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Volumn 90, Issue 12, 2006, Pages 4558-4573

Gaussian-weighted RMSD superposition of proteins: A structural comparison for flexible proteins and predicted protein structures

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PROTEIN DERIVATIVE;

EID: 33744807436     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.066654     Document Type: Article
Times cited : (114)

References (59)
  • 1
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • Tsai, C. J., S. Kumar, B. Ma, and R. Nussinov. 1999. Folding funnels, binding funnels, and protein function. Protein Sci. 8:1181-1190.
    • (1999) Protein Sci. , vol.8 , pp. 1181-1190
    • Tsai, C.J.1    Kumar, S.2    Ma, B.3    Nussinov, R.4
  • 2
    • 0036147568 scopus 로고    scopus 로고
    • Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
    • Ma, B., M. Shatsky, H. J. Wolfson, and R. Nussinov. 2002. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 11:184-197.
    • (2002) Protein Sci. , vol.11 , pp. 184-197
    • Ma, B.1    Shatsky, M.2    Wolfson, H.J.3    Nussinov, R.4
  • 3
    • 9944225262 scopus 로고    scopus 로고
    • Molecular mechanisms for multitasking: Recent crystal structures of moonlighting proteins
    • Jeffery, C. J. 2004. Molecular mechanisms for multitasking: recent crystal structures of moonlighting proteins. Curr. Opin. Struct. Biol. 14:663-668.
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 663-668
    • Jeffery, C.J.1
  • 6
    • 0032530836 scopus 로고    scopus 로고
    • A database of macromolecular movements
    • Gerstein, M., and W. Krebs. 1998. A database of macromolecular movements. Nucleic Acids Res. 26:4280-4290.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 4280-4290
    • Gerstein, M.1    Krebs, W.2
  • 7
    • 0034655949 scopus 로고    scopus 로고
    • The morph server: A standardized system for analyzing and visualizing macromolecular motions in a database framework
    • Krebs, W. G., and M. Gerstein. 2000. The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res. 28:1665-1675.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1665-1675
    • Krebs, W.G.1    Gerstein, M.2
  • 8
    • 0037246863 scopus 로고    scopus 로고
    • MolMovDB: Analysis and visualization of conformational change and structural flexibility
    • Echols, N., D. Milburn, and M. Gerstein. 2003. MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res. 31:478-482.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 478-482
    • Echols, N.1    Milburn, D.2    Gerstein, M.3
  • 9
    • 1042275603 scopus 로고    scopus 로고
    • Exploring the range of protein flexibility, from a structural proteomics perspective
    • Gerstein, M., and N. Echols. 2004. Exploring the range of protein flexibility, from a structural proteomics perspective. Curr. Opin. Chem. Biol. 8:14-19.
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 14-19
    • Gerstein, M.1    Echols, N.2
  • 10
    • 1542465044 scopus 로고    scopus 로고
    • Organization and functions of interacting domains for signaling by protein-protein interactions
    • Buck, E., and R. Iyengar. 2003. Organization and functions of interacting domains for signaling by protein-protein interactions. Sci. STKE. 209:Re14.
    • (2003) Sci. STKE , vol.209
    • Buck, E.1    Iyengar, R.2
  • 11
    • 0037453510 scopus 로고    scopus 로고
    • Assembly of cell regulatory systems through protein interaction domains
    • Pawson, T., and P. Nash. 2003. Assembly of cell regulatory systems through protein interaction domains. Science. 300:445-452.
    • (2003) Science , vol.300 , pp. 445-452
    • Pawson, T.1    Nash, P.2
  • 12
    • 0032544060 scopus 로고    scopus 로고
    • The structural distribution of cooperative interactions in proteins: Analysis of the native state ensemble
    • Hilser, V. J., D. Dowdy, T. G. Oas, and E. Freire. 1998. The structural distribution of cooperative interactions in proteins: analysis of the native state ensemble. Proc. Natl. Acad. Sci. USA. 95:9903-9908.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 9903-9908
    • Hilser, V.J.1    Dowdy, D.2    Oas, T.G.3    Freire, E.4
  • 13
    • 0033642945 scopus 로고    scopus 로고
    • Structural stability of binding sites: Consequences for binding affinity and allosteric effects
    • Luque, I., and E. Freire. 2000. Structural stability of binding sites: consequences for binding affinity and allosteric effects. Proteins. S4:63-71.
    • (2000) Proteins , vol.S4 , pp. 63-71
    • Luque, I.1    Freire, E.2
  • 14
    • 0033974667 scopus 로고    scopus 로고
    • Accommodating protein flexibility in computational drug design
    • Carlson, H. A., and J. A. McCammon. 2000. Accommodating protein flexibility in computational drug design. Mol. Pharmacol. 57:213-218.
    • (2000) Mol. Pharmacol. , vol.57 , pp. 213-218
    • Carlson, H.A.1    McCammon, J.A.2
  • 15
    • 0014965896 scopus 로고
    • Chymotrypsinogen: 2.5 Å crystal structure, comparison with α-chymotrypsin, and implications for zymogen activation
    • Freer, S. T., J. Kraut, J. D. Robertus, H. T. Wright, and N. H. Xuong. 1970. Chymotrypsinogen: 2.5 Å crystal structure, comparison with α-chymotrypsin, and implications for zymogen activation. Biochemistry. 9:1997-2009.
    • (1970) Biochemistry , vol.9 , pp. 1997-2009
    • Freer, S.T.1    Kraut, J.2    Robertus, J.D.3    Wright, H.T.4    Xuong, N.H.5
  • 16
    • 0029091249 scopus 로고
    • Average core structures and variability measures for protein families: Application to the immunoglobulins
    • Gerstein, M., and R. B. Altman. 1995. Average core structures and variability measures for protein families: application to the immunoglobulins. J. Mol. Biol. 251:161-175.
    • (1995) J. Mol. Biol. , vol.251 , pp. 161-175
    • Gerstein, M.1    Altman, R.B.2
  • 17
    • 0035865982 scopus 로고    scopus 로고
    • Protein structural alignments and functional genomics
    • Irving, J. A., J. C. Whisstock, and A. M. Lesk. 2001. Protein structural alignments and functional genomics. Proteins. 42:378-382.
    • (2001) Proteins , vol.42 , pp. 378-382
    • Irving, J.A.1    Whisstock, J.C.2    Lesk, A.M.3
  • 18
    • 0030883755 scopus 로고    scopus 로고
    • Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates
    • Wriggers, W., and K. Schulten. 1997. Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins. 29:1-14.
    • (1997) Proteins , vol.29 , pp. 1-14
    • Wriggers, W.1    Schulten, K.2
  • 19
    • 0036681439 scopus 로고    scopus 로고
    • Flexible protein alignment and hinge detection
    • Shatsky, M., R. Nussinov, and H. J. Wolfson. 2002. Flexible protein alignment and hinge detection. Proteins. 48:242-256.
    • (2002) Proteins , vol.48 , pp. 242-256
    • Shatsky, M.1    Nussinov, R.2    Wolfson, H.J.3
  • 20
    • 0141448920 scopus 로고    scopus 로고
    • Protein structural alignment for detection of maximally conserved regions
    • Kotlovyi, V., W. L. Nichols, and L. F. Ten Eych. 2003. Protein structural alignment for detection of maximally conserved regions. Biophys. Chem. 105:595-608.
    • (2003) Biophys. Chem. , vol.105 , pp. 595-608
    • Kotlovyi, V.1    Nichols, W.L.2    Ten Eych, L.F.3
  • 21
    • 0037460952 scopus 로고    scopus 로고
    • MINRMS: An efficient algorithm for determining protein structure similarity using root-mean-squared-distance
    • Jewett, A. I., C. C. Huang, and T. E. Ferrin. 2003. MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. Bioinformatics. 19:625-634.
    • (2003) Bioinformatics , vol.19 , pp. 625-634
    • Jewett, A.I.1    Huang, C.C.2    Ferrin, T.E.3
  • 22
    • 2942547529 scopus 로고    scopus 로고
    • Using 3D hidden Markov models that explicitly represent spatial coordinates to model and compare protein structures
    • Alexandrov, V., and M. Gerstein. 2004. Using 3D hidden Markov models that explicitly represent spatial coordinates to model and compare protein structures. BMC Bioinformatcs. 5:2.
    • (2004) BMC Bioinformatcs , vol.5 , pp. 2
    • Alexandrov, V.1    Gerstein, M.2
  • 23
    • 3042533398 scopus 로고    scopus 로고
    • Database searching by flexible protein structure alignment
    • Ye, Y., and A. Godzik. 2004. Database searching by flexible protein structure alignment. Protein Sci. 13:1841-1850.
    • (2004) Protein Sci. , vol.13 , pp. 1841-1850
    • Ye, Y.1    Godzik, A.2
  • 24
    • 0036008503 scopus 로고    scopus 로고
    • A genetic algorithm for the identification of conformationally invariant regions in protein molecules
    • Schneider, T. R. 2002. A genetic algorithm for the identification of conformationally invariant regions in protein molecules. Acta Crystallogr. D58:195-208.
    • (2002) Acta Crystallogr. , vol.D58 , pp. 195-208
    • Schneider, T.R.1
  • 25
    • 16644386895 scopus 로고    scopus 로고
    • Domain identification by iterative analysis of error-scaled difference distance matrices
    • Schneider, T. R. 2004. Domain identification by iterative analysis of error-scaled difference distance matrices. Acta Crystallogr. D60:2269-2275.
    • (2004) Acta Crystallogr. , vol.D60 , pp. 2269-2275
    • Schneider, T.R.1
  • 26
    • 0029159748 scopus 로고
    • Rigid domains in proteins: An algorithmic approach to their identification
    • Nichols, W. L., G. D. Rose, L. F. Ten Eyck, and B. H. Zimm. 1995. Rigid domains in proteins: an algorithmic approach to their identification. Proteins. 23:38-48.
    • (1995) Proteins , vol.23 , pp. 38-48
    • Nichols, W.L.1    Rose, G.D.2    Ten Eyck, L.F.3    Zimm, B.H.4
  • 28
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch, W. 1976. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A32:922-923.
    • (1976) Acta Crystallogr. , vol.A32 , pp. 922-923
    • Kabsch, W.1
  • 29
    • 0032606104 scopus 로고    scopus 로고
    • RMS/coverage graphs: A qualitative method for comparing three-dimensional protein structure predictions
    • Hubbard, T. J. P. 1999. RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions. Proteins. S3:15-21.
    • (1999) Proteins , vol.S3 , pp. 15-21
    • Hubbard, T.J.P.1
  • 31
    • 0037046143 scopus 로고    scopus 로고
    • Anisotropic dynamics of the Je-2147-HIV protease complex: Drug resistance and thermodynamic binding mode examined in a 1.09 Å structure
    • Reiling, K. K., N. F. Endres, D. S. Dauber, C. S. Craik, and R. M. Stroud. 2002. Anisotropic dynamics of the Je-2147-HIV protease complex: drug resistance and thermodynamic binding mode examined in a 1.09 Å structure. Biochemistry. 41:4582-4594.
    • (2002) Biochemistry , vol.41 , pp. 4582-4594
    • Reiling, K.K.1    Endres, N.F.2    Dauber, D.S.3    Craik, C.S.4    Stroud, R.M.5
  • 32
    • 0026344399 scopus 로고
    • The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU
    • Spinelli, S., Q. Z. Liu, P. M. Alzari, P. H. Hirel, and R. J. Poljak. 1991. The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU. Biochimie. 73:1391-1396.
    • (1991) Biochimie. , vol.73 , pp. 1391-1396
    • Spinelli, S.1    Liu, Q.Z.2    Alzari, P.M.3    Hirel, P.H.4    Poljak, R.J.5
  • 33
    • 0028331080 scopus 로고
    • cAMP-dependent protein kinase: Crystallographic insights into substrate recognition and phosphotransfer
    • Madhusudan, E. A. Trafny, N. H. Xuong, J. A. Adams, L. F. Ten Eyck, S. S. Taylor, and J. M. Sowadski. 1994. cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer. Protein Sci. 3:176-187.
    • (1994) Protein Sci. , vol.3 , pp. 176-187
    • Madhusudan1    Trafny, E.A.2    Xuong, N.H.3    Adams, J.A.4    Ten Eyck, L.F.5    Taylor, S.S.6    Sowadski, J.M.7
  • 34
    • 0027429591 scopus 로고
    • Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations
    • Zheng, J., D. R. Knighton, N. H. Xuong, S. S. Tayor, J. M. Sowadski, and L. F. Ten Eyck. 1993. Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations. Protein Sci. 2:1559-1573.
    • (1993) Protein Sci. , vol.2 , pp. 1559-1573
    • Zheng, J.1    Knighton, D.R.2    Xuong, N.H.3    Tayor, S.S.4    Sowadski, J.M.5    Ten Eyck, L.F.6
  • 36
    • 0027980558 scopus 로고
    • The crystal structure of elongation factor G complexed with GDP, at 2.7 Å resolution
    • Czworkowski, J., J. Wang, T. A. Steitz, and P. B. Moore. 1994. The crystal structure of elongation factor G complexed with GDP, at 2.7 Å resolution. EMBO J. 13:3661-3668.
    • (1994) EMBO J. , vol.13 , pp. 3661-3668
    • Czworkowski, J.1    Wang, J.2    Steitz, T.A.3    Moore, P.B.4
  • 37
    • 0032446607 scopus 로고    scopus 로고
    • The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen
    • Shiau, A. K., D. Barstad, P. M. Loria, L. Cheng, P. J. Kushner, D. A. Agard, and G. L. Green. 1998. The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell. 95:927-937.
    • (1998) Cell , vol.95 , 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    Green, G.L.7
  • 38
    • 0035369086 scopus 로고    scopus 로고
    • Structure of the replicating complex of a Pol α family DNA polymerase
    • Franklin, M. C., J. Wang, and T. A. Steitz. 2001. Structure of the replicating complex of a Pol α family DNA polymerase. Cell. 105:657-667.
    • (2001) Cell , vol.105 , pp. 657-667
    • Franklin, M.C.1    Wang, J.2    Steitz, T.A.3
  • 40
    • 0028885711 scopus 로고
    • Conformational variability in the refined structure of the chaperonin GroEL at 2.8 Å resolution
    • Braig, K., P. D. Adams, and A. T. Brunger. 1995. Conformational variability in the refined structure of the chaperonin GroEL at 2.8 Å resolution. Nat. Struct. Biol. 2:1083-1094.
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 1083-1094
    • Braig, K.1    Adams, P.D.2    Brunger, A.T.3
  • 41
    • 0033522118 scopus 로고    scopus 로고
    • Structure of a Ran-binding domain complexed with Ran bound to a GTP analogue: Implications for nuclear transport
    • Vetter, I. R., C. Nowak, T. Nishimoto, J. Kuhlmann, and A. Wittinghofer. 1999. Structure of a Ran-binding domain complexed with Ran bound to a GTP analogue: implications for nuclear transport. Nature. 398:39-46.
    • (1999) Nature , vol.398 , pp. 39-46
    • Vetter, I.R.1    Nowak, C.2    Nishimoto, T.3    Kuhlmann, J.4    Wittinghofer, A.5
  • 42
    • 0032545173 scopus 로고    scopus 로고
    • The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)
    • Stewart, M., H. M. Kent, and A. J. McCoy. 1998. The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2). J. Mol. Biol. 284:1517-1527.
    • (1998) J. Mol. Biol. , vol.284 , pp. 1517-1527
    • Stewart, M.1    Kent, H.M.2    McCoy, A.J.3
  • 43
    • 0033579380 scopus 로고    scopus 로고
    • Structure of a transcribing T7 RNA polymerase initiation complex
    • Cheetham, G. M. T., and T. A. Steitz. 1999. Structure of a transcribing T7 RNA polymerase initiation complex. Science. 286:2305-2309.
    • (1999) Science , vol.286 , pp. 2305-2309
    • Cheetham, G.M.T.1    Steitz, T.A.2
  • 44
    • 0037112082 scopus 로고    scopus 로고
    • Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase
    • Yin, Y. W., and T. A. Steitz. 2002. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science. 298:1387-1395.
    • (2002) Science , vol.298 , pp. 1387-1395
    • Yin, Y.W.1    Steitz, T.A.2
  • 45
    • 0242267517 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP)-Round V
    • Moult, J., K. Fidelis, A. Zemla, and T. Hubbard. 2003. Critical assessment of methods of protein structure prediction (CASP)-Round V. Proteins. 53:334-339.
    • (2003) Proteins , vol.53 , pp. 334-339
    • Moult, J.1    Fidelis, K.2    Zemla, A.3    Hubbard, T.4
  • 46
  • 47
    • 0037387121 scopus 로고    scopus 로고
    • Crystal structure of CapZ: Structural basis for actin filament barbed end capping
    • Yamashita, A., K. Maeda, and Y. Maeda. 2003. Crystal structure of CapZ: structural basis for actin filament barbed end capping. EMBO J. 22:1529-1538.
    • (2003) EMBO J. , vol.22 , pp. 1529-1538
    • Yamashita, A.1    Maeda, K.2    Maeda, Y.3
  • 48
    • 0036407694 scopus 로고    scopus 로고
    • The structure of an FF domain from human HYPA/FBP11
    • Allen, M., A. Friedler, O. Schon, and M. Bycroft. 2002. The structure of an FF domain from human HYPA/FBP11. J. Mol. Biol. 323:411-416.
    • (2002) J. Mol. Biol. , vol.323 , pp. 411-416
    • Allen, M.1    Friedler, A.2    Schon, O.3    Bycroft, M.4
  • 49
    • 0038309557 scopus 로고    scopus 로고
    • Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain
    • Miller, D. J., N. Ouellette, E. Evdokimova, A. Savchenko, A. Edwards, and W. F. Anderson. 2003. Crystal complexes of a predicted S-adenosylmethionine- dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain. Protein Sci. 12:1432-1442.
    • (2003) Protein Sci. , vol.12 , pp. 1432-1442
    • Miller, D.J.1    Ouellette, N.2    Evdokimova, E.3    Savchenko, A.4    Edwards, A.5    Anderson, W.F.6
  • 52
    • 0033505579 scopus 로고    scopus 로고
    • Rotational superposition: A review of methods
    • Flower, D. R. 1999. Rotational superposition: a review of methods. J. Mol. Graph. Model. 17:238-244.
    • (1999) J. Mol. Graph. Model , vol.17 , pp. 238-244
    • Flower, D.R.1
  • 53
    • 0001382861 scopus 로고
    • A note on the rotational superposition problem
    • Diamond, R. 1988. A note on the rotational superposition problem. Acta Crystallogr. A44:211-216.
    • (1988) Acta Crystallogr. , vol.A44 , pp. 211-216
    • Diamond, R.1
  • 54
    • 0027053207 scopus 로고
    • On the multiple simultaneous superposition of molecular structures by rigid body transformations
    • Diamond, R. 1992. On the multiple simultaneous superposition of molecular structures by rigid body transformations. Protein Sci. 1:1279-1287.
    • (1992) Protein Sci. , vol.1 , pp. 1279-1287
    • Diamond, R.1
  • 55
    • 0029982530 scopus 로고    scopus 로고
    • The structural alignment between two proteins: Is there a unique answer?
    • Godzik, A. 1996. The structural alignment between two proteins: is there a unique answer? Protein Sci. 5:1325-1338.
    • (1996) Protein Sci. , vol.5 , pp. 1325-1338
    • Godzik, A.1
  • 56
    • 0242330730 scopus 로고    scopus 로고
    • Assessment of homology-based predictions in CASP5
    • Tramontano, A., and V. Morea. 2003. Assessment of homology-based predictions in CASP5. Proteins. 53:352-368.
    • (2003) Proteins , vol.53 , pp. 352-368
    • Tramontano, A.1    Morea, V.2
  • 58
    • 0242299187 scopus 로고    scopus 로고
    • Predictions without templates: New folds, secondary structure, and contacts in CASP5
    • Aloy, P., A. Stark, C. Hadley, and R. B. Russell. 2003. Predictions without templates: new folds, secondary structure, and contacts in CASP5. Proteins. 53:436-456.
    • (2003) Proteins , vol.53 , pp. 436-456
    • Aloy, P.1    Stark, A.2    Hadley, C.3    Russell, R.B.4
  • 59
    • 0042622381 scopus 로고    scopus 로고
    • LGA: A method for finding 3D similarities in protein structures
    • Zemla, A. 2003. LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res. 31:3370-3374.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3370-3374
    • Zemla, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.