메뉴 건너뛰기




Volumn 10, Issue 1, 2009, Pages 67-81

Distance matrix-based approach to protein structure prediction

Author keywords

Distance geometry; Distance matrix; Elastic networks; Protein structure prediction; Protein structure refinement; Spectral analysis

Indexed keywords

PROTEINASE;

EID: 60849087655     PISSN: 1345711X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10969-009-9062-2     Document Type: Article
Times cited : (40)

References (62)
  • 2
    • 0343621535 scopus 로고    scopus 로고
    • AAindex: Amino acid index database
    • 10.1093/nar/28.1.374
    • S Kawashima M Kanehisa 2000 AAindex: amino acid index database Nucleic Acids Res 28 374 10.1093/nar/28.1.374
    • (2000) Nucleic Acids Res , vol.28 , pp. 374
    • Kawashima, S.1    Kanehisa, M.2
  • 5
    • 10844225367 scopus 로고    scopus 로고
    • Principal eigenvector of contact matrices and hydrophobicity profiles in proteins
    • 10.1002/prot.20240
    • U Bastolla M Porto HE Roman M Vendruscolo 2005 Principal eigenvector of contact matrices and hydrophobicity profiles in proteins Proteins: Struct Funct Bioinform 58 22 30 10.1002/prot.20240
    • (2005) Proteins: Struct Funct Bioinform , vol.58 , pp. 22-30
    • Bastolla, U.1    Porto, M.2    Roman, H.E.3    Vendruscolo, M.4
  • 6
    • 1642389927 scopus 로고    scopus 로고
    • Local feature frequency profile: A method to measure structural similarity in proteins
    • 10.1073/pnas.0308656100
    • IG Choi J Kwon SH Kim 2004 Local feature frequency profile: a method to measure structural similarity in proteins Proc Natl Acad Sci USA 101 3797 3802 10.1073/pnas.0308656100
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 3797-3802
    • Choi, I.G.1    Kwon, J.2    Kim, S.H.3
  • 7
    • 36549054018 scopus 로고    scopus 로고
    • Conformational analysis of alternative protein structures
    • 10.1093/bioinformatics/btm499
    • FS Domingues J Rahnenfuhrer T Lengauer 2007 Conformational analysis of alternative protein structures Bioinformatics 23 3131 3138 10.1093/ bioinformatics/btm499
    • (2007) Bioinformatics , vol.23 , pp. 3131-3138
    • Domingues, F.S.1    Rahnenfuhrer, J.2    Lengauer, T.3
  • 8
    • 0027504807 scopus 로고
    • Regularities in interaction patterns of globular-proteins
    • 10.1093/protein/6.8.801
    • A Godzik J Skolnick A Kolinski 1993 Regularities in interaction patterns of globular-proteins Protein Eng 6 801 810 10.1093/protein/6.8.801
    • (1993) Protein Eng , vol.6 , pp. 801-810
    • Godzik, A.1    Skolnick, J.2    Kolinski, A.3
  • 9
    • 8444243745 scopus 로고    scopus 로고
    • Accurate detection of very sparse sequence motifs
    • 10.1089/cmb.2004.11.843
    • A Heger M Lappe L Holm 2004 Accurate detection of very sparse sequence motifs J Comput Biol 11 843 857 10.1089/cmb.2004.11.843
    • (2004) J Comput Biol , vol.11 , pp. 843-857
    • Heger, A.1    Lappe, M.2    Holm, L.3
  • 10
    • 0033824470 scopus 로고    scopus 로고
    • DaliLite workbench for protein structure comparison
    • 10.1093/bioinformatics/16.6.566
    • L Holm J Park 2000 DaliLite workbench for protein structure comparison Bioinformatics 16 566 567 10.1093/bioinformatics/16.6.566
    • (2000) Bioinformatics , vol.16 , pp. 566-567
    • Holm, L.1    Park, J.2
  • 11
    • 32544461476 scopus 로고    scopus 로고
    • Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions
    • 10.1093/bioinformatics/bti828
    • YM Huang C Bystroff 2006 Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions Bioinformatics 22 413 422 10.1093/bioinformatics/bti828
    • (2006) Bioinformatics , vol.22 , pp. 413-422
    • Huang, Y.M.1    Bystroff, C.2
  • 12
    • 0036081436 scopus 로고    scopus 로고
    • In search for more accurate alignments in the twilight zone
    • 10.1110/ps.4820102
    • L Jaroszewski WZ Li A Godzik 2002 In search for more accurate alignments in the twilight zone Protein Sci 11 1702 1713 10.1110/ps.4820102
    • (2002) Protein Sci , vol.11 , pp. 1702-1713
    • Jaroszewski, L.1    Li, W.Z.2    Godzik, A.3
  • 13
    • 4344656723 scopus 로고    scopus 로고
    • Approximate protein structural alignment in polynomial time
    • 10.1073/pnas.0404383101
    • R Kolodny N Linial 2004 Approximate protein structural alignment in polynomial time Proc Natl Acad Sci USA 101 12201 12206 10.1073/pnas.0404383101
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 12201-12206
    • Kolodny, R.1    Linial, N.2
  • 15
    • 54349091030 scopus 로고    scopus 로고
    • Protein co-evolution, co-adaptation and interactions
    • 10.1038/emboj.2008.189
    • F Pazos A Valencia 2008 Protein co-evolution, co-adaptation and interactions EMBO J 27 2648 2655 10.1038/emboj.2008.189
    • (2008) EMBO J , vol.27 , pp. 2648-2655
    • Pazos, F.1    Valencia, A.2
  • 16
    • 21144481493 scopus 로고
    • Analysis of the 3-dimensional structure of proteins in terms of residue contact matrices. 1. the contact criterion
    • MA Rodionov SG Galaktionov 1992 Analysis of the 3-dimensional structure of proteins in terms of residue contact matrices. 1. The contact criterion Mol Biol 26 773 776
    • (1992) Mol Biol , vol.26 , pp. 773-776
    • Rodionov, M.A.1    Galaktionov, S.G.2
  • 17
    • 24144476642 scopus 로고    scopus 로고
    • The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships
    • 10.1093/bioinformatics/bti564
    • T Sato Y Yamanishi M Kanehisa H Toh 2005 The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships Bioinformatics 21 3482 3489 10.1093/bioinformatics/bti564
    • (2005) Bioinformatics , vol.21 , pp. 3482-3489
    • Sato, T.1    Yamanishi, Y.2    Kanehisa, M.3    Toh, H.4
  • 18
    • 33749870873 scopus 로고    scopus 로고
    • Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions
    • 10.1093/bioinformatics/btl419
    • T Sato Y Yamanishi K Horimoto M Kanehisa H Toh 2006 Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions Bioinformatics 22 2488 2492 10.1093/bioinformatics/btl419
    • (2006) Bioinformatics , vol.22 , pp. 2488-2492
    • Sato, T.1    Yamanishi, Y.2    Horimoto, K.3    Kanehisa, M.4    Toh, H.5
  • 19
    • 0034084540 scopus 로고    scopus 로고
    • Objective comparison of protein structures: Error-scaled difference distance matrices
    • 10.1107/S0907444900003723
    • TR Schneider 2000 Objective comparison of protein structures: error-scaled difference distance matrices Acta Crystallogr D Biol Crystallogr 56 714 721 10.1107/S0907444900003723
    • (2000) Acta Crystallogr D Biol Crystallogr , vol.56 , pp. 714-721
    • Schneider, T.R.1
  • 20
    • 18844415920 scopus 로고    scopus 로고
    • Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles
    • 10.1002/prot.20402
    • DA Snyder GT Montelione 2005 Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles Proteins: Struct Funct Bioinform 59 673 686 10.1002/prot.20402
    • (2005) Proteins: Struct Funct Bioinform , vol.59 , pp. 673-686
    • Snyder, D.A.1    Montelione, G.T.2
  • 22
    • 0033997724 scopus 로고    scopus 로고
    • Protein structure alignment using a genetic algorithm
    • 10.1002/(SICI)1097-0134(20000301)38:4<428::AID-PROT8>3.0.CO;2-N
    • JD Szustakowski ZP Weng 2000 Protein structure alignment using a genetic algorithm Proteins-Structure Funct Genet 38 428 440 10.1002/(SICI)1097- 0134(20000301)38:4<428::AID-PROT8>3.0.CO;2-N
    • (2000) Proteins-Structure Funct Genet , vol.38 , pp. 428-440
    • Szustakowski, J.D.1    Weng, Z.P.2
  • 23
    • 8444245971 scopus 로고    scopus 로고
    • Approximate multiple protein structure alignment using the sum-of-pairs distance
    • 10.1089/cmb.2004.11.986
    • JP Ye R Janardan 2004 Approximate multiple protein structure alignment using the sum-of-pairs distance J Comput Biol 11 986 1000 10.1089/cmb.2004.11. 986
    • (2004) J Comput Biol , vol.11 , pp. 986-1000
    • Ye, J.P.1    Janardan, R.2
  • 24
    • 33644640467 scopus 로고    scopus 로고
    • Protein structure similarity from principle component correlation analysis
    • 10pp
    • Zhou XB, Chou J, Wong STC (2006) Protein structure similarity from principle component correlation analysis. BMC Bioinformatics 7:40 (10pp)
    • (2006) BMC Bioinformatics , vol.7 , pp. 40
    • Zhou, X.B.1    Chou, J.2    Wong, S.T.C.3
  • 25
    • 0017024625 scopus 로고
    • Statistical thermodynamics of random networks
    • Flory PJ (1976) Statistical thermodynamics of random networks. Proc R Soc Lond A: Math Phys Eng Sci 351:351-380
    • (1976) Proc R Soc Lond A: Math Phys Eng Sci , vol.351 , pp. 351-380
    • Flory, P.J.1
  • 26
    • 0024621473 scopus 로고
    • Chain dimensions and fluctuations in random elastomeric networks 1 phantom Gaussian networks in the undeformed state
    • 10.1021/ma00193a070
    • A Kloczkowski JE Mark B Erman 1989 Chain dimensions and fluctuations in random elastomeric networks 1 phantom Gaussian networks in the undeformed state Macromolecules 22 1423 1432 10.1021/ma00193a070
    • (1989) Macromolecules , vol.22 , pp. 1423-1432
    • Kloczkowski, A.1    Mark, J.E.2    Erman, B.3
  • 27
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • 10.1016/S1359-0278(97)00024-2
    • I Bahar AR Atilgan B Erman 1997 Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential Fold Des 2 173 181 10.1016/S1359-0278(97)00024-2
    • (1997) Fold des , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 28
    • 0345973041 scopus 로고    scopus 로고
    • Gaussian dynamics of folded proteins
    • 10.1103/PhysRevLett.79.3090
    • T Haliloglu I Bahar B Erman 1997 Gaussian dynamics of folded proteins Phys Rev Lett 79 3090 3093 10.1103/PhysRevLett.79.3090
    • (1997) Phys Rev Lett , vol.79 , pp. 3090-3093
    • Haliloglu, T.1    Bahar, I.2    Erman, B.3
  • 29
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • 10.1103/PhysRevLett.77.1905
    • MM Tirion 1996 Large amplitude elastic motions in proteins from a single-parameter, atomic analysis Phys Rev Lett 77 1905 1908 10.1103/PhysRevLett.77.1905
    • (1996) Phys Rev Lett , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 30
    • 0035996990 scopus 로고    scopus 로고
    • Dynamics of proteins in crystals: Comparison of experiment with simple models
    • 10.1016/S0006-3495(02)75203-X
    • S Kundu JS Melton DC Sorensen GN Phillips 2002 Dynamics of proteins in crystals: comparison of experiment with simple models Biophys J 83 723 732 10.1016/S0006-3495(02)75203-X
    • (2002) Biophys J , vol.83 , pp. 723-732
    • Kundu, S.1    Melton, J.S.2    Sorensen, D.C.3    Phillips, G.N.4
  • 31
    • 33748189629 scopus 로고    scopus 로고
    • The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models
    • 10.1021/ct600060d
    • TZ Sen YP Feng JV Garcia A Kloczkowski RL Jernigan 2006 The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models J Chem Theory Comput 2 696 704 10.1021/ct600060d
    • (2006) J Chem Theory Comput , vol.2 , pp. 696-704
    • Sen, T.Z.1    Feng, Y.P.2    Garcia, J.V.3    Kloczkowski, A.4    Jernigan, R.L.5
  • 32
    • 0035132230 scopus 로고    scopus 로고
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model
    • 10.1016/S0006-3495(01)76033-X
    • AR Atilgan SR Durell RL Jernigan MC Demirel O Keskin I Bahar 2001 Anisotropy of fluctuation dynamics of proteins with an elastic network model Biophys J 80 505 515 10.1016/S0006-3495(01)76033-X
    • (2001) Biophys J , vol.80 , pp. 505-515
    • Atilgan, A.R.1    Durell, S.R.2    Jernigan, R.L.3    Demirel, M.C.4    Keskin, O.5    Bahar, I.6
  • 33
    • 0037080323 scopus 로고    scopus 로고
    • Molecular mechanisms of chaperonin GroEL-GroES function
    • 10.1021/bi011393x
    • O Keskin I Bahar D Flatow DG Covell RL Jernigan 2002 Molecular mechanisms of chaperonin GroEL-GroES function Biochemistry 41 491 501 10.1021/bi011393x
    • (2002) Biochemistry , vol.41 , pp. 491-501
    • Keskin, O.1    Bahar, I.2    Flatow, D.3    Covell, D.G.4    Jernigan, R.L.5
  • 34
    • 0035996975 scopus 로고    scopus 로고
    • Relating molecular flexibility to function: A case study of tubulin
    • 10.1016/S0006-3495(02)75199-0
    • O Keskin SR Durell I Bahar RL Jernigan DG Covell 2002 Relating molecular flexibility to function: a case study of tubulin Biophys J 83 663 680 10.1016/S0006-3495(02)75199-0
    • (2002) Biophys J , vol.83 , pp. 663-680
    • Keskin, O.1    Durell, S.R.2    Bahar, I.3    Jernigan, R.L.4    Covell, D.G.5
  • 35
    • 1042291214 scopus 로고    scopus 로고
    • Myosin flexibility: Structural domains and collective vibrations
    • 10.1002/prot.10476
    • I Navizet R Lavery RL Jernigan 2004 Myosin flexibility: structural domains and collective vibrations Proteins-Structure Funct Genet 54 384 393 10.1002/prot.10476
    • (2004) Proteins-Structure Funct Genet , vol.54 , pp. 384-393
    • Navizet, I.1    Lavery, R.2    Jernigan, R.L.3
  • 36
    • 4344685227 scopus 로고    scopus 로고
    • Global ribosome motions revealed with elastic network model
    • 10.1016/j.jsb.2004.01.005
    • YM Wang AJ Rader I Bahar RL Jernigan 2004 Global ribosome motions revealed with elastic network model J Struct Biol 147 302 314 10.1016/j.jsb.2004.01.005
    • (2004) J Struct Biol , vol.147 , pp. 302-314
    • Wang, Y.M.1    Rader, A.J.2    Bahar, I.3    Jernigan, R.L.4
  • 37
    • 27744512500 scopus 로고    scopus 로고
    • Comparison of tRNA motions in the free and ribosomal bound structures
    • 10.1529/biophysj.105.064840
    • YM Wang RL Jernigan 2005 Comparison of tRNA motions in the free and ribosomal bound structures Biophys J 89 3399 3409 10.1529/biophysj.105.064840
    • (2005) Biophys J , vol.89 , pp. 3399-3409
    • Wang, Y.M.1    Jernigan, R.L.2
  • 38
    • 58149157892 scopus 로고    scopus 로고
    • Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome
    • Yan A, Wang Y, Kloczkowski A, Jernigan RL (2008) Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome. J Chem Theory Comput 4:1757-1767
    • (2008) J Chem Theory Comput , vol.4 , pp. 1757-1767
    • Yan, A.1    Wang, Y.2    Kloczkowski, A.3    Jernigan, R.L.4
  • 39
    • 0000892481 scopus 로고
    • Stable calculation of coordinates from distance information
    • 10.1107/S0567739478000522
    • GM Crippen TF Havel 1978 Stable calculation of coordinates from distance information Acta Crystallogr A 34 282 284 10.1107/S0567739478000522
    • (1978) Acta Crystallogr A , vol.34 , pp. 282-284
    • Crippen, G.M.1    Havel, T.F.2
  • 40
    • 84985641098 scopus 로고
    • Effects of distance constraints on macromolecular conformation. 2. Simulation of experimental results and theoretical predictions
    • 10.1002/bip.1979.360180108
    • TF Havel GM Crippen ID Kuntz 1979 Effects of distance constraints on macromolecular conformation. 2. Simulation of experimental results and theoretical predictions Biopolymers 18 73 81 10.1002/bip.1979.360180108
    • (1979) Biopolymers , vol.18 , pp. 73-81
    • Havel, T.F.1    Crippen, G.M.2    Kuntz, I.D.3
  • 41
    • 0021097083 scopus 로고
    • The combinatorial distance geometry method for the calculation of molecular-conformation. 1. A new approach to an old problem
    • 10.1016/0022-5193(83)90112-1
    • TF Havel ID Kuntz GM Crippen 1983 The combinatorial distance geometry method for the calculation of molecular-conformation. 1. A new approach to an old problem J Theor Biol 104 359 381 10.1016/0022-5193(83)90112-1
    • (1983) J Theor Biol , vol.104 , pp. 359-381
    • Havel, T.F.1    Kuntz, I.D.2    Crippen, G.M.3
  • 42
    • 0021097106 scopus 로고
    • The combinatorial distance geometry method for the calculation of molecular-conformation. 2. Sample problems and computational statistics
    • 10.1016/0022-5193(83)90113-3
    • TF Havel GM Crippen ID Kuntz JM Blaney 1983 The combinatorial distance geometry method for the calculation of molecular-conformation. 2. Sample problems and computational statistics J Theor Biol 104 383 400 10.1016/0022-5193(83)90113-3
    • (1983) J Theor Biol , vol.104 , pp. 383-400
    • Havel, T.F.1    Crippen, G.M.2    Kuntz, I.D.3    Blaney, J.M.4
  • 44
    • 60849120170 scopus 로고
    • Crystallographic approaches to the dynamics of ligand-binding to myoglobin
    • GA Petsko H Frauenfelder 1980 Crystallographic approaches to the dynamics of ligand-binding to myoglobin Fed Proc 39 1648
    • (1980) Fed Proc , vol.39 , pp. 1648
    • Petsko, G.A.1    Frauenfelder, H.2
  • 45
    • 0037022347 scopus 로고    scopus 로고
    • Flexibility and packing in proteins
    • 10.1073/pnas.032522499
    • B Halle 2002 Flexibility and packing in proteins Proc Natl Acad Sci USA 99 1274 1279 10.1073/pnas.032522499
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 1274-1279
    • Halle, B.1
  • 46
    • 33846965982 scopus 로고    scopus 로고
    • Prediction of protein B-factors using multi-class bounded SVM
    • 10.2174/092986607779816078
    • P Chen B Wang HS Wong DS Huang 2007 Prediction of protein B-factors using multi-class bounded SVM Protein Pept Lett 14 185 190 10.2174/092986607779816078
    • (2007) Protein Pept Lett , vol.14 , pp. 185-190
    • Chen, P.1    Wang, B.2    Wong, H.S.3    Huang, D.S.4
  • 47
    • 38949218425 scopus 로고    scopus 로고
    • Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes
    • 10.1016/j.str.2007.12.011
    • L Yang G Song A Carriquiry RL Jernigan 2008 Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes Structure 16 321 330 10.1016/j.str.2007.12. 011
    • (2008) Structure , vol.16 , pp. 321-330
    • Yang, L.1    Song, G.2    Carriquiry, A.3    Jernigan, R.L.4
  • 48
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force-an approach to the knowledge-based prediction of local structures in globular-proteins
    • Sippl MJ (1990) Calculation of conformational ensembles from potentials of mean force-an approach to the knowledge-based prediction of local structures in globular-proteins. J Mol Biol 213:859-883
    • (1990) J Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 49
    • 0026704815 scopus 로고
    • Detection of native-like models for amino-acid-sequences of unknown 3-dimensional structure in a data-base of known protein conformations
    • MJ Sippl 1992 Detection of native-like models for amino-acid-sequences of unknown 3-dimensional structure in a data-base of known protein conformations Proteins 13 258 271
    • (1992) Proteins , vol.13 , pp. 258-271
    • Sippl, M.J.1
  • 50
    • 0027490731 scopus 로고
    • Recognition of errors in 3-dimensional structures of proteins
    • 10.1002/prot.340170404
    • MJ Sippl 1993 Recognition of errors in 3-dimensional structures of proteins Proteins-Structure Funct Genet 17 355 362 10.1002/prot.340170404
    • (1993) Proteins-Structure Funct Genet , vol.17 , pp. 355-362
    • Sippl, M.J.1
  • 51
    • 0029000696 scopus 로고
    • Knowledge-based potentials for proteins
    • Sippl MJ (1995) Knowledge-based potentials for proteins. Curr Opin Struct Biol 5:229-235
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 52
    • 0022704535 scopus 로고
    • Cayley-Menger coordinates
    • 10.1073/pnas.83.8.2283
    • MJ Sippl HA Scheraga 1986 Cayley-Menger coordinates Proc Natl Acad Sci USA 83 2283 2287 10.1073/pnas.83.8.2283
    • (1986) Proc Natl Acad Sci USA , vol.83 , pp. 2283-2287
    • Sippl, M.J.1    Scheraga, H.A.2
  • 53
    • 0022048703 scopus 로고
    • Solution of the embedding problem and decomposition of symmetric-matrices
    • 10.1073/pnas.82.8.2197
    • MJ Sippl HA Scheraga 1985 Solution of the embedding problem and decomposition of symmetric-matrices Proc Natl Acad Sci USA 82 2197 2201 10.1073/pnas.82.8.2197
    • (1985) Proc Natl Acad Sci USA , vol.82 , pp. 2197-2201
    • Sippl, M.J.1    Scheraga, H.A.2
  • 54
    • 0031582083 scopus 로고    scopus 로고
    • Novel knowledge-based mean force potential at atomic level
    • 10.1006/jmbi.1996.0868
    • F Melo E Feytmans 1997 Novel knowledge-based mean force potential at atomic level J Mol Biol 267 207 222 10.1006/jmbi.1996.0868
    • (1997) J Mol Biol , vol.267 , pp. 207-222
    • Melo, F.1    Feytmans, E.2
  • 55
    • 0032540222 scopus 로고    scopus 로고
    • Assessing protein structures with a non-local atomic interaction energy
    • 10.1006/jmbi.1998.1665
    • F Melo E Feytmans 1998 Assessing protein structures with a non-local atomic interaction energy J Mol Biol 277 1141 1152 10.1006/jmbi.1998.1665
    • (1998) J Mol Biol , vol.277 , pp. 1141-1152
    • Melo, F.1    Feytmans, E.2
  • 56
    • 19544370004 scopus 로고    scopus 로고
    • Comparison of X-ray and NMR structures: Is there a systematic difference in residue contacts between X-ray and NMR-resolved protein structures?
    • 10.1002/prot.20491
    • SO Garbuzynskiy BS Melnik MY Lobanov AV Finkelstein OV Galzitskaya 2005 Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray and NMR-resolved protein structures? Proteins: Struct Funct Bioinform 60 139 147 10.1002/prot.20491
    • (2005) Proteins: Struct Funct Bioinform , vol.60 , pp. 139-147
    • Garbuzynskiy, S.O.1    Melnik, B.S.2    Lobanov, M.Y.3    Finkelstein, A.V.4    Galzitskaya, O.V.5
  • 57
    • 33846086348 scopus 로고    scopus 로고
    • PIDD: Database for protein inter-atomic distance distributions
    • 10.1093/nar/gkl802
    • D Wu F Cui R Jernigan ZJ Wu 2007 PIDD: database for protein inter-atomic distance distributions Nucleic Acids Res 35 D202 D207 10.1093/nar/gkl802
    • (2007) Nucleic Acids Res , vol.35
    • Wu, D.1    Cui, F.2    Jernigan, R.3    Wu, Z.J.4
  • 60
    • 37049014272 scopus 로고    scopus 로고
    • Version 1.2 of the crystallography and NMR system
    • 10.1038/nprot.2007.406
    • AT Brunger 2007 Version 1.2 of the crystallography and NMR system Nat Protoc 2 2728 2733 10.1038/nprot.2007.406
    • (2007) Nat Protoc , vol.2 , pp. 2728-2733
    • Brunger, A.T.1
  • 61
    • 34249874640 scopus 로고    scopus 로고
    • Refinement of NMR-determined protein structures with database derived mean-force potentials
    • 10.1002/prot.21358
    • D Wu R Jernigan ZJ Wu 2007 Refinement of NMR-determined protein structures with database derived mean-force potentials Proteins: Struct Funct Bioinform 68 232 242 10.1002/prot.21358
    • (2007) Proteins: Struct Funct Bioinform , vol.68 , pp. 232-242
    • Wu, D.1    Jernigan, R.2    Wu, Z.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.