메뉴 건너뛰기




Volumn 11, Issue SUPPLL.1, 2010, Pages

HORI: A web server to compute Higher Order Residue Interactions in protein structures

Author keywords

[No Author keywords available]

Indexed keywords

GLOBAL INTERACTION; IMPORTANT FEATURES; OVERALL STABILITIES; POTENTIAL ENERGY LANDSCAPES; PROTEIN STRUCTURES; STRUCTURAL BIOINFORMATICS; THREE-DIMENSIONAL STRUCTURE; THREE-DIMENSIONAL STRUCTURE OF PROTEIN; PROTEIN STRUCTURE ANALYSIS;

EID: 75149166625     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S1-S24     Document Type: Article
Times cited : (7)

References (42)
  • 1
    • 0002006297 scopus 로고
    • Are there pathways for protein folding?
    • Levinthal C. Are there pathways for protein folding?. J Chim Phys 1968, 65:44.
    • (1968) J Chim Phys , vol.65 , pp. 44
    • Levinthal, C.1
  • 2
    • 0015361994 scopus 로고
    • The formation and stabilization of protein structure
    • 1173893, 4565129
    • Anfinsen CB. The formation and stabilization of protein structure. Biochem J 1972, 128(4):737-749. 1173893, 4565129.
    • (1972) Biochem J , vol.128 , Issue.4 , pp. 737-749
    • Anfinsen, C.B.1
  • 3
    • 0033005899 scopus 로고    scopus 로고
    • Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
    • 2144252, 10048329
    • Betancourt MR, Thirumalai D. Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 1999, 8(2):361-369. 2144252, 10048329.
    • (1999) Protein Sci , vol.8 , Issue.2 , pp. 361-369
    • Betancourt, M.R.1    Thirumalai, D.2
  • 4
    • 0030806961 scopus 로고    scopus 로고
    • Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment
    • 10.1002/pro.5560060711, 2143734, 9232648
    • Munson PJ, Singh RK. Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment. Protein Sci 1997, 6(7):1467-1481. 10.1002/pro.5560060711, 2143734, 9232648.
    • (1997) Protein Sci , vol.6 , Issue.7 , pp. 1467-1481
    • Munson, P.J.1    Singh, R.K.2
  • 5
    • 0030059689 scopus 로고    scopus 로고
    • Forces contributing to the conformational stability of proteins
    • Pace CN, Shirley BA, McNutt M, Gajiwala K. Forces contributing to the conformational stability of proteins. FASEB J 1996, 10(1):75-83.
    • (1996) FASEB J , vol.10 , Issue.1 , pp. 75-83
    • Pace, C.N.1    Shirley, B.A.2    McNutt, M.3    Gajiwala, K.4
  • 6
    • 0029000696 scopus 로고
    • Knowledge-based potentials for proteins
    • 10.1016/0959-440X(95)80081-6, 7648326
    • Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995, 5(2):229-235. 10.1016/0959-440X(95)80081-6, 7648326.
    • (1995) Curr Opin Struct Biol , vol.5 , Issue.2 , pp. 229-235
    • Sippl, M.J.1
  • 7
    • 0033168866 scopus 로고    scopus 로고
    • Knowledge-based interaction potentials for proteins
    • 10.1002/(SICI)1097-0134(19990701)36:1<54::AID-PROT5>3.0.CO;2-B, 10373006
    • Rojnuckarin A, Subramaniam S. Knowledge-based interaction potentials for proteins. Proteins 1999, 36(1):54-67. 10.1002/(SICI)1097-0134(19990701)36:1<54::AID-PROT5>3.0.CO;2-B, 10373006.
    • (1999) Proteins , vol.36 , Issue.1 , pp. 54-67
    • Rojnuckarin, A.1    Subramaniam, S.2
  • 9
    • 38349144394 scopus 로고    scopus 로고
    • Understanding the molecular machinery of genetics through 3D structures
    • 10.1038/nrg2273, 18160966
    • Laskowski RA, Thornton JM. Understanding the molecular machinery of genetics through 3D structures. Nat Rev Genet 2008, 9(2):141-151. 10.1038/nrg2273, 18160966.
    • (2008) Nat Rev Genet , vol.9 , Issue.2 , pp. 141-151
    • Laskowski, R.A.1    Thornton, J.M.2
  • 10
    • 36448988254 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structure
    • 10.1038/nrm2281, 18037900
    • Lee D, Redfern O, Orengo C. Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 2007, 8(12):995-1005. 10.1038/nrm2281, 18037900.
    • (2007) Nat Rev Mol Cell Biol , vol.8 , Issue.12 , pp. 995-1005
    • Lee, D.1    Redfern, O.2    Orengo, C.3
  • 12
    • 0036667733 scopus 로고    scopus 로고
    • Knowledge-based potential functions in protein design
    • 10.1016/S0959-440X(02)00346-9, 12163066
    • Russ WP, Ranganathan R. Knowledge-based potential functions in protein design. Curr Opin Struct Biol 2002, 12(4):447-452. 10.1016/S0959-440X(02)00346-9, 12163066.
    • (2002) Curr Opin Struct Biol , vol.12 , Issue.4 , pp. 447-452
    • Russ, W.P.1    Ranganathan, R.2
  • 13
    • 33746592898 scopus 로고    scopus 로고
    • Knowledge-based potentials in protein design
    • 10.1016/j.sbi.2006.06.013, 16843652
    • Poole AM, Ranganathan R. Knowledge-based potentials in protein design. Curr Opin Struct Biol 2006, 16(4):508-513. 10.1016/j.sbi.2006.06.013, 16843652.
    • (2006) Curr Opin Struct Biol , vol.16 , Issue.4 , pp. 508-513
    • Poole, A.M.1    Ranganathan, R.2
  • 14
    • 68149166344 scopus 로고    scopus 로고
    • Graphical models of protein-protein interaction specificity from correlated mutations and interaction data
    • 10.1002/prot.22398, 19306342
    • Thomas J, Ramakrishnan N, Bailey-Kellogg C. Graphical models of protein-protein interaction specificity from correlated mutations and interaction data. Proteins 2009, 76(4):911-929. 10.1002/prot.22398, 19306342.
    • (2009) Proteins , vol.76 , Issue.4 , pp. 911-929
    • Thomas, J.1    Ramakrishnan, N.2    Bailey-Kellogg, C.3
  • 15
    • 43849095772 scopus 로고    scopus 로고
    • Graphical models of residue coupling in protein families
    • 10.1109/TCBB.2007.70225, 18451428
    • Thomas J, Ramakrishnan N, Bailey-Kellogg C. Graphical models of residue coupling in protein families. IEEE/ACM Trans Comput Biol Bioinform 2008, 5(2):183-197. 10.1109/TCBB.2007.70225, 18451428.
    • (2008) IEEE/ACM Trans Comput Biol Bioinform , vol.5 , Issue.2 , pp. 183-197
    • Thomas, J.1    Ramakrishnan, N.2    Bailey-Kellogg, C.3
  • 16
    • 0030054951 scopus 로고    scopus 로고
    • Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues
    • 10.1089/cmb.1996.3.213, 8811483
    • Singh RK, Tropsha A, Vaisman II. Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues. J Comput Biol 1996, 3(2):213-221. 10.1089/cmb.1996.3.213, 8811483.
    • (1996) J Comput Biol , vol.3 , Issue.2 , pp. 213-221
    • Singh, R.K.1    Tropsha, A.2    Vaisman, I.I.3
  • 17
    • 0026726481 scopus 로고
    • Topology fingerprint approach to the inverse protein folding problem
    • 10.1016/0022-2836(92)90693-E, 1522587
    • Godzik A, Kolinski A, Skolnick J. Topology fingerprint approach to the inverse protein folding problem. J Mol Biol 1992, 227(1):227-238. 10.1016/0022-2836(92)90693-E, 1522587.
    • (1992) J Mol Biol , vol.227 , Issue.1 , pp. 227-238
    • Godzik, A.1    Kolinski, A.2    Skolnick, J.3
  • 18
    • 0242369082 scopus 로고    scopus 로고
    • RAPTOR: optimal protein threading by linear programming
    • 10.1142/S0219720003000186, 15290783
    • Xu J, Li M, Kim D, Xu Y. RAPTOR: optimal protein threading by linear programming. J Bioinform Comput Biol 2003, 1(1):95-117. 10.1142/S0219720003000186, 15290783.
    • (2003) J Bioinform Comput Biol , vol.1 , Issue.1 , pp. 95-117
    • Xu, J.1    Li, M.2    Kim, D.3    Xu, Y.4
  • 19
    • 0042889108 scopus 로고    scopus 로고
    • Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations
    • 10.1093/bioinformatics/btg186, 12912835
    • Krishnamoorthy B, Tropsha A. Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics 2003, 19(12):1540-1548. 10.1093/bioinformatics/btg186, 12912835.
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1540-1548
    • Krishnamoorthy, B.1    Tropsha, A.2
  • 20
    • 33746124556 scopus 로고    scopus 로고
    • Biomolecules in the Computer: Jmol to the rescue
    • Herráez A. Biomolecules in the Computer: Jmol to the rescue. Biochem Educ 2006, 34:7.
    • (2006) Biochem Educ , vol.34 , pp. 7
    • Herráez, A.1
  • 21
    • 0029119568 scopus 로고
    • RASMOL: biomolecular graphics for all
    • 10.1016/S0968-0004(00)89080-5, 7482707
    • Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem Sci 1995, 20(9):374. 10.1016/S0968-0004(00)89080-5, 7482707.
    • (1995) Trends Biochem Sci , vol.20 , Issue.9 , pp. 374
    • Sayle, R.A.1    Milner-White, E.J.2
  • 22
    • 84888276251 scopus 로고    scopus 로고
    • PDB Wiki
    • PDB Wiki. , http://pdbwiki.org/index.php/PDB_FAQ#Q:_How_do_I_define_or_select_intera cting_residues.3F
  • 23
    • 84855229636 scopus 로고    scopus 로고
    • PIC: Protein Interactions Calculator
    • Web Server, 10.1093/nar/gkm423, 1933215, 17584791
    • Tina KG, Bhadra R, Srinivasan N. PIC: Protein Interactions Calculator. Nucleic Acids Res 2007, (35 Web Server):W473-476. 10.1093/nar/gkm423, 1933215, 17584791.
    • (2007) Nucleic Acids Res , Issue.35
    • Tina, K.G.1    Bhadra, R.2    Srinivasan, N.3
  • 24
    • 33644876493 scopus 로고    scopus 로고
    • SCOPPI: a structural classification of protein-protein interfaces
    • Database, 10.1093/nar/gkj099, 1347461, 16381874
    • Winter C, Henschel A, Kim WK, Schroeder M. SCOPPI: a structural classification of protein-protein interfaces. Nucleic Acids Res 2006, (34 Database):D310-314. 10.1093/nar/gkj099, 1347461, 16381874.
    • (2006) Nucleic Acids Res , Issue.34
    • Winter, C.1    Henschel, A.2    Kim, W.K.3    Schroeder, M.4
  • 25
    • 23144462926 scopus 로고    scopus 로고
    • SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment
    • Web Server, 10.1093/nar/gki398, 1160159, 15980496
    • Sobolev V, Eyal E, Gerzon S, Potapov V, Babor M, Prilusky J, Edelman M. SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment. Nucleic Acids Res 2005, (33 Web Server):W39-43. 10.1093/nar/gki398, 1160159, 15980496.
    • (2005) Nucleic Acids Res , Issue.33
    • Sobolev, V.1    Eyal, E.2    Gerzon, S.3    Potapov, V.4    Babor, M.5    Prilusky, J.6    Edelman, M.7
  • 26
    • 13044272912 scopus 로고    scopus 로고
    • Automated analysis of interatomic contacts in proteins
    • 10.1093/bioinformatics/15.4.327, 10320401
    • Sobolev V, Sorokine A, Prilusky J, Abola EE, Edelman M. Automated analysis of interatomic contacts in proteins. Bioinformatics 1999, 15(4):327-332. 10.1093/bioinformatics/15.4.327, 10320401.
    • (1999) Bioinformatics , vol.15 , Issue.4 , pp. 327-332
    • Sobolev, V.1    Sorokine, A.2    Prilusky, J.3    Abola, E.E.4    Edelman, M.5
  • 27
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247(4):536-540.
    • (1995) J Mol Biol , vol.247 , Issue.4 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 29
    • 0035896377 scopus 로고    scopus 로고
    • The TIM-barrel fold: a versatile framework for efficient enzymes
    • 10.1016/S0014-5793(01)02236-0, 11257493
    • Wierenga RK. The TIM-barrel fold: a versatile framework for efficient enzymes. FEBS Lett 2001, 492(3):193-198. 10.1016/S0014-5793(01)02236-0, 11257493.
    • (2001) FEBS Lett , vol.492 , Issue.3 , pp. 193-198
    • Wierenga, R.K.1
  • 30
    • 0015834475 scopus 로고
    • Comparison of super-secondary structures in proteins
    • 10.1016/0022-2836(73)90388-4, 4737475
    • Rao ST, Rossmann MG. Comparison of super-secondary structures in proteins. J Mol Biol 1973, 76(2):241-256. 10.1016/0022-2836(73)90388-4, 4737475.
    • (1973) J Mol Biol , vol.76 , Issue.2 , pp. 241-256
    • Rao, S.T.1    Rossmann, M.G.2
  • 31
    • 33744502382 scopus 로고    scopus 로고
    • Structure of a high-resolution crystal form of human triosephosphate isomerase: improvement of crystals using the gel-tube method
    • 10.1107/S1744309105008341, 1952429, 16511037
    • Kinoshita T, Maruki R, Warizaya M, Nakajima H, Nishimura S. Structure of a high-resolution crystal form of human triosephosphate isomerase: improvement of crystals using the gel-tube method. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005, 61(Pt 4):346-349. 10.1107/S1744309105008341, 1952429, 16511037.
    • (2005) Acta Crystallogr Sect F Struct Biol Cryst Commun , vol.61 , Issue.PART 4 , pp. 346-349
    • Kinoshita, T.1    Maruki, R.2    Warizaya, M.3    Nakajima, H.4    Nishimura, S.5
  • 32
    • 0034405702 scopus 로고    scopus 로고
    • Crystal structure of the peptidyl-cysteine decarboxylase EpiD complexed with a pentapeptide substrate
    • 10.1093/emboj/19.23.6299, 305864, 11101502
    • Blaesse M, Kupke T, Huber R, Steinbacher S. Crystal structure of the peptidyl-cysteine decarboxylase EpiD complexed with a pentapeptide substrate. EMBO J 2000, 19(23):6299-6310. 10.1093/emboj/19.23.6299, 305864, 11101502.
    • (2000) EMBO J , vol.19 , Issue.23 , pp. 6299-6310
    • Blaesse, M.1    Kupke, T.2    Huber, R.3    Steinbacher, S.4
  • 33
    • 0024413884 scopus 로고
    • Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-A resolution
    • 10.1021/bi00440a051, 2775751
    • Birktoft JJ, Rhodes G, Banaszak LJ. Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-A resolution. Biochemistry 1989, 28(14):6065-6081. 10.1021/bi00440a051, 2775751.
    • (1989) Biochemistry , vol.28 , Issue.14 , pp. 6065-6081
    • Birktoft, J.J.1    Rhodes, G.2    Banaszak, L.J.3
  • 34
    • 0001554681 scopus 로고
    • Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin
    • 10.1073/pnas.81.19.6014, 391849, 16593516
    • Teeter MM. Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin. Proc Natl Acad Sci USA 1984, 81(19):6014-6018. 10.1073/pnas.81.19.6014, 391849, 16593516.
    • (1984) Proc Natl Acad Sci USA , vol.81 , Issue.19 , pp. 6014-6018
    • Teeter, M.M.1
  • 35
    • 84888278707 scopus 로고    scopus 로고
    • HORI Results for 1CRN
    • HORI Results for 1CRN. , http://caps.ncbs.res.in/hori/hori_results/er_hori_SatDec13185917IST2008. html
  • 36
    • 0031574909 scopus 로고    scopus 로고
    • Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereochemical analysis
    • 10.1006/jmbi.1997.1000, 9175860
    • Longhi S, Czjzek M, Lamzin V, Nicolas A, Cambillau C. Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereochemical analysis. J Mol Biol 1997, 268(4):779-799. 10.1006/jmbi.1997.1000, 9175860.
    • (1997) J Mol Biol , vol.268 , Issue.4 , pp. 779-799
    • Longhi, S.1    Czjzek, M.2    Lamzin, V.3    Nicolas, A.4    Cambillau, C.5
  • 37
    • 0026583770 scopus 로고
    • Fusarium solani cutinase is a lipolytic enzyme with a catalytic serine accessible to solvent
    • 10.1038/356615a0, 1560844
    • Martinez C, De Geus P, Lauwereys M, Matthyssens G, Cambillau C. Fusarium solani cutinase is a lipolytic enzyme with a catalytic serine accessible to solvent. Nature 1992, 356(6370):615-618. 10.1038/356615a0, 1560844.
    • (1992) Nature , vol.356 , Issue.6370 , pp. 615-618
    • Martinez, C.1    De Geus, P.2    Lauwereys, M.3    Matthyssens, G.4    Cambillau, C.5
  • 38
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
    • Database, 10.1093/nar/gkh028, 308762, 14681376
    • Porter CT, Bartlett GJ, Thornton JM. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 2004, (32 Database):D129-133. 10.1093/nar/gkh028, 308762, 14681376.
    • (2004) Nucleic Acids Res , Issue.32
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 39
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 40
    • 0031662892 scopus 로고    scopus 로고
    • Engineering an intertwined form of CD2 for stability and assembly
    • 10.1038/1816, 9731771
    • Murray AJ, Head JG, Barker JJ, Brady RL. Engineering an intertwined form of CD2 for stability and assembly. Nat Struct Biol 1998, 5(9):778-782. 10.1038/1816, 9731771.
    • (1998) Nat Struct Biol , vol.5 , Issue.9 , pp. 778-782
    • Murray, A.J.1    Head, J.G.2    Barker, J.J.3    Brady, R.L.4
  • 41
    • 0036108484 scopus 로고    scopus 로고
    • 3D domain swapping: as domains continue to swap
    • 10.1110/ps.0201402, 2373619, 12021428
    • Liu Y, Eisenberg D. 3D domain swapping: as domains continue to swap. Protein Sci 2002, 11(6):1285-1299. 10.1110/ps.0201402, 2373619, 12021428.
    • (2002) Protein Sci , vol.11 , Issue.6 , pp. 1285-1299
    • Liu, Y.1    Eisenberg, D.2
  • 42
    • 84888284622 scopus 로고    scopus 로고
    • HORI Results for 1A64
    • HORI Results for 1A64. , http://caps.ncbs.res.in/hori/hori_results/er_hori_SatDec13182345IST2008. html


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.