메뉴 건너뛰기




Volumn 3, Issue 5, 1998, Pages 379-388

Empirical modifications to the Amber/OPLS potential for predicting the solution conformations of cyclic peptides by vacuum calculations

Author keywords

Cyclic peptides; Empirical potential; Structure prediction

Indexed keywords

AMINO ACID; CYCLOPEPTIDE; HYDROGEN; PROLINE;

EID: 0031757623     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(98)00051-0     Document Type: Article
Times cited : (8)

References (20)
  • 1
    • 0019958979 scopus 로고
    • Conformational restrictions of biologically active peptides via amino acid sidechain groups
    • Hruby, V.J. (1982). Conformational restrictions of biologically active peptides via amino acid sidechain groups. Life Sci. 31, 189-199.
    • (1982) Life Sci. , vol.31 , pp. 189-199
    • Hruby, V.J.1
  • 2
    • 0019862208 scopus 로고
    • A potent cyclic hexapeptide analog of somatostatin
    • Veber, D.F., et al., & Hirschmann, R. (1981). A potent cyclic hexapeptide analog of somatostatin. Nature 292, 55-58.
    • (1981) Nature , vol.292 , pp. 55-58
    • Veber, D.F.1    Hirschmann, R.2
  • 3
    • 0025606733 scopus 로고
    • Design of biologically active conformationally constrained GnRH antagonists
    • Stuthers, R.S., et al., & Hagler, A.T. (1990). Design of biologically active conformationally constrained GnRH antagonists. Proteins 8, 295-304.
    • (1990) Proteins , vol.8 , pp. 295-304
    • Stuthers, R.S.1    Hagler, A.T.2
  • 4
    • 0024285003 scopus 로고
    • Theoretical studies of the structure and molecular dynamics of a peptide crystal
    • Kitson, D.H. & Hagler, A.T. (1988). Theoretical studies of the structure and molecular dynamics of a peptide crystal. Biochemistry 27, 5246-5257.
    • (1988) Biochemistry , vol.27 , pp. 5246-5257
    • Kitson, D.H.1    Hagler, A.T.2
  • 5
    • 0028150192 scopus 로고
    • Hydrophobic "collapse" in a cyclic hexapeptide: Computer simulations of CHDLFC and CAAAAC in water
    • Simmerling, C. & Elber, R. (1994). Hydrophobic "collapse" in a cyclic hexapeptide: Computer simulations of CHDLFC and CAAAAC in water. J. Am. Chem. Soc. 116, 2534-2547.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 2534-2547
    • Simmerling, C.1    Elber, R.2
  • 6
    • 0025974617 scopus 로고
    • Simulation of the structure and dynamics of the bis(penicillamine) enkephalin zwitterion
    • Smith, P.E., Dang, L.X. & Pettitt, B.M. (1990). Simulation of the structure and dynamics of the bis(penicillamine) enkephalin zwitterion. J. Am. Chem. Soc. 113, 67-73.
    • (1990) J. Am. Chem. Soc. , vol.113 , pp. 67-73
    • Smith, P.E.1    Dang, L.X.2    Pettitt, B.M.3
  • 7
    • 33645941402 scopus 로고
    • The OPLS potential function for proteins. Energy minimization of cyclic peptides and crambin
    • Jorgensen, W.L. & Tirado-Rives, J. (1988). The OPLS potential function for proteins. Energy minimization of cyclic peptides and crambin. J. Am. Chem. Soc. 110, 1657-1666.
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 1657-1666
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 8
    • 0021757436 scopus 로고
    • A new force field for molecular mechanical simulation of nucleic acids and proteins
    • Wiener, S.J., et al., & Weiner, P. (1984). A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-772.
    • (1984) J. Am. Chem. Soc. , vol.106 , pp. 765-772
    • Wiener, S.J.1    Weiner, P.2
  • 10
    • 0026055156 scopus 로고
    • Analysis of the steric strain in the polypeptide backbone of protein molecules
    • Herzberg O. & Moult J. (1991). Analysis of the steric strain in the polypeptide backbone of protein molecules. Proteins 11, 223-229.
    • (1991) Proteins , vol.11 , pp. 223-229
    • Herzberg, O.1    Moult, J.2
  • 11
    • 0029633178 scopus 로고
    • MOIL: A program for simulations of macromolecules
    • Elber, R., et al., & Ulitski, A. (1995). MOIL: a program for simulations of macromolecules. Comput. Phys. Commun. 91, 159-189.
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 159-189
    • Elber, R.1    Ulitski, A.2
  • 12
    • 0031587288 scopus 로고    scopus 로고
    • Kinetics of peptide folding: Computer simulations of SYPFDV and peptide variants in water
    • Mohanty, D., Elber, R., Thirumalai, D., Beglov, D. & Roux, B. (1997). Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J. Mol. Biol. 272, 423-442.
    • (1997) J. Mol. Biol. , vol.272 , pp. 423-442
    • Mohanty, D.1    Elber, R.2    Thirumalai, D.3    Beglov, D.4    Roux, B.5
  • 13
    • 0030596007 scopus 로고    scopus 로고
    • Deviations from planarity of the peptide bond in peptides and proteins
    • MacArthur, M.W. & Thomton, J.M. (1996). Deviations from planarity of the peptide bond in peptides and proteins. J. Mol. Biol. 264, 1180-1195.
    • (1996) J. Mol. Biol. , vol.264 , pp. 1180-1195
    • MacArthur, M.W.1    Thomton, J.M.2
  • 14
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick, K.S., Gelatt, C.D. & Vecchi, M.P. (1983). Optimization by simulated annealing. Science, 220, 671-675.
    • (1983) Science , vol.220 , pp. 671-675
    • Kirkpatrick, K.S.1    Gelatt, C.D.2    Vecchi, M.P.3
  • 16
    • 15644375594 scopus 로고    scopus 로고
    • A backbone-cyclic, receptor 5-selective somatostatin analog: Synthesis, bioactivity, and nuclear magnetic resonance conformational analysis
    • Gilon C., et al., & Kessler H. (1998). A backbone-cyclic, receptor 5-selective somatostatin analog: synthesis, bioactivity, and nuclear magnetic resonance conformational analysis. J. Med. Chem. 41, 919-929.
    • (1998) J. Med. Chem. , vol.41 , pp. 919-929
    • Gilon, C.1    Kessler, H.2
  • 17
    • 0028340334 scopus 로고
    • Comparison of the conformation of active and non-active backbone cyclic analogs of substance P as a tool to elucidate features of the bioactive conformation: NMR and molecular dynamics in DMSO and water
    • Grdadolink, S.G., Mierke, D.F., Byk, G. Zeltser, I., Gilon, C. & Kessler, H. (1994). Comparison of the conformation of active and non-active backbone cyclic analogs of substance P as a tool to elucidate features of the bioactive conformation: NMR and molecular dynamics in DMSO and water. J. Med. Chem. 37, 2145-2152.
    • (1994) J. Med. Chem. , vol.37 , pp. 2145-2152
    • Grdadolink, S.G.1    Mierke, D.F.2    Byk, G.3    Zeltser, I.4    Gilon, C.5    Kessler, H.6
  • 18
    • 0029742128 scopus 로고    scopus 로고
    • NMR and X-ray crystallographic studies on cyclic tetrapeptide, cyclo(D-Phe-Pro-Sar-Gly)
    • Jois, D.S.S., Suresh, S., Vijayan, V. & Easwaran, K.R.K. (1996). NMR and X-ray crystallographic studies on cyclic tetrapeptide, cyclo(D-Phe-Pro-Sar-Gly). Int. J. Peptide Prot. Res. 48, 12-20.
    • (1996) Int. J. Peptide Prot. Res. , vol.48 , pp. 12-20
    • Jois, D.S.S.1    Suresh, S.2    Vijayan, V.3    Easwaran, K.R.K.4
  • 19
    • 0030028449 scopus 로고    scopus 로고
    • Conformational analysis of cyclic hexapeptides designed as constrained ligands for the SH2 domain of the p85 subunit of phosphatidylinositol-3-OH Kinase
    • Barchi, J.J., Nomizu, M., Otaka, A., Roller, P.P., Burke, T.R. (1996) Conformational analysis of cyclic hexapeptides designed as constrained ligands for the SH2 domain of the p85 subunit of phosphatidylinositol-3-OH Kinase. Biopolymers 38, 191-208.
    • (1996) Biopolymers , vol.38 , pp. 191-208
    • Barchi, J.J.1    Nomizu, M.2    Otaka, A.3    Roller, P.P.4    Burke, T.R.5
  • 20
    • 0030424261 scopus 로고    scopus 로고
    • Solution and solid state structure of an AIB containing cyclodecapeptide inhibiting the cholate uptake in hepatocytes
    • Rossi, F., et al., & Benedetti, E. (1997) Solution and solid state structure of an AIB containing cyclodecapeptide inhibiting the cholate uptake in hepatocytes. Biopolymers 40, 465-478.
    • (1997) Biopolymers , vol.40 , pp. 465-478
    • Rossi, F.1    Benedetti, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.