Heuser,P., Wohlfahrt,G. and Schomburg,D. (2004) Efficient methods for filtering and ranking fragments for the prediction of structurally variable regions in proteins. Proteins, 54, 583-595.
    • (2004) Proteins , vol.54 , pp. 583-595
    • Heuser, P.1    Wohlfahrt, G.2    Schomburg, D.3
  • 76
    • 0346882663 scopus 로고    scopus 로고
    • ModLoop: Automated modeling of loops in protein structures
    • Fiser,A. and Sali,A. (2003) ModLoop: Automated modeling of loops in protein structures. Bioinformatics, 19, 2500.
    • (2003) Bioinformatics , vol.19 , pp. 2500
    • Fiser, A.1    Sali, A.2
  • 77
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123.
    • (1993) J. Mol. Biol. , vol.233 , pp. 123
    • Holm, L.1    Sander, C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.