메뉴 건너뛰기




Volumn 29, Issue SUPPL. 1, 1997, Pages 29-37

Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search

Author keywords

Deformation zones; Homology modeling; Prediction map building

Indexed keywords

ARTICLE; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; CHEMICAL STRUCTURE; PEPTIDE MAPPING; PROTEIN CONFORMATION; REPRODUCIBILITY;

EID: 0031296786     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(1997)1+<29::AID-PROT5>3.0.CO;2-J     Document Type: Article
Times cited : (71)

References (24)
  • 1
    • 0022701772 scopus 로고
    • Using known substructures in protein model building and crystallography
    • Jones, T.A., Thirup, S. Using known substructures in protein model building and crystallography. EMBO J. 5:819-822, 1986.
    • (1986) EMBO J. , vol.5 , pp. 819-822
    • Jones, T.A.1    Thirup, S.2
  • 2
    • 0023278330 scopus 로고
    • Canonical structures for the hypervariable regions of immunoglobulins
    • Chothia, C., Lesk, A.M. Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196:901-917, 1987.
    • (1987) J. Mol. Biol. , vol.196 , pp. 901-917
    • Chothia, C.1    Lesk, A.M.2
  • 3
    • 0024287213 scopus 로고
    • Knowledge-based protein modelling and design
    • Blundell, T., Carney, D., Gardner, S., et al. Knowledge-based protein modelling and design. Eur. J. Biochem. 172:513-520, 1988.
    • (1988) Eur. J. Biochem. , vol.172 , pp. 513-520
    • Blundell, T.1    Carney, D.2    Gardner, S.3
  • 4
    • 0026754015 scopus 로고
    • Accurate modeling of protein conformation by automatic segment matching
    • Levitt, M. Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol. 226:507-533, 1992.
    • (1992) J. Mol. Biol. , vol.226 , pp. 507-533
    • Levitt, M.1
  • 5
    • 0022788691 scopus 로고
    • An algorithm for determining the conformation of polypeptide segments in proteins by systematic search
    • Moult, J., James, M.N.G. An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins 1:146-163, 1986.
    • (1986) Proteins , vol.1 , pp. 146-163
    • Moult, J.1    James, M.N.G.2
  • 6
    • 0023173201 scopus 로고
    • Prediction of the folding of short polypeptide segments by uniform conformational sampling
    • Bruccoleri, R.E., Karplus, M. Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 26:137-168, 1987.
    • (1987) Biopolymers , vol.26 , pp. 137-168
    • Bruccoleri, R.E.1    Karplus, M.2
  • 7
    • 0023807627 scopus 로고
    • Structure of antibody hypervariable loops reproduced by a conformational search algorithm
    • Bruccoleri, R.E., Haber, E., Novotny, J. Structure of antibody hypervariable loops reproduced by a conformational search algorithm. Nature 335:564-568, 1988.
    • (1988) Nature , vol.335 , pp. 564-568
    • Bruccoleri, R.E.1    Haber, E.2    Novotny, J.3
  • 8
    • 0027146064 scopus 로고
    • The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: The correct modeling of an eight-residue loop
    • Borchert, T.V., Abagyan, R.A., Kishan, K.V.R., Zeelen, J.Ph., Wierenga, R.K. The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: The correct modeling of an eight-residue loop. Structure 1:205-213, 1993.
    • (1993) Structure , vol.1 , pp. 205-213
    • Borchert, T.V.1    Abagyan, R.A.2    Kishan, K.V.R.3    Zeelen, J.Ph.4    Wierenga, R.K.5
  • 9
    • 0028849881 scopus 로고
    • Homology modeling by the ICM method
    • Cardozo, T., Totrov, M., Abagyan, R. Homology modeling by the ICM method. Proteins 23:403-414, 1995.
    • (1995) Proteins , vol.23 , pp. 403-414
    • Cardozo, T.1    Totrov, M.2    Abagyan, R.3
  • 10
    • 0001290941 scopus 로고
    • Conformational energy calculations on polypeptide and proteins
    • Vasquez, M., Nemethy, G., Scheraga, H.A. Conformational energy calculations on polypeptide and proteins. Chem. Rev. 94:2183-2239, 1994.
    • (1994) Chem. Rev. , vol.94 , pp. 2183-2239
    • Vasquez, M.1    Nemethy, G.2    Scheraga, H.A.3
  • 11
    • 0024609784 scopus 로고
    • New methodology for computer-aided modelling of biomolecular structure and dynamics. I. Non-cyclic structures
    • Mazur, A.K., Abagyan, R.A. New methodology for computer-aided modelling of biomolecular structure and dynamics. I. Non-cyclic structures. J. Biomol. Struct. Dyn. 6:815-832, 1989.
    • (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 815-832
    • Mazur, A.K.1    Abagyan, R.A.2
  • 12
    • 0024609825 scopus 로고
    • New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles
    • Abagyan, R.A., Mazur, A.K. New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles. J. Biomol. Struct. Dyn. 6:833-845, 1989.
    • (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 833-845
    • Abagyan, R.A.1    Mazur, A.K.2
  • 13
    • 84986522918 scopus 로고
    • ICM: A new method for structure modeling and design - Applications to docking and structure prediction from the distorted native conformation
    • Abagyan, R.A., Totrov, M.M., Kuznetsov, D.A. ICM: A new method for structure modeling and design - Applications to docking and structure prediction from the distorted native conformation. J. Comp. Chem. 15:488-506, 1994.
    • (1994) J. Comp. Chem. , vol.15 , pp. 488-506
    • Abagyan, R.A.1    Totrov, M.M.2    Kuznetsov, D.A.3
  • 14
    • 0027955787 scopus 로고
    • Biased Probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • Abagyan, R.A., Totrov, M.M. Biased Probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235:983-1002, 1994.
    • (1994) J. Mol. Biol. , vol.235 , pp. 983-1002
    • Abagyan, R.A.1    Totrov, M.M.2
  • 15
    • 0031054817 scopus 로고    scopus 로고
    • Protein engineering with monomeric triosephosphate isomerase (monoTIM): The modelling and structure verification of a seven residue loop
    • Thanki, N., Zeelen, J.Ph., Mathieu, M., Jaenicke, R., Abagyan, R.A., Wierenga, R.K., Schliebs, W. Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven residue loop. Protein Eng. 10:159-167, 1997.
    • (1997) Protein Eng. , vol.10 , pp. 159-167
    • Thanki, N.1    Zeelen, J.Ph.2    Mathieu, M.3    Jaenicke, R.4    Abagyan, R.A.5    Wierenga, R.K.6    Schliebs, W.7
  • 16
    • 0030053370 scopus 로고    scopus 로고
    • ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling
    • Peitsch, M.C. ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. Biochem. Soc. Trans. 24:274-279, 1996.
    • (1996) Biochem. Soc. Trans. , vol.24 , pp. 274-279
    • Peitsch, M.C.1
  • 17
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S., Henikoff, J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 89:10915-10919, 1992.
    • (1992) Proc. Natl. Acad. Sci. U.S.A. , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 18
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman, S.B., Wunsch, C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443-453, 1970.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 19
    • 0031576355 scopus 로고    scopus 로고
    • Do aligned sequences share the same fold?
    • Abagyan, R.A., Batalov, S.V. Do aligned sequences share the same fold? J. Mol. Biol. 273:355-368, 1997.
    • (1997) J. Mol. Biol. , vol.273 , pp. 355-368
    • Abagyan, R.A.1    Batalov, S.V.2
  • 20
    • 84995046262 scopus 로고
    • A large-scale experiment to assess protein structure prediction methods
    • Moult, J., Judson, R., Fidelis, K. A, Pedersen, J. T. A large-scale experiment to assess protein structure prediction methods. Proteins 23:ii-iv, 1995.
    • (1995) Proteins , vol.23
    • Moult, J.1    Judson, R.2    Fidelis, K.A.3    Pedersen, J.T.4
  • 21
    • 0028864205 scopus 로고
    • A critical assessment of comparative molecular modeling of tertiary structures of proteins
    • Mosimann, S., Meleshko, R., James, M.N.G. A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins 23:301-317, 1995.
    • (1995) Proteins , vol.23 , pp. 301-317
    • Mosimann, S.1    Meleshko, R.2    James, M.N.G.3
  • 22
    • 0031560777 scopus 로고    scopus 로고
    • Contact Area Difference (CAD): A robust measure to evaluate accuracy of protein models
    • Abagyan, R.A., Totrov, M. Contact Area Difference (CAD): A robust measure to evaluate accuracy of protein models. J. Mol. Biol. 268:678-685, 1997.
    • (1997) J. Mol. Biol. , vol.268 , pp. 678-685
    • Abagyan, R.A.1    Totrov, M.2
  • 24
    • 0025398721 scopus 로고
    • WHAT IF: A molecular modeling and drug design program
    • Vriend, G. WHAT IF: A molecular modeling and drug design program. J. Mol. Graphics 8:52-56, 1990.
    • (1990) J. Mol. Graphics , vol.8 , pp. 52-56
    • Vriend, G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.