메뉴 건너뛰기




Volumn 80, Issue 9, 2012, Pages 2305-2310

GSAFold: A new application of GSA to protein structure prediction

Author keywords

GSA; GSAFold; Mastoparan X; Molecular modeling; Protein folding

Indexed keywords

MASTOPARAN; MASTOPARAN X; UNCLASSIFIED DRUG;

EID: 84864409332     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24120     Document Type: Article
Times cited : (7)

References (45)
  • 3
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill KA. Dominant forces in protein folding. Biochemistry 1990; 29: 7133-7155.
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 4
    • 0348062818 scopus 로고    scopus 로고
    • The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models
    • Kopp J. The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res 2004; 32: 230D-234D.
    • (2004) Nucleic Acids Res , vol.32
    • Kopp, J.1
  • 5
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
    • Arnold K, Bordoli L, Kopp J, Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 2006; 22: 195-201.
    • (2006) Bioinformatics , vol.22 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 6
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie J, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991; 253: 164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.1    Luthy, R.2    Eisenberg, D.3
  • 7
    • 0027122748 scopus 로고
    • Proteins. One thousand families for the molecular biologist
    • Chothia C. Proteins. One thousand families for the molecular biologist. Nature 1992; 357: 543-544.
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 9
    • 13444273448 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt)
    • Database Issue
    • Bairoch A. The Universal Protein Resource (UniProt). Nucleic Acids Res 2004; 33(Database issue): D154-D159.
    • (2004) Nucleic Acids Res , vol.33
    • Bairoch, A.1
  • 10
    • 33645523756 scopus 로고    scopus 로고
    • A comparative study of available software for high accuracy homology modeling: from sequence alignments to structural models
    • Nayeem A, Sitkoff D, Krystek S, Jr. A comparative study of available software for high accuracy homology modeling: from sequence alignments to structural models. Protein Sci 2006; 15: 808-824.
    • (2006) Protein Sci , vol.15 , pp. 808-824
    • Nayeem, A.1    Sitkoff, D.2    Krystek Jr., S.3
  • 11
    • 41149134509 scopus 로고    scopus 로고
    • Sequence-similar, structure-dissimilar protein pairs in the PDB
    • Kosloff M, Kolodny R. Sequence-similar, structure-dissimilar protein pairs in the PDB. Proteins 2008; 71: 891-902.
    • (2008) Proteins , vol.71 , pp. 891-902
    • Kosloff, M.1    Kolodny, R.2
  • 12
    • 0007992814 scopus 로고    scopus 로고
    • Protein plasticity to the extreme: changing the topology of a 4-alpha-helical bundle with a single amino acid substitution
    • Glykos NM, Cesareni G, Kokkinidis M. Protein plasticity to the extreme: changing the topology of a 4-alpha-helical bundle with a single amino acid substitution. Structure 1999; 7: 597-603.
    • (1999) Structure , vol.7 , pp. 597-603
    • Glykos, N.M.1    Cesareni, G.2    Kokkinidis, M.3
  • 13
    • 1842337282 scopus 로고
    • Gene mutations in human haemoglobin: the chemical difference between normal and sickle cell haemoglobin
    • Ingram VM. Gene mutations in human haemoglobin: the chemical difference between normal and sickle cell haemoglobin. Nature 1957; 180: 326-328.
    • (1957) Nature , vol.180 , pp. 326-328
    • Ingram, V.M.1
  • 14
    • 3042681604 scopus 로고    scopus 로고
    • Protein tolerance to random amino acid change
    • Guo HH, Choe J, Loeb LA. Protein tolerance to random amino acid change. Proc Natl Acad Sci USA 2004; 101: 9205-9210.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 9205-9210
    • Guo, H.H.1    Choe, J.2    Loeb, L.A.3
  • 15
    • 0032568596 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    • Brenner SE, Chothia C, Hubbard TJP. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci USA 1998; 95: 6073-6078.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 6073-6078
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.P.3
  • 16
    • 33744478372 scopus 로고    scopus 로고
    • Statistical limits to the identification of ion channel domains by sequence similarity
    • Fodor AA, Aldrich RW. Statistical limits to the identification of ion channel domains by sequence similarity. J Gen Physiol 2006; 127: 755-766.
    • (2006) J Gen Physiol , vol.127 , pp. 755-766
    • Fodor, A.A.1    Aldrich, R.W.2
  • 19
    • 45949121309 scopus 로고
    • Fast simulated annealing
    • Szu H, Hartley R. Fast simulated annealing. Phys Lett A 1987; 122: 157-162.
    • (1987) Phys Lett A , vol.122 , pp. 157-162
    • Szu, H.1    Hartley, R.2
  • 21
    • 4244100012 scopus 로고    scopus 로고
    • Scaling behavior of stochastic minimization algorithms in a perfect funnel landscape
    • Hamacher K, Wenzel W. Scaling behavior of stochastic minimization algorithms in a perfect funnel landscape. Phys Rev E 1999; 59: 938-941.
    • (1999) Phys Rev E , vol.59 , pp. 938-941
    • Hamacher, K.1    Wenzel, W.2
  • 22
    • 52449087215 scopus 로고    scopus 로고
    • Atomic basis sets optimization using the generalized simulated annealing approach: new basis sets for the first row elements
    • Andrade MD De, Nascimento MAC, Mundim KC, Sobrinho AMC, Malbouisson LAC. Atomic basis sets optimization using the generalized simulated annealing approach: new basis sets for the first row elements. Int J Quantum Chem 2008; 108: 2486-2498.
    • (2008) Int J Quantum Chem , vol.108 , pp. 2486-2498
    • Andrade, M.D.1    Nascimento, M.A.C.2    Mundim, K.C.3    Sobrinho, A.M.C.4    Malbouisson, L.A.C.5
  • 23
    • 0032051222 scopus 로고    scopus 로고
    • Optimization of non-linear gravity models through generalized simulated annealing
    • Mundim K, Lemaire T, Bassrei A. Optimization of non-linear gravity models through generalized simulated annealing. Phys A: Stat Mech Appl 1998; 252: 405-416.
    • (1998) Phys A: Stat Mech Appl , vol.252 , pp. 405-416
    • Mundim, K.1    Lemaire, T.2    Bassrei, A.3
  • 24
    • 0001663232 scopus 로고    scopus 로고
    • Geometry optimization and conformational analysis through generalized simulated annealing
    • Mundim KC, Tsallis C. Geometry optimization and conformational analysis through generalized simulated annealing. Int J Quantum Chem 1996; 58: 373-381.
    • (1996) Int J Quantum Chem , vol.58 , pp. 373-381
    • Mundim, K.C.1    Tsallis, C.2
  • 27
    • 52449135129 scopus 로고    scopus 로고
    • Studies of molecular docking between fibroblast growth factor and heparin using generalized simulated annealing
    • Rocha Pita SS da, Fernandes TVA, Caffarena ER, Pascutti PG. Studies of molecular docking between fibroblast growth factor and heparin using generalized simulated annealing. Int J Quantum Chem 2008; 108: 2608-2614.
    • (2008) Int J Quantum Chem , vol.108 , pp. 2608-2614
    • Rocha Pita, S.d.1    Fernandes, T.V.A.2    Caffarena, E.R.3    Pascutti, P.G.4
  • 29
    • 33646516485 scopus 로고
    • Possible generalization of Boltzmann-Gibbs statistics
    • Tsallis C. Possible generalization of Boltzmann-Gibbs statistics. J Stat Phys 1988; 52: 479-487.
    • (1988) J Stat Phys , vol.52 , pp. 479-487
    • Tsallis, C.1
  • 30
    • 79960653151 scopus 로고    scopus 로고
    • Combined use of replica-exchange molecular dynamics and magic-angle-spinning solid-state NMR spectral simulations for determining the structure and orientation of membrane-bound peptide
    • Ikeda K, Kameda T, Harada E, Akutsu H, Fujiwara T. Combined use of replica-exchange molecular dynamics and magic-angle-spinning solid-state NMR spectral simulations for determining the structure and orientation of membrane-bound peptide. J Phys Chem B 2011; 115: 9327-9336.
    • (2011) J Phys Chem B , vol.115 , pp. 9327-9336
    • Ikeda, K.1    Kameda, T.2    Harada, E.3    Akutsu, H.4    Fujiwara, T.5
  • 31
    • 36849087359 scopus 로고    scopus 로고
    • Role of helix nucleation in the kinetics of binding of mastoparan X to phospholipid bilayers
    • Tang J, Signarvic RS, DeGrado WF, Gai F. Role of helix nucleation in the kinetics of binding of mastoparan X to phospholipid bilayers. Biochemistry 2007; 46: 13856-13863.
    • (2007) Biochemistry , vol.46 , pp. 13856-13863
    • Tang, J.1    Signarvic, R.S.2    DeGrado, W.F.3    Gai, F.4
  • 32
    • 38949129729 scopus 로고    scopus 로고
    • Characterization of the structure and dynamics of mastoparan-X during folding in aqueous TFE by CD and NMR spectroscopy
    • Crandall YM, Bruch MD. Characterization of the structure and dynamics of mastoparan-X during folding in aqueous TFE by CD and NMR spectroscopy. Biopolymers 2008; 89: 197-209.
    • (2008) Biopolymers , vol.89 , pp. 197-209
    • Crandall, Y.M.1    Bruch, M.D.2
  • 33
    • 33751191168 scopus 로고    scopus 로고
    • An exact D-dimensional Tsallis random number generator for generalized simulated annealing
    • Schanze T. An exact D-dimensional Tsallis random number generator for generalized simulated annealing. Comput Phys Commun 2006; 175: 708-712.
    • (2006) Comput Phys Commun , vol.175 , pp. 708-712
    • Schanze, T.1
  • 34
    • 3042713195 scopus 로고    scopus 로고
    • Urbana, IL: Theoretical biophysics group, University of Illinois at Urbana-Champaign
    • Gullingsrud J, Saam J, Phillips J. PSFGEN user's guide. Urbana, IL: Theoretical biophysics group, University of Illinois at Urbana-Champaign; 2002.
    • (2002) PSFGEN user's guide
    • Gullingsrud, J.1    Saam, J.2    Phillips, J.3
  • 36
    • 0032492664 scopus 로고    scopus 로고
    • G protein-bound conformation of mastoparan-X: heteronuclear multidimensional transferred nuclear Overhauser effect analysis of peptide uniformly enriched with 13C and 15N
    • Kusunoki H, Wakamatsu K, Sato K, Miyazawa T, Kohno T. G protein-bound conformation of mastoparan-X: heteronuclear multidimensional transferred nuclear Overhauser effect analysis of peptide uniformly enriched with 13C and 15N. Biochemistry 1998; 37: 4782-4790.
    • (1998) Biochemistry , vol.37 , pp. 4782-4790
    • Kusunoki, H.1    Wakamatsu, K.2    Sato, K.3    Miyazawa, T.4    Kohno, T.5
  • 38
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • MacKerell AD, Feig M, Brooks CL. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 2004; 25: 1400-1415.
    • (2004) J Comput Chem , vol.25 , pp. 1400-1415
    • MacKerell, A.D.1    Feig, M.2    Brooks, C.L.3
  • 39
    • 0003042571 scopus 로고    scopus 로고
    • Is re-association in folded proteins a case of nonextensivity?
    • Tsallis C, Bemski G, Mendes RS. Is re-association in folded proteins a case of nonextensivity? Phys Lett A 1999; 257: 93-98.
    • (1999) Phys Lett A , vol.257 , pp. 93-98
    • Tsallis, C.1    Bemski, G.2    Mendes, R.S.3
  • 40
    • 0000932767 scopus 로고    scopus 로고
    • Stochastic molecular optimization using generalized simulated annealing
    • Moret MA, Pascutti PG, Bisch PM, Mundim KC. Stochastic molecular optimization using generalized simulated annealing. J Comput Chem 1998; 19: 647-657.
    • (1998) J Comput Chem , vol.19 , pp. 647-657
    • Moret, M.A.1    Pascutti, P.G.2    Bisch, P.M.3    Mundim, K.C.4
  • 41
    • 0026876981 scopus 로고
    • A parallel Monte Carlo search algorithm for the conformational analysis of polypeptides
    • Ripoll DR, Thomas SJ. A parallel Monte Carlo search algorithm for the conformational analysis of polypeptides. J Supercomput 1992; 6: 163-185.
    • (1992) J Supercomput , vol.6 , pp. 163-185
    • Ripoll, D.R.1    Thomas, S.J.2
  • 42
    • 36849087359 scopus 로고    scopus 로고
    • Role of helix nucleation in the kinetics of binding of mastoparan X to phospholipid bilayers
    • Tang J, Signarvic RS, DeGrado WF, Gai F. Role of helix nucleation in the kinetics of binding of mastoparan X to phospholipid bilayers. Biochemistry 2007; 46: 13856-13863.
    • (2007) Biochemistry , vol.46 , pp. 13856-13863
    • Tang, J.1    Signarvic, R.S.2    DeGrado, W.F.3    Gai, F.4
  • 43
    • 52449087215 scopus 로고    scopus 로고
    • Atomic basis set optimization using the generalized simulated annealing approach: new basis sets for the first row elements
    • De Andrade MD, Nascimento MAC, Mundim KC, Sobrinho AMC, Malbouisson LAC. Atomic basis set optimization using the generalized simulated annealing approach: new basis sets for the first row elements. Int J Quantum Chem 2008; 108: 2486-2498.
    • (2008) Int J Quantum Chem , vol.108 , pp. 2486-2498
    • De Andrade, M.D.1    Nascimento, M.A.C.2    Mundim, K.C.3    Sobrinho, A.M.C.4    Malbouisson, L.A.C.5
  • 44
    • 52449135129 scopus 로고    scopus 로고
    • Studies of molecular docking between fibroblast growth factor and heparin using generalized simulated annealing
    • Pita SSR, Fernandes TVA, Caffarena ER, Pascutti PG. Studies of molecular docking between fibroblast growth factor and heparin using generalized simulated annealing. Int J Quantum Chem 2008; 108: 2608-2614.
    • (2008) Int J Quantum Chem , vol.108 , pp. 2608-2614
    • Pita, S.S.R.1    Fernandes, T.V.A.2    Caffarena, E.R.3    Pascutti, P.G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.