메뉴 건너뛰기




Volumn 21, Issue 8, 2005, Pages 1472-1478

M-ZDOCK: A grid-based approach for Cn symmetric multimer docking

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOLIPASE A2; RIBONUCLEASE A; TRYPSIN INHIBITOR; VIRUS ENVELOPE PROTEIN;

EID: 17444385658     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti229     Document Type: Article
Times cited : (145)

References (37)
  • 2
    • 0344980718 scopus 로고    scopus 로고
    • Construction of molecular assemblies via docking: Modeling of tetramers with D2 symmetry
    • Berchanski,A. and Eisenstein,M. (2003) Construction of molecular assemblies via docking: modeling of tetramers with D2 symmetry. Proteins, 53, 817-829.
    • (2003) Proteins , vol.53 , pp. 817-829
    • Berchanski, A.1    Eisenstein, M.2
  • 5
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking
    • Chen,R. and Weng,Z. (2003) A novel shape complementarity scoring function for protein-protein docking. Proteins, 51, 397-408.
    • (2003) Proteins , vol.51 , pp. 397-408
    • Chen, R.1    Weng, Z.2
  • 6
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: An initial-stage protein-docking algorithm
    • Chen,R., Li,L. and Weng,Z. (2003a) ZDOCK: an initial-stage protein-docking algorithm. Proteins, 52, 80-87.
    • (2003) Proteins , vol.52 , pp. 80-87
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 7
    • 0037561868 scopus 로고    scopus 로고
    • ZDOCK predictions for the CAPRI challenge
    • Chen,R., Tong,W., Mintseris,J., Li,L. and Weng,Z. (2003b) ZDOCK predictions for the CAPRI challenge. Proteins, 52, 68-73.
    • (2003) Proteins , vol.52 , pp. 68-73
    • Chen, R.1    Tong, W.2    Mintseris, J.3    Li, L.4    Weng, Z.5
  • 8
    • 17444429573 scopus 로고    scopus 로고
    • The PyMOL Molecular Graphics System
    • Delano,W.L. (2002). The PyMOL Molecular Graphics System.
    • (2002)
    • Delano, W.L.1
  • 9
    • 0031566966 scopus 로고    scopus 로고
    • Modeling supra-molecular helices: Extension of the molecular surface recognition algorithm and application to the protein coat of the tobacco mosaic virus
    • Eisenstein,M., Shariv,I., Koren,G., Friesem,A.A. and Katchalski-Katzir,E. (1997) Modeling supra-molecular helices: extension of the molecular surface recognition algorithm and application to the protein coat of the tobacco mosaic virus. J. Mol. Biol., 266, 135-143.
    • (1997) J. Mol. Biol. , vol.266 , pp. 135-143
    • Eisenstein, M.1    Shariv, I.2    Koren, G.3    Friesem, A.A.4    Katchalski-Katzir, E.5
  • 10
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • Gabb,H.A., Jackson,R.M. and Sternberg,M.J. (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol., 272, 106-120.
    • (1997) J. Mol. Biol. , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.3
  • 12
    • 0003437218 scopus 로고
    • Addison-Wesley Publishing Co., Reading, Mass
    • Goldstein,H. (1980). Classical Mechanics. Addison-Wesley Publishing Co., Reading, Mass.
    • (1980) Classical Mechanics
    • Goldstein, H.1
  • 13
    • 0033151762 scopus 로고    scopus 로고
    • Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography
    • Gonin,P., Xu,Y., Milon,L., Dabernat,S., Morr,M., Kumar,R., Lacombe,M.L., Janin,J. and Lascu,I. (1999) Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography. Biochemistry, 38 7265-7272.
    • (1999) Biochemistry , vol.38 , pp. 7265-7272
    • Gonin, P.1    Xu, Y.2    Milon, L.3    Dabernat, S.4    Morr, M.5    Kumar, R.6    Lacombe, M.L.7    Janin, J.8    Lascu, I.9
  • 16
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • Halperin,I., Ma,B., Wolfson,H. and Nussinov,R. (2002) Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins, 47, 409-443.
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 17
    • 0034737315 scopus 로고    scopus 로고
    • The BPTI decamer observed in acidic pH crystal forms pre-exists as a stable species in solution
    • Hamiaux,C., Perez,J., Prange,T., Veesler,S., Ries-Kautt,M. and Vachette,P. (2000) The BPTI decamer observed in acidic pH crystal forms pre-exists as a stable species in solution. J. Mol. Biol., 297, 697-712.
    • (2000) J. Mol. Biol. , vol.297 , pp. 697-712
    • Hamiaux, C.1    Perez, J.2    Prange, T.3    Veesler, S.4    Ries-Kautt, M.5    Vachette, P.6
  • 18
    • 0030792944 scopus 로고    scopus 로고
    • Structural adaptations in the specialized bacteriophage T4 co-chaperonin Gp31 expand the size of the Anfinsen cage
    • Hunt,J.F., van der Vies,S.M., Henry,L. and Deisenhofer,J. (1997) Structural adaptations in the specialized bacteriophage T4 co-chaperonin Gp31 expand the size of the Anfinsen cage. Cell, 90, 361-371.
    • (1997) Cell , vol.90 , pp. 361-371
    • Hunt, J.F.1    van der Vies, S.M.2    Henry, L.3    Deisenhofer, J.4
  • 19
    • 4344596245 scopus 로고    scopus 로고
    • Structure of adeno-associated virus type 2 Rep40-ADP complex: Insight into nucleotide recognition and catalysis by superfamily 3 helicases
    • James,J.A., Aggarwal,A.K., Linden,R.M. and Escalante,C.R. (2004) Structure of adeno-associated virus type 2 Rep40-ADP complex: insight into nucleotide recognition and catalysis by superfamily 3 helicases. Proc. Natl Acad. Sci. USA, 101, 12455-12460.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 12455-12460
    • James, J.A.1    Aggarwal, A.K.2    Linden, R.M.3    Escalante, C.R.4
  • 20
    • 0026572775 scopus 로고
    • Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
    • Katchalski-Katzir,E., Shariv,I., Eisenstein,M., Friesem,A.A., Aflalo,C. and Vakser,I.A. (1992) Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl Acad. Sci. USA, 89, 2195-2199.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.A.4    Aflalo, C.5    Vakser, I.A.6
  • 22
    • 11244255410 scopus 로고    scopus 로고
    • Oligomerization of the GABA transporter-1 is driven by an interplay of polar and hydrophobic interactions in transmembrane helix II
    • Korkhov,V.M., Farhan,H., Freissmuth,M. and Sitte,H.H. (2004) Oligomerization of the GABA transporter-1 is driven by an interplay of polar and hydrophobic interactions in transmembrane helix II. J. Biol. Chem., 279, 55728-55736.
    • (2004) J. Biol. Chem. , vol.279 , pp. 55728-55736
    • Korkhov, V.M.1    Farhan, H.2    Freissmuth, M.3    Sitte, H.H.4
  • 23
    • 0029902763 scopus 로고    scopus 로고
    • Computational methods for biomolecular docking
    • Lengauer,T. and Rarey,M. (1996) Computational methods for biomolecular docking. Curr. Opin. Struct. Biol., 6, 402-406.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 402-406
    • Lengauer, T.1    Rarey, M.2
  • 24
    • 0036145653 scopus 로고    scopus 로고
    • Structures of the two 3D domain-swapped RNase A trimers
    • Liu,Y., Gotte,G., Libonati,M. and Eisenberg,D. (2002) Structures of the two 3D domain-swapped RNase A trimers. Protein Sci. 11, 371-380.
    • (2002) Protein Sci. , vol.11 , pp. 371-380
    • Liu, Y.1    Gotte, G.2    Libonati, M.3    Eisenberg, D.4
  • 26
    • 0029154302 scopus 로고
    • Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium
    • Morera,S., Chiadmi,M., LeBras,G., Lascu,I. and Janin,J. (1995) Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium. Biochemistry, 34, 11062-11070.
    • (1995) Biochemistry , vol.34 , pp. 11062-11070
    • Morera, S.1    Chiadmi, M.2    LeBras, G.3    Lascu, I.4    Janin, J.5
  • 27
    • 4344587654 scopus 로고    scopus 로고
    • Mycobacterium tuberculosis GroEL homologues unusually exist as lower oligomers and retain the ability to suppress aggregation of substrate proteins
    • Qamra,R., Srinivas,V. and Mande,S.C. (2004) Mycobacterium tuberculosis GroEL homologues unusually exist as lower oligomers and retain the ability to suppress aggregation of substrate proteins. J. Mol. Biol., 342, 605-617.
    • (2004) J. Mol. Biol. , vol.342 , pp. 605-617
    • Qamra, R.1    Srinivas, V.2    Mande, S.C.3
  • 28
    • 0029014434 scopus 로고
    • The envelope glycoprotein from fick-borne encephalitis virus at 2A resolution
    • Rey,F.A., Heinz,F.X., Mandl,C., Kunz,C. and Harrison,S.C. (1995) The envelope glycoprotein from fick-borne encephalitis virus at 2A resolution. Nature, 375, 291-298.
    • (1995) Nature , vol.375 , pp. 291-298
    • Rey, F.A.1    Heinz, F.X.2    Mandl, C.3    Kunz, C.4    Harrison, S.C.5
  • 31
    • 0030962437 scopus 로고    scopus 로고
    • Structure of a product complex of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase
    • Taylor,T.C. and Andersson,I. (1997) Structure of a product complex of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase. Biochemistry, 36, 4041-4046.
    • (1997) Biochemistry , vol.36 , pp. 4041-4046
    • Taylor, T.C.1    Andersson, I.2
  • 32
    • 0026606219 scopus 로고
    • Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K
    • Tilton,R.F.,Jr Dewan,J.C. and Petsko,G.A. (1992) Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K. Biochemistry, 31, 2469-2481.
    • (1992) Biochemistry , vol.31 , pp. 2469-2481
    • Tilton Jr., R.F.1    Dewan, J.C.2    Petsko, G.A.3
  • 33
    • 0028984540 scopus 로고
    • Protein docking for low-resolution structures
    • Vakser,I.A. (1995) Protein docking for low-resolution structures. Protein Eng., 8, 371-377.
    • (1995) Protein Eng. , vol.8 , pp. 371-377
    • Vakser, I.A.1
  • 34
    • 0031565721 scopus 로고    scopus 로고
    • Channel specificity: Structural basis for sugar discrimination and differential flux rates in maltoporin
    • Wang,Y.F., Dutzler,R., Pizkallah,P.J., Rosenbusch,J.P. and Schirmer,T. (1997) Channel specificity: structural basis for sugar discrimination and differential flux rates in maltoporin. J. Mol. Biol., 272, 56-63.
    • (1997) J. Mol. Biol. , vol.272 , pp. 56-63
    • Wang, Y.F.1    Dutzler, R.2    Pizkallah, P.J.3    Rosenbusch, J.P.4    Schirmer, T.5
  • 35
    • 0037051999 scopus 로고    scopus 로고
    • Crystal structure of human nicotinamide mononucleotide adenylyltransferase in complex with NMN
    • Werner,E., Ziegler,M., Lerner,F., Schweiger,M. and Heinemann,U. (2002) Crystal structure of human nicotinamide mononucleotide adenylyltransferase in complex with NMN. FEBS Lett., 516, 239-244.
    • (2002) FEBS Lett. , vol.516 , pp. 239-244
    • Werner, E.1    Ziegler, M.2    Lerner, F.3    Schweiger, M.4    Heinemann, U.5
  • 36
    • 0021603710 scopus 로고
    • Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II
    • Wlodawer,A., Walter,J., Huber,R. and Sjolin,L. (1984) Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II. J. Mol. Biol., 180, 301-329.
    • (1984) J. Mol. Biol. , vol.180 , pp. 301-329
    • Wlodawer, A.1    Walter, J.2    Huber, R.3    Sjolin, L.4
  • 37
    • 0031552370 scopus 로고    scopus 로고
    • Determination of atomic desolvation energies from the structures of crystallized proteins
    • Zhang,C., Vasmatzis,G., Cornette,J.L. and DeLisi,C. (1997) Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol., 267, 707-726.
    • (1997) J. Mol. Biol. , vol.267 , pp. 707-726
    • Zhang, C.1    Vasmatzis, G.2    Cornette, J.L.3    DeLisi, C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.