메뉴 건너뛰기




Volumn 49, Issue , 2012, Pages 127-140

A new approach for investigating protein flexibility based on Constraint Logic Programming. The first application in the case of the estrogen receptor

Author keywords

C.L.P.; Estrogen receptor; Protein flexibility; Protein folding

Indexed keywords

17ALPHA ESTRADIOL; AFIMOXIFENE; ESTROGEN RECEPTOR; ESTROGEN RECEPTOR ALPHA; N BUTYL 11 (3,17BETA DIHYDROXYESTRA 1,3,5(10) TRIEN 7ALPHA YL) N METHYLUNDECANAMIDE;

EID: 84857234772     PISSN: 02235234     EISSN: 17683254     Source Type: Journal    
DOI: 10.1016/j.ejmech.2012.01.003     Document Type: Article
Times cited : (4)

References (72)
  • 2
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic personalities of proteins
    • DOI 10.1038/nature06522, PII NATURE06522
    • K. Henzler-Wildman, and D. Kern Dynamic personalities of proteins Nature 450 2007 964 972 (Pubitemid 350273626)
    • (2007) Nature , vol.450 , Issue.7172 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 3
    • 65349192770 scopus 로고    scopus 로고
    • Probing the flexibility of large conformational changes in protein structures through local perturbations
    • B.K. Ho, and D.A. Agard Probing the flexibility of large conformational changes in protein structures through local perturbations PLoS Comput. Biol. 5 2009 e1000343
    • (2009) PLoS Comput. Biol. , vol.5 , pp. 1000343
    • Ho, B.K.1    Agard, D.A.2
  • 4
    • 78649898335 scopus 로고    scopus 로고
    • Protein flexibility and ligand recognition: Challenges for molecular modeling
    • F. Spyrakis, A. BidonChanal, X. Barril, and F.J. Luque Protein flexibility and ligand recognition: challenges for molecular modeling Curr. Top. Med. Chem. 11 2011 192 210
    • (2011) Curr. Top. Med. Chem. , vol.11 , pp. 192-210
    • Spyrakis, F.1    Bidonchanal, A.2    Barril, X.3    Luque, F.J.4
  • 5
    • 33646943202 scopus 로고    scopus 로고
    • Molecular dynamics: Survey of methods for simulating the activity of proteins
    • DOI 10.1021/cr040426m
    • S.A. Adcock, and J.A. McCammon Molecular dynamics: survey of methods for simulating the activity of proteins Chem. Rev. 106 2006 1589 1615 (Pubitemid 43792773)
    • (2006) Chemical Reviews , vol.106 , Issue.5 , pp. 1589-1615
    • Adcock, S.A.1    McCammon, J.A.2
  • 6
    • 17044393884 scopus 로고    scopus 로고
    • Coarse-grained models for proteins
    • V. Tozzini Coarse-grained models for proteins Curr. Opin. Struct. Biol. 15 2005 144 150
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 144-150
    • Tozzini, V.1
  • 7
    • 0025865704 scopus 로고
    • Computational studies of ligand diffusion in globins: I
    • R. Czerminski, and R. Elber Computational studies of ligand diffusion in globins: I Leghemoglobin, Proteins 10 1991 70 80
    • (1991) Leghemoglobin, Proteins , vol.10 , pp. 70-80
    • Czerminski, R.1    Elber, R.2
  • 8
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • PII S0009261499011239
    • Y. Sugita, and Y. Okamoto Replica-exchanged molecular dynamcs method for protein folding Chem. Phys. Lett. 314 1999 141 151 (Pubitemid 129556751)
    • (1999) Chemical Physics Letters , vol.314 , Issue.1-2 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 9
    • 13244275057 scopus 로고    scopus 로고
    • Constraint Logic Programming approach to protein structure prediction
    • A. Dal Palú, A. Dovier, and F. Fogolari Constraint Logic Programming approach to protein structure prediction BMC Bioinform. 5 2004 186
    • (2004) BMC Bioinform. , vol.5 , pp. 186
    • Dal Palú, A.1    Dovier, A.2    Fogolari, F.3
  • 10
    • 4243532938 scopus 로고
    • Constraint Logic Programming: A survey
    • J. Jaffar, and M.J. Maher Constraint Logic Programming: a survey J. Logic Programming 19 20 1994 503 581
    • (1994) J. Logic Programming , vol.19 , Issue.20 , pp. 503-581
    • Jaffar, J.1    Maher, M.J.2
  • 13
    • 0001737878 scopus 로고    scopus 로고
    • Practical applications of constraint programming
    • M. Wallace Practical applications of constraint programming Constraints 1 1996 139 168 (Pubitemid 126709718)
    • (1996) Constraints , vol.1 , Issue.1-2 , pp. 139-168
    • Wallace, M.1
  • 14
    • 0031451570 scopus 로고    scopus 로고
    • Evolution of the nuclear receptor superfamily: Early diversification from an ancestral orphan receptor
    • DOI 10.1677/jme.0.0190207
    • V. Laudet Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor J. Mol. Endocrinol. 19 1997 207 226 (Pubitemid 28023157)
    • (1997) Journal of Molecular Endocrinology , vol.19 , Issue.3 , pp. 207-226
    • Laudet, V.1
  • 15
    • 0034463085 scopus 로고    scopus 로고
    • Crucial role of the H11-H12 loop in stabilizing the active conformation of the human mineralocorticoid receptor
    • DOI 10.1210/me.14.8.1210
    • C. Hellal-Levy, J. Fagart, A. Souque, J.M. Wurtz, D. Moras, and M.E. Rafestin-Oblin Crucial role of the H11-H12 loop in stabilizing the active conformation of the human mineralocorticoid receptor Mol. Endocrinol. 14 2000 1210 1221 (Pubitemid 32260482)
    • (2000) Molecular Endocrinology , vol.14 , Issue.8 , pp. 1210-1221
    • Hellal-Levy, C.1    Fagart, J.2    Souque, A.3    Wurtz, J.-M.4    Moras, D.5    Rafestin-Oblin, M.-E.6
  • 16
    • 0018548076 scopus 로고
    • Mechanism of action of estrogen agonists and antagonists
    • J.H. Clark, J.W. Hardin, and S.A. McCormack Mechanism of action of estrogen agonists and antagonists J. Anim. Sci. 49 Suppl 2 1979 46 65
    • (1979) J. Anim. Sci. , vol.49 , Issue.SUPPL. 2 , pp. 46-65
    • Clark, J.H.1    Hardin, J.W.2    McCormack, S.A.3
  • 17
    • 0032813510 scopus 로고    scopus 로고
    • Oestrogen receptors - An overview
    • DOI 10.1046/j.1365-2796.1999.00545.x
    • E. Enmark, and J.A. Gustafsson Oestrogen receptors - an overview J. Intern. Med. 246 1999 133 138 (Pubitemid 29378917)
    • (1999) Journal of Internal Medicine , vol.246 , Issue.2 , pp. 133-138
    • Enmark, E.1    Gustafsson, J.-A.2
  • 18
    • 0035289768 scopus 로고    scopus 로고
    • Assessing latex allergy among health care employees using workers' compensation data
    • I.B. Horwitz, J.D. Kammeyer-Mueller, and B.P. McCall Assessing latex allergy among health care employees using workers' compensation data Minn. Med. 84 2001 47 50
    • (2001) Minn. Med. , vol.84 , pp. 47-50
    • Horwitz, I.B.1    Kammeyer-Mueller, J.D.2    McCall, B.P.3
  • 19
    • 0032835740 scopus 로고    scopus 로고
    • Steroid hormones use non-genomic mechanisms to control brain functions and behaviors: A review of evidence
    • DOI 10.1159/000006610
    • F.L. Moore, and S.J. Evans Steroid hormones use non-genomic mechanisms to control brain functions and behaviors: a review of evidence Brain Behav. Evol. 54 1999 41 50 (Pubitemid 29448881)
    • (1999) Brain, Behavior and Evolution , vol.54 , Issue.1 , pp. 41-50
    • Moore, F.L.1    Evans, S.J.2
  • 20
    • 70349394877 scopus 로고
    • Some biochemical and Clinical aspects of the action of Androgens and Estrogens
    • A. Segaloff Some biochemical and Clinical aspects of the action of Androgens and Estrogens Cancer Res. 23 1963 1459 1464
    • (1963) Cancer Res. , vol.23 , pp. 1459-1464
    • Segaloff, A.1
  • 21
    • 0030071445 scopus 로고    scopus 로고
    • Tripartite steroid hormone receptor pharmacology: Interaction with multiple effector sites as a basis for the cell- and promoter-specific action of these hormones
    • DOI 10.1210/me.10.2.119
    • J.A. Katzenellenbogen, B.W. O'Malley, and B.S. Katzenellenbogen Tripartite steroid hormone receptor pharmacology: interaction with multiple effector sites as a basis for the cell- and promoter-specific action of these hormones Mol. Endocrinol. 10 1996 119 131 (Pubitemid 26042544)
    • (1996) Molecular Endocrinology , vol.10 , Issue.2 , pp. 119-131
    • Katzenellenbogen, J.A.1    O'Malley, B.W.2    Katzenellenbogen, B.S.3
  • 23
    • 0037203973 scopus 로고    scopus 로고
    • Designing non-peptide peptidomimetics in the 21st century: Inhibitors targeting conformational ensembles
    • DOI 10.1021/jm010425b
    • M.G. Bursavich, and D.H. Rich Designing non-peptide peptidomimetics in the 21st century: inhibitors targeting conformational ensembles J. Med. Chem. 45 2002 541 558 (Pubitemid 34145701)
    • (2002) Journal of Medicinal Chemistry , vol.45 , Issue.3 , pp. 541-558
    • Bursavich, M.G.1    Rich, D.H.2
  • 24
    • 33847114057 scopus 로고    scopus 로고
    • Conformational dynamics of the estrogen receptor α: Molecular dynamics simulations of the influence of binding site structure on protein dynamics
    • DOI 10.1021/bi061656t
    • L. Celik, J.D. Lund, and B. Schiott Conformational dynamics of the estrogen receptor alpha: molecular dynamics simulations of the influence of binding site structure on protein dynamics Biochemistry 46 2007 1743 1758 (Pubitemid 46290551)
    • (2007) Biochemistry , vol.46 , Issue.7 , pp. 1743-1758
    • Celik, L.1    Lund, J.D.D.2    Schiott, B.3
  • 25
    • 46149089650 scopus 로고    scopus 로고
    • Preliminary molecular dynamic simulations of the estrogen receptor alpha ligand binding domain from antagonist to apo
    • DOI 10.3390/ijerph2008050014
    • T.D. McGee, J. Edwards, and A.E. Roitberg Preliminary molecular dynamic simulations of the estrogen receptor alpha ligand binding domain from antagonist to apo Int. J. Environ. Res. Public Health 5 2008 111 114 (Pubitemid 351904786)
    • (2008) International Journal of Environmental Research and Public Health , vol.5 , Issue.2 , pp. 111-114
    • McGee, T.D.1    Edwards, J.2    Roitberg, A.E.3
  • 26
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • DOI 10.1126/science.282.5389.740
    • Y. Duan, and P.A. Kollman Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution Science 282 1998 740 744 (Pubitemid 28489385)
    • (1998) Science , vol.282 , Issue.5389 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 29
    • 0032446607 scopus 로고    scopus 로고
    • The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen
    • DOI 10.1016/S0092-8674(00)81717-1
    • A.K. Shiau, D. Barstad, P.M. Loria, L. Cheng, P.J. Kushner, D.A. Agard, and G.L. Greene The structural basis of estrogen receptor/co-activator recognition and the antagonism of this interaction by tamoxifen Cell 95 1998 927 937 (Pubitemid 29019045)
    • (1998) Cell , vol.95 , Issue.7 , pp. 927-937
    • Shiau, A.K.1    Barstad, D.2    Loria, P.M.3    Cheng, L.4    Kushner, P.J.5    Agard, D.A.6    Greene, G.L.7
  • 31
    • 0034956939 scopus 로고    scopus 로고
    • Overexpression, purification, and crystal structure of native ERα LBD
    • DOI 10.1006/prep.2001.1409
    • S. Eiler, M. Gangloff, S. Duclaud, D. Moras, and M. Ruff Overexpression, purification, and crystal structure of native ER alpha LBD Protein Expr. Purif. 22 2001 165 173 (Pubitemid 32608541)
    • (2001) Protein Expression and Purification , vol.22 , Issue.2 , pp. 165-173
    • Eiler, S.1    Gangloff, M.2    Duclaud, S.3    Moras, D.4    Ruff, M.5
  • 32
    • 18944381947 scopus 로고    scopus 로고
    • Structural basis for an unexpected mode of SERM-Mediated ER antagonism
    • DOI 10.1016/j.molcel.2005.04.014, PII S1097276505012773
    • Y.L. Wu, X. Yang, Z. Ren, D.P. McDonnell, J.D. Norris, T.M. Willson, and G.L. Greene Structural basis for an unexpected mode of SERM-mediated ER antagonism Mol. Cell 18 2005 413 424 (Pubitemid 40704756)
    • (2005) Molecular Cell , vol.18 , Issue.4 , pp. 413-424
    • Wu, Y.-L.1    Yang, X.2    Ren, Z.3    McDonnell, D.P.4    Norris, J.D.5    Willson, T.M.6    Greene, G.L.7
  • 34
    • 0030734795 scopus 로고    scopus 로고
    • Altered ligand binding properties and enhanced stability of a constitutively active estrogen receptor: Evidence that an open pocket conformation is required for ligand interaction
    • DOI 10.1021/bi971746l
    • K.E. Carlson, I. Choi, A. Gee, B.S. Katzenellenbogen, and J.A. Katzenellenbogen Altered ligand binding properties and enhanced stability of a constitutively active estrogen receptor: evidence that an open pocket conformation is required for ligand interaction Biochemistry 36 1997 14897 14905 (Pubitemid 27524414)
    • (1997) Biochemistry , vol.36 , Issue.48 , pp. 14897-14905
    • Carlson, K.E.1    Choi, I.2    Gee, A.3    Katzenellenbogen, B.S.4    Katzenellenbogen, J.A.5
  • 35
    • 0029012163 scopus 로고
    • Crystal structure of the ligand-binding domain of the human nuclear receptor RXR-alpha
    • W. Bourguet, M. Ruff, P. Chambon, H. Gronemeyer, and D. Moras Crystal structure of the ligand-binding domain of the human nuclear receptor RXR-alpha Nature 375 1995 377 382
    • (1995) Nature , vol.375 , pp. 377-382
    • Bourguet, W.1    Ruff, M.2    Chambon, P.3    Gronemeyer, H.4    Moras, D.5
  • 36
    • 70349386285 scopus 로고    scopus 로고
    • How computational methods try to disclose the estrogen receptor secrecy-modeling the flexibility
    • F. Spyrakis, and P. Cozzini How computational methods try to disclose the estrogen receptor secrecy-modeling the flexibility Curr. Med. Chem. 16 2009 2987 3027
    • (2009) Curr. Med. Chem. , vol.16 , pp. 2987-3027
    • Spyrakis, F.1    Cozzini, P.2
  • 37
    • 0345874610 scopus 로고    scopus 로고
    • Steroid-hormone rapid actions, membrane receptors and a conformational ensemble model
    • A.W. Norman, M.T. Mizwicki, and D.P. Norman Steroid-hormone rapid actions, membrane receptors and a conformational ensemble model Nat. Rev. Drug Discov. 3 2004 27 41 (Pubitemid 38088696)
    • (2004) Nature Reviews Drug Discovery , vol.3 , Issue.1 , pp. 27-41
    • Norman, A.W.1    Mizwicki, M.T.2    Norman, D.P.G.3
  • 38
    • 0141974927 scopus 로고    scopus 로고
    • Global mapping of nucleic acid conformational space: Dinucleoside monophosphate conformations and transition pathways among conformational classes
    • DOI 10.1093/nar/gkg750
    • G.E. Sims, and S.H. Kim Global mapping of nucleic acid conformational space: dinucleoside monophosphate conformations and transition pathways among conformational classes Nucleic Acids Res. 31 2003 5607 5616 (Pubitemid 37441932)
    • (2003) Nucleic Acids Research , vol.31 , Issue.19 , pp. 5607-5616
    • Sims, G.E.1    Kim, S.-H.2
  • 39
    • 2442560527 scopus 로고    scopus 로고
    • Signature of the oligomeric behaviour of nuclear receptors at the sequence and structural level
    • DOI 10.1038/sj.embor.7400119
    • Y. Brelivet, S. Kammerer, N. Rochel, O. Poch, and D. Moras Signature of the oligomeric behaviour of nuclear receptors at the sequence and structural level EMBO Rep. 5 2004 423 429 (Pubitemid 38618287)
    • (2004) EMBO Reports , vol.5 , Issue.4 , pp. 423-429
    • Brelivet, Y.1    Kammerer, S.2    Rochel, N.3    Poch, O.4    Moras, D.5
  • 40
    • 60849124513 scopus 로고    scopus 로고
    • Generalized ensemble methods for de novo structure prediction
    • A. Shmygelska, and M. Levitt Generalized ensemble methods for de novo structure prediction Proc. Natl. Acad. Sci. U S A 106 2009 1415 1420
    • (2009) Proc. Natl. Acad. Sci. U S A , vol.106 , pp. 1415-1420
    • Shmygelska, A.1    Levitt, M.2
  • 41
    • 34347404689 scopus 로고    scopus 로고
    • Effective optimization algorithms for fragment-assembly based protein structure prediction
    • PII S0219720007002618
    • K.W. Deronne, and G. Karypis Effective optimization algorithms for fragment-assembly based protein structure prediction J. Bioinform. Comput. Biol. 5 2007 335 352 (Pubitemid 47018581)
    • (2007) Journal of Bioinformatics and Computational Biology , vol.5 , Issue.2 A , pp. 335-352
    • Deronne, K.W.1    Karypis, G.2
  • 42
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • DOI 10.1006/jmbi.1997.0959
    • K.T. Simons, C. Kooperberg, E. Huang, and D. Baker Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions J. Mol. Biol. 268 1997 209 225 (Pubitemid 27192690)
    • (1997) Journal of Molecular Biology , vol.268 , Issue.1 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 44
    • 4043058565 scopus 로고    scopus 로고
    • Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing
    • DOI 10.1002/prot.20150
    • J. Lee, S.Y. Kim, K. Joo, and I. Kim Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing Proteins 56 2004 704 714 (Pubitemid 39063314)
    • (2004) Proteins: Structure, Function and Genetics , vol.56 , Issue.4 , pp. 704-714
    • Lee, J.1    Kim, S.-Y.2    Joo, K.3    Kim, I.4    Lee, J.5
  • 45
    • 0029101826 scopus 로고
    • Recognizing native folds by the arrangement of hydrophobic and polar residues
    • E.S. Huang, S. Subbiah, and M. Levitt Recognizing native folds by the arrangement of hydrophobic and polar residues J. Mol. Biol. 252 1995 709 720
    • (1995) J. Mol. Biol. , vol.252 , pp. 709-720
    • Huang, E.S.1    Subbiah, S.2    Levitt, M.3
  • 46
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • DOI 10.1006/jmbi.1996.0114
    • S. Miyazawa, and R.L. Jernigan Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading J. Mol. Biol. 256 1996 623 644 (Pubitemid 26107211)
    • (1996) Journal of Molecular Biology , vol.256 , Issue.3 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 47
    • 0027650879 scopus 로고
    • Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
    • M.J. Sippl Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures J. Comput. Aided Mol. Des 7 1993 473 501
    • (1993) J. Comput. Aided Mol. des , vol.7 , pp. 473-501
    • Sippl, M.J.1
  • 48
    • 84857236981 scopus 로고    scopus 로고
    • De Novo protein structure prediction using fragment based potential and conformational space annealing
    • M. Sasai, C. Seok, and J. Lee de Novo protein structure prediction using fragment based potential and conformational space annealing Biophysical J. 98 2010 461a
    • (2010) Biophysical J. , vol.98
    • Sasai, M.1    Seok, C.2    Lee, J.3
  • 49
    • 0041417422 scopus 로고    scopus 로고
    • Building three-dimensional ribonucleic acid structures
    • F. Major Building three-dimensional ribonucleic acid structures Comput. Sci. Eng. 5 2003 44 53
    • (2003) Comput. Sci. Eng. , vol.5 , pp. 44-53
    • Major, F.1
  • 50
    • 0037343306 scopus 로고    scopus 로고
    • Protein decoy assembly using short fragments under geometric constraints
    • DOI 10.1002/bip.10262
    • R. Kolodny, and M. Levitt Protein decoy assembly using short fragments under geometric constraints Biopolymers 68 2003 278 285 (Pubitemid 36342867)
    • (2003) Biopolymers , vol.68 , Issue.3 , pp. 278-285
    • Kolodny, R.1    Levitt, M.2
  • 51
    • 0035366744 scopus 로고    scopus 로고
    • The protein structure prediction problem: A constraint optimization approach using a new lower bound
    • DOI 10.1023/A:1011485622743
    • R. Backofen The protein structure prediction problem: a constraint optimization approach using a new lower bound Constraints 6 2001 223 255 (Pubitemid 32543258)
    • (2001) Constraints , vol.6 , Issue.2-3 , pp. 223-255
    • Backofen, R.1
  • 53
    • 0036662961 scopus 로고    scopus 로고
    • PSICO: Solving protein structures with constraint programming and optimization
    • DOI 10.1023/A:1020577603762
    • L. Krippahl, and P. Barahona PSICO: solving protein structures with constraint programming and optimization Constraints 7 2002 317 331 (Pubitemid 35393796)
    • (2002) Constraints , vol.7 , Issue.3-4 , pp. 317-331
    • Krippahl, L.1    Barahona, P.2
  • 54
    • 44449128110 scopus 로고    scopus 로고
    • CPSP-tools-exact and complete algorithms for high-throughput 3D lattice protein studies
    • M. Mann, S. Will, and R. Backofen CPSP-tools-exact and complete algorithms for high-throughput 3D lattice protein studies BMC Bioinform. 9 2008 230
    • (2008) BMC Bioinform. , vol.9 , pp. 230
    • Mann, M.1    Will, S.2    Backofen, R.3
  • 55
    • 34547830871 scopus 로고    scopus 로고
    • Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: A lattice study
    • E. Jacob, A. Horovitz, and R. Unger Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: a lattice study Bioinformatics 23 2007 240 248
    • (2007) Bioinformatics , vol.23 , pp. 240-248
    • Jacob, E.1    Horovitz, A.2    Unger, R.3
  • 56
    • 24944493938 scopus 로고    scopus 로고
    • Biochemistry: Toward high-resolution de novo structure prediction for small proteins
    • DOI 10.1126/science.1113801
    • P. Bradley, K.M. Misura, and D. Baker Toward high-resolution de novo structure prediction for small proteins Science 309 2005 1868 1871 (Pubitemid 41325099)
    • (2005) Science , vol.309 , Issue.5742 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.S.2    Baker, D.3
  • 57
    • 27344449197 scopus 로고    scopus 로고
    • Progress in modeling of protein structures and interactions
    • DOI 10.1126/science.1112160
    • O. Schueler-Furman, C. Wang, P. Bradley, K. Misura, and D. Baker Progress in modeling of protein structures and interactions Science 310 2005 638 642 (Pubitemid 41528148)
    • (2005) Science , vol.310 , Issue.5748 , pp. 638-642
    • Schueler-Furman, O.1    Wang, C.2    Bradley, P.3    Misura, K.4    Baker, D.5
  • 58
    • 0032613288 scopus 로고    scopus 로고
    • Ab initio folding of proteins using restraints derived from evolutionary information
    • DOI 10.1002/(SICI)1097-0134(1999)37:3+<177::AID-PROT22>3.0.CO;2-E
    • A.R. Ortiz, A. Kolinski, P. Rotkiewicz, B. Ilkowski, and J. Skolnick Ab initio folding of proteins using restraints derived from evolutionary information Proteins Suppl 3 1999 177 185 (Pubitemid 29463529)
    • (1999) Proteins: Structure, Function and Genetics , vol.37 , Issue.SUPPL. 3 , pp. 177-185
    • Ortiz, A.R.1    Kolinski, A.2    Rotkiewicz, P.3    Ilkowski, B.4    Skolnick, J.5
  • 59
    • 0036681386 scopus 로고    scopus 로고
    • Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding
    • DOI 10.1002/prot.10141
    • Y. Zhang, D. Kihara, and J. Skolnick Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding Proteins 48 2002 192 201 (Pubitemid 34743409)
    • (2002) Proteins: Structure, Function and Genetics , vol.48 , Issue.2 , pp. 192-201
    • Zhang, Y.1    Kihara, D.2    Skolnick, J.3
  • 60
    • 1942455272 scopus 로고    scopus 로고
    • Generalized-ensemble algorithms: Enhanced sampling techniques for Monte Carlo and molecular dynamics simulations
    • DOI 10.1016/j.jmgm.2003.12.009, PII S1093326303001980
    • Y. Okamoto Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations J. Mol. Graph Model. 22 2004 425 439 (Pubitemid 38510308)
    • (2004) Journal of Molecular Graphics and Modelling , vol.22 , Issue.5 , pp. 425-439
    • Okamoto, Y.1
  • 61
    • 0037157317 scopus 로고    scopus 로고
    • On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
    • DOI 10.1063/1.1472510
    • H. Fukunishi, O. Watanabe, and S. Takada On the Hamiltonian replica exchange method for efficient sampling, of biomolecular systems: application to protein structure prediction J. Chem. Phys. 116 2002 9058 9067 (Pubitemid 34631453)
    • (2002) Journal of Chemical Physics , vol.116 , Issue.20 , pp. 9058-9067
    • Fukunishi, H.1    Watanabe, O.2    Takada, S.3
  • 63
    • 0027080363 scopus 로고
    • KEY, and LOCK LOCKSMITH: Complementary hydropathic map predictions of drug structure from a known receptor-receptor structure from known drugs
    • 226
    • G.E. Kellogg, D.J. Abraham, KEY, and LOCK LOCKSMITH: complementary hydropathic map predictions of drug structure from a known receptor-receptor structure from known drugs J. Mol. Graph 10 1992 212 217 226
    • (1992) J. Mol. Graph , vol.10 , pp. 212-217
    • Kellogg, G.E.1    Abraham, D.J.2
  • 66
    • 0030203710 scopus 로고    scopus 로고
    • Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
    • G.M. Morris, D.S. Goodsell, R. Huey, and A.J. Olson Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4 J. Comput. Aided Mol. Des 10 1996 293 304 (Pubitemid 126712824)
    • (1996) Journal of Computer-Aided Molecular Design , vol.10 , Issue.4 , pp. 293-304
    • Morris, G.M.1    Goodsell, D.S.2    Huey, R.3    Olson, A.J.4
  • 67
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • DOI 10.1006/jmbi.1996.0477
    • M. Rarey, B. Kramer, T. Lengauer, and G. Klebe A fast flexible docking method using an incremental construction algorithm J. Mol. Biol. 261 1996 470 489 (Pubitemid 26335901)
    • (1996) Journal of Molecular Biology , vol.261 , Issue.3 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 68
    • 1442351132 scopus 로고    scopus 로고
    • Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
    • DOI 10.1016/j.jmb.2004.01.003
    • C.N. Cavasotto, and R.A. Abagyan Protein flexibility in ligand docking and virtual screening to protein kinases J. Mol. Biol. 337 2004 209 225 (Pubitemid 38270258)
    • (2004) Journal of Molecular Biology , vol.337 , Issue.1 , pp. 209-225
    • Cavasotto, C.N.1    Abagyan, R.A.2
  • 69
    • 0035957528 scopus 로고    scopus 로고
    • FLEXE: Efficient molecular docking considering protein structure variations
    • DOI 10.1006/jmbi.2001.4551
    • H. Claussen, C. Buning, M. Rarey, and T. Lengauer FlexE: efficient molecular docking considering protein structure variations J. Mol. Biol. 308 2001 377 395 (Pubitemid 33043576)
    • (2001) Journal of Molecular Biology , vol.308 , Issue.2 , pp. 377-395
    • Claussen, H.1    Buning, C.2    Rarey, M.3    Lengauer, T.4
  • 70
    • 0036137713 scopus 로고    scopus 로고
    • Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in autodock
    • DOI 10.1002/prot.10028
    • F. Osterberg, G.M. Morris, M.F. Sanner, A.J. Olson, and D.S. Goodsell Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock Proteins 46 2002 34 40 (Pubitemid 34033574)
    • (2002) Proteins: Structure, Function and Genetics , vol.46 , Issue.1 , pp. 34-40
    • Osterberg, F.1    Morris, G.M.2    Sanner, M.F.3    Olson, A.J.4    Goodsell, D.S.5
  • 71
    • 0034284383 scopus 로고    scopus 로고
    • Recurrent oligomers in proteins: An optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies
    • C. Micheletti, F. Seno, and A. Maritan Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies Proteins 40 2000 662 674
    • (2000) Proteins , vol.40 , pp. 662-674
    • Micheletti, C.1    Seno, F.2    Maritan, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.