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Volumn 11, Issue 1, 2004, Pages 83-106

FlexProt: Alignment of flexible protein structures without a predefinition of hinge regions

Author keywords

Efficient algorithm; Flexible structural comparison; Hinge detection; Hinge bending; Protein structural alignment; Structural comparison

Indexed keywords

FLEXIBLE PROTEIN; PEPTIDE FRAGMENT; PROTEIN; UNCLASSIFIED DRUG;

EID: 1842450688     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652704773416902     Document Type: Article
Times cited : (59)

References (40)
  • 1
    • 0030464952 scopus 로고    scopus 로고
    • Detection of non-topological motifs in protein structures
    • Alesker, V., Nussinov, R., and Wolfson, H. 1996. Detection of non-topological motifs in protein structures. Protein Eng. 9, 1103-1119.
    • (1996) Protein Eng. , vol.9 , pp. 1103-1119
    • Alesker, V.1    Nussinov, R.2    Wolfson, H.3
  • 4
    • 0028958868 scopus 로고
    • Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics
    • Collins, J.R., Burt, S.K., and Erickson, J.W. 1995. Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics. Nat. Struct. Biol. 2, 334-338.
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 334-338
    • Collins, J.R.1    Burt, S.K.2    Erickson, J.W.3
  • 6
    • 0034531045 scopus 로고    scopus 로고
    • Structure comparison and structure pattern
    • Eidhammer, I., Jonassen, I., and Taylor, W.R. 2001. Structure comparison and structure pattern. J. Comp. Biol. 7, 685-716.
    • (2001) J. Comp. Biol. , vol.7 , pp. 685-716
    • Eidhammer, I.1    Jonassen, I.2    Taylor, W.R.3
  • 8
    • 84969049944 scopus 로고
    • 3-d substructure matching in protein molecules
    • Tucson, Arizona, Springer Verlag, Lecture Notes in Computer Science, 644
    • Fischer, D., Nussinov, R., and Wolfson, H. 1992. 3-d substructure matching in protein molecules, in Third Symp. on Combinatorial Pattern Matching, 136-150, Tucson, Arizona, Springer Verlag, Lecture Notes in Computer Science, 644.
    • (1992) Third Symp. on Combinatorial Pattern Matching , pp. 136-150
    • Fischer, D.1    Nussinov, R.2    Wolfson, H.3
  • 9
    • 0032530836 scopus 로고    scopus 로고
    • A database of macromolecular motions
    • bioinfo.mbb.yale.edu/MolMovDB/
    • Gerstein, M., and Krebs, W. 1998. A database of macromolecular motions. Nucl. Acids Res. 26, 4280-4290. bioinfo. mbb.yale.edu/MolMovDB/.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 4280-4290
    • Gerstein, M.1    Krebs, W.2
  • 10
    • 0028335096 scopus 로고
    • Structural mechanisms for domain movements in proteins
    • Gerstein, M., Lesk, A.M., and Chothia, C. 1994. Structural mechanisms for domain movements in proteins. Biochemistry 33, 6739-6749.
    • (1994) Biochemistry , vol.33 , pp. 6739-6749
    • Gerstein, M.1    Lesk, A.M.2    Chothia, C.3
  • 12
    • 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, 123-138.
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 13
    • 0032919371 scopus 로고    scopus 로고
    • Protein folds and families: Sequence and structure alignments
    • Holm, L., and Sander, C. 1999. Protein folds and families: Sequence and structure alignments. Nucl. Acids Res. 27, 244-247.
    • (1999) Nucl. Acids Res. , vol.27 , pp. 244-247
    • Holm, L.1    Sander, C.2
  • 14
    • 84975553202 scopus 로고
    • Closed form solution of absolute orientation using unit quaternions
    • Horn, B.K.P. 1987. Closed form solution of absolute orientation using unit quaternions. J. Optical Society A, 4(4), 629-642.
    • (1987) J. Optical Society A , vol.4 , Issue.4 , pp. 629-642
    • Horn, B.K.P.1
  • 15
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch, W. 1978. A solution for the best rotation to relate two sets of vectors. Acta Crystal A32, 922-923.
    • (1978) Acta Crystal , vol.A32 , pp. 922-923
    • Kabsch, W.1
  • 16
    • 0034029144 scopus 로고    scopus 로고
    • Proteins with similar architecture exhibit similar large-scale dynamic behavior
    • Keskin, O., Jernigan, R.L., and Bahar, I. 2000. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys. J. 78, 2093-2106.
    • (2000) Biophys. J. , vol.78 , pp. 2093-2106
    • Keskin, O.1    Jernigan, R.L.2    Bahar, I.3
  • 18
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: Dynamic landscapes and population shifts
    • Kumar, S., Ma, B., Tsai, C. -J., Sinha, N., and Nussinov, R. 2000. Folding and binding cascades: Dynamic landscapes and population shifts. Protein Sci. 9, 10-19.
    • (2000) Protein Sci. , vol.9 , pp. 10-19
    • Kumar, S.1    Ma, B.2    Tsai, C.J.3    Sinha, N.4    Nussinov, R.5
  • 19
    • 0031670902 scopus 로고    scopus 로고
    • Conformational switching in an aspartic proteinase
    • Lee, A.Y., Gulnik, S.V., and Erickson, J.W. 1998. Conformational switching in an aspartic proteinase. Nat. Struc. Biol. 5, 866-871.
    • (1998) Nat. Struc. Biol. , vol.5 , pp. 866-871
    • Lee, A.Y.1    Gulnik, S.V.2    Erickson, J.W.3
  • 20
    • 0034924161 scopus 로고    scopus 로고
    • MUSTA: A general, efficient automated method for multiple structure alignment and detection of a common motif
    • Leibowitz, N., Nussinov, R., and Wolfson, H.J. 2001. MUSTA: A general, efficient automated method for multiple structure alignment and detection of a common motif. J. Comp. Biol. 8, 93-121.
    • (2001) J. Comp. Biol. , vol.8 , pp. 93-121
    • Leibowitz, N.1    Nussinov, R.2    Wolfson, H.J.3
  • 21
    • 0034065350 scopus 로고    scopus 로고
    • Computational methods for structural alignment of molecules
    • Lemmen, C., and Lengauer, T. 2000. Computational methods for structural alignment of molecules. J. Computer-Aided Mol. Design 14, 215-232.
    • (2000) J. Computer-Aided Mol. Design , vol.14 , pp. 215-232
    • Lemmen, C.1    Lengauer, T.2
  • 22
    • 0032824805 scopus 로고    scopus 로고
    • Folding funnels and binding mechanisms
    • Ma, B., Kumar, S., Tsai, C.-J., and Nussinov, R. 1999. Folding funnels and binding mechanisms. Protein Eng. 12, 713-720.
    • (1999) Protein Eng. , vol.12 , pp. 713-720
    • Ma, B.1    Kumar, S.2    Tsai, C.-J.3    Nussinov, R.4
  • 24
    • 0030939896 scopus 로고    scopus 로고
    • A new method for modeling large-scale rearrangements of protein domains
    • Maiorov, V., and Abagian R. 1997. A new method for modeling large-scale rearrangements of protein domains. Proteins 27, 410-424.
    • (1997) Proteins , vol.27 , pp. 410-424
    • Maiorov, V.1    Abagian, R.2
  • 25
    • 0022272122 scopus 로고
    • Comparison of protein structures
    • Matthews, B.W., and Rossman, M.G. 1985. Comparison of protein structures. Methods Enzymol., 115, 397-420.
    • (1985) Methods Enzymol. , vol.115 , pp. 397-420
    • Matthews, B.W.1    Rossman, M.G.2
  • 27
    • 0031837984 scopus 로고    scopus 로고
    • Hinge bending within the cytokine receptor superfamily revealed by the 2.4Å crystal structure of the extracellular domain of the rabbit tissue factor
    • Muller, Y., Kelley, R.F., and De Vos, A.M. 1998. Hinge bending within the cytokine receptor superfamily revealed by the 2.4Å crystal structure of the extracellular domain of the rabbit tissue factor. Protein Sci. 7, 1106-1115.
    • (1998) Protein Sci. , vol.7 , pp. 1106-1115
    • Muller, Y.1    Kelley, R.F.2    De Vos, A.M.3
  • 28
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 30
    • 1842422157 scopus 로고    scopus 로고
    • Flexible 3D-substructure matching and novel conformer derivation in very large databases of 3D-molecular information
    • T.J. Watson Research Center, Yorktown Heights, NY
    • Rigoutsos, I., Platt, D., and Califano, A. 1996. Flexible 3D-substructure matching and novel conformer derivation in very large databases of 3D-molecular information, IBM Research Division, T.J. Watson Research Center, Yorktown Heights, NY
    • (1996) IBM Research Division
    • Rigoutsos, I.1    Platt, D.2    Califano, A.3
  • 31
    • 0032562224 scopus 로고    scopus 로고
    • Domain flexibility in retroviral proteases: Structural implications for drug resistant mutations
    • Rose, R.B., Craik, C.S., and Stroud, R.M. 1998. Domain flexibility in retroviral proteases: Structural implications for drug resistant mutations. Biochemistry 37, 2607-2621.
    • (1998) Biochemistry , vol.37 , pp. 2607-2621
    • Rose, R.B.1    Craik, C.S.2    Stroud, R.M.3
  • 32
    • 0024438910 scopus 로고
    • High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligomer inhibitor: The analysis of the inhibitor binding and description of the rigid body shift in the enzyme
    • Sali, A., Cooper, J.B., Foundling, S.I., Hoover, D.J., and Blundell, T.L. 1989. High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligomer inhibitor: The analysis of the inhibitor binding and description of the rigid body shift in the enzyme. EMBO J. 8, 2179-2188.
    • (1989) EMBO J. , vol.8 , pp. 2179-2188
    • Sali, A.1    Cooper, J.B.2    Foundling, S.I.3    Hoover, D.J.4    Blundell, T.L.5
  • 33
    • 0023364263 scopus 로고
    • Identification of partially obscured objects in two dimensions by matching of noisy characteristic curves
    • Schwartz, J.T., and Sharir, M. 1987. Identification of partially obscured objects in two dimensions by matching of noisy characteristic curves. Int. J. Robotics Res. 6, 29-44.
    • (1987) Int. J. Robotics Res. , vol.6 , pp. 29-44
    • Schwartz, J.T.1    Sharir, M.2
  • 37
    • 0025744920 scopus 로고
    • Detection of common three dimensional substructures in proteins
    • Vriend, G., and Sander, C. 1991. Detection of common three dimensional substructures in proteins. Proteins: Struct., Funct., and Genetics 11, 52-58.
    • (1991) Proteins: Struct., Funct., and Genetics , vol.11 , pp. 52-58
    • Vriend, G.1    Sander, C.2
  • 38
    • 37249044407 scopus 로고
    • Model based object recognition by 'Geometric Hashing'
    • Springer Verlag, Lecture Notes in Computer Science 427
    • Wolfson, H.J. 1990. Model based object recognition by 'Geometric Hashing'. Proc. European Conf. on Computer Vision, 526-536, Springer Verlag, Lecture Notes in Computer Science 427.
    • (1990) Proc. European Conf. on Computer Vision , pp. 526-536
    • Wolfson, H.J.1
  • 39
    • 0026301147 scopus 로고
    • Generalizing the generalized Hough transform
    • Wolfson, H.J. 1991. Generalizing the generalized Hough transform. Pattern Recognition Lett. 12, 565-573.
    • (1991) Pattern Recognition Lett. , vol.12 , pp. 565-573
    • Wolfson, H.J.1
  • 40
    • 0030883755 scopus 로고    scopus 로고
    • Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates
    • Wriggers, W., and Schulten, K. 1997. Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins: Struct., Funct., and Genetics 29, 1-14.
    • (1997) Proteins: Struct., Funct., and Genetics , vol.29 , pp. 1-14
    • Wriggers, W.1    Schulten, K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.