메뉴 건너뛰기




Volumn 39, Issue SUPPL. 1, 2011, Pages

A series of PDB related databases for everyday needs

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ACCURACY; AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; BIOINFORMATICS; DATA ANALYSIS SOFTWARE; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT; X RAY CRYSTALLOGRAPHY;

EID: 78651277458     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1105     Document Type: Article
Times cited : (598)

References (55)
  • 3
    • 0345059376 scopus 로고    scopus 로고
    • Announcing the worldwide Protein Data Bank
    • DOI 10.1038/nsb1203-980
    • Berman, H., Henrick, K. and Nakamura, H. (2003) Announcing the worldwide Protein Data Bank. Nat. Struct. Biol., 10, 980. (Pubitemid 37500485)
    • (2003) Nature Structural Biology , vol.10 , Issue.12 , pp. 980
    • Berman, H.1    Henrick, K.2    Nakamura, H.3
  • 4
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
    • Berman, H., Henrick, K., Nakamura, H. and Markley, J.L. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 35, D301-D303.
    • (2007) Nucleic Acids Res. , vol.35
    • Berman, H.1    Henrick, K.2    Nakamura, H.3    Markley, J.L.4
  • 5
    • 38549097071 scopus 로고    scopus 로고
    • The universal protein resource (UniProt)
    • The UniProt Consortium
    • The UniProt Consortium. (2008) The universal protein resource (UniProt). Nucleic Acids Res, 36, D190-D195.
    • (2008) Nucleic Acids Res , vol.36
  • 7
    • 34447498926 scopus 로고    scopus 로고
    • PDB improvement starts with data deposition
    • Joosten, R.P. and Vriend, G. (2007) PDB improvement starts with data deposition. Science, 317, 195-196.
    • (2007) Science , vol.317 , pp. 195-196
    • Joosten, R.P.1    Vriend, G.2
  • 9
    • 76649141763 scopus 로고    scopus 로고
    • Prediction of protein structural classes for low-homology sequences based on predicted secondary structure
    • Yang, J., Peng, Z. and Chen, X. (2010) Prediction of protein structural classes for low-homology sequences based on predicted secondary structure. BMC Bioinformatics, 11(Suppl. 1), S9.
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL. 1
    • Yang, J.1    Peng, Z.2    Chen, X.3
  • 10
    • 77949635993 scopus 로고    scopus 로고
    • Improving protein secondary structure prediction using a simple k-mer model
    • Madera, M., Calmus, R., Thiltgen, G., Karplus, K. and Gough, J. (2010) Improving protein secondary structure prediction using a simple k-mer model. Bioinformatics, 26, 596-602.
    • (2010) Bioinformatics , vol.26 , pp. 596-602
    • Madera, M.1    Calmus, R.2    Thiltgen, G.3    Karplus, K.4    Gough, J.5
  • 11
    • 77957895860 scopus 로고    scopus 로고
    • Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks
    • Babaei, S., Geranmayeh, A. and Seyyedsalehi, S.A. (2010) Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. Comput. Methods Programs Biomed., 100, 237-247.
    • (2010) Comput. Methods Programs Biomed. , vol.100 , pp. 237-247
    • Babaei, S.1    Geranmayeh, A.2    Seyyedsalehi, S.A.3
  • 12
    • 79954443219 scopus 로고    scopus 로고
    • IFC(2): An integrated web-server for improved prediction of protein structural class, fold type, and secondary structure content
    • [doi;10.1007/s00726-010-0721-1, Epub ahead of print 21 Aug 2010]
    • Chen, K., Stach, W., Homaeian, L. and Kurgan, L. (2010) iFC(2): An integrated web-server for improved prediction of protein structural class, fold type, and secondary structure content. Amino Acids, [doi;10.1007/s00726-010- 0721-1, Epub ahead of print 21 Aug 2010].
    • (2010) Amino Acids
    • Chen, K.1    Stach, W.2    Homaeian, L.3    Kurgan, L.4
  • 13
    • 77952748293 scopus 로고    scopus 로고
    • Protein secondary structure prediction
    • Pirovano, W. and Heringa, J. (2010) Protein secondary structure prediction. Methods Mol. Biol., 609, 327-348.
    • (2010) Methods Mol. Biol. , vol.609 , pp. 327-348
    • Pirovano, W.1    Heringa, J.2
  • 15
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 16
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 17
    • 0026030641 scopus 로고
    • Database of homology-derived protein structures and the structural meaning of sequence alignment
    • Sander, C. and Schneider, R. (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins, 9, 56-68.
    • (1991) Proteins , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 18
    • 0028071565 scopus 로고
    • The HSSP database of protein structure-sequence alignments
    • Sander, C. and Schneider, R. (1994) The HSSP database of protein structure-sequence alignments. Nucleic Acids Res., 22, 3597-3599.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 3597-3599
    • Sander, C.1    Schneider, R.2
  • 19
    • 0029960050 scopus 로고    scopus 로고
    • The HSSP database of protein structure-sequence alignments
    • Schneider, R. and Sander, C. (1996) The HSSP database of protein structure-sequence alignments. Nucleic Acids Res., 24, 201-205.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 201-205
    • Schneider, R.1    Sander, C.2
  • 20
    • 0030879419 scopus 로고    scopus 로고
    • The HSSP database of protein structure-sequence alignments
    • Schneider, R., de Daruvar, A. and Sander, C. (1997) The HSSP database of protein structure-sequence alignments. Nucleic Acids Res., 25, 226-230.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 226-230
    • Schneider, R.1    De Daruvar, A.2    Sander, C.3
  • 21
    • 0031841279 scopus 로고    scopus 로고
    • The HSSP database of protein structure-sequence alignments and family profiles
    • Dodge, C., Schneider, R. and Sander, C. (1998) The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Res., 26, 313-315.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 313-315
    • Dodge, C.1    Schneider, R.2    Sander, C.3
  • 23
    • 0025398721 scopus 로고
    • WHAT IF: A molecular modeling and drug design program
    • Vriend, G. (1990) WHAT IF: A molecular modeling and drug design program. J. Mol. Graph, 8, 52-56, 29.
    • (1990) J. Mol. Graph , vol.8 , Issue.52-56 , pp. 29
    • Vriend, G.1
  • 24
    • 0014432781 scopus 로고
    • Solvent content of protein crystals
    • Matthews, B.W. (1968) Solvent content of protein crystals. J. Mol. Biol., 33, 491-497.
    • (1968) J. Mol. Biol. , vol.33 , pp. 491-497
    • Matthews, B.W.1
  • 25
    • 1842692143 scopus 로고
    • General definition of ring puckering coordinates
    • Cremer, D. and Pople, J.A. (1975) General definition of ring puckering coordinates. J. Am. Chem. Soc., 97, 1354-1358.
    • (1975) J. Am. Chem. Soc. , vol.97 , pp. 1354-1358
    • Cremer, D.1    Pople, J.A.2
  • 26
    • 79952608525 scopus 로고
    • Accurate bond and angle parameters for X-ray protein structure refinement
    • Engh, R.A. and Huber, R. (1991) Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. Sect. A, 47, 392-400.
    • (1991) Acta Crystallogr. Sect. A , vol.47 , pp. 392-400
    • Engh, R.A.1    Huber, R.2
  • 27
    • 0027542118 scopus 로고
    • Quality control of protein models: Directional atomic contact analysis
    • Vriend, G. and Sander, C. (1993) Quality control of protein models: directional atomic contact analysis. J. Appl. Crystallogr., 26, 47-60.
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 47-60
    • Vriend, G.1    Sander, C.2
  • 28
    • 0028746097 scopus 로고
    • Reconstruction of symmetry-related molecules from protein data bank (PDB) files
    • Hooft, R.W.W., Sander, C. and Vriend, G. (1994) Reconstruction of symmetry-related molecules from protein data bank (PDB) files. J. Appl. Crystallogr., 27, 1006-1009.
    • (1994) J. Appl. Crystallogr. , vol.27 , pp. 1006-1009
    • Hooft, R.W.W.1    Sander, C.2    Vriend, G.3
  • 30
    • 0030442990 scopus 로고    scopus 로고
    • Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
    • Hooft, R.W., Sander, C. and Vriend, G. (1996) Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins, 26, 363-376.
    • (1996) Proteins , vol.26 , pp. 363-376
    • Hooft, R.W.1    Sander, C.2    Vriend, G.3
  • 31
    • 0030870075 scopus 로고    scopus 로고
    • Objectively judging the quality of a protein structure from a Ramachandran plot
    • Hooft, R.W., Sander, C. and Vriend, G. (1997) Objectively judging the quality of a protein structure from a Ramachandran plot. Comput. Appl. Biosci., 13, 425-430.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 425-430
    • Hooft, R.W.1    Sander, C.2    Vriend, G.3
  • 33
    • 0035182073 scopus 로고    scopus 로고
    • Use of TLS parameters to model anisotropic displacements in macromolecular refinement
    • Winn, M.D., Isupov, M.N. and Murshudov, G.N. (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D Biol. Crystallogr., 57, 122-133.
    • (2001) Acta Crystallogr. D Biol. Crystallogr. , vol.57 , pp. 122-133
    • Winn, M.D.1    Isupov, M.N.2    Murshudov, G.N.3
  • 36
    • 0001841380 scopus 로고
    • On the rigid-body motion of molecules in crystals
    • Schomaker, V. and Trueblood, K.N. (1968) On the rigid-body motion of molecules in crystals. Acta Crystallogr. Sect.B, 24, 63-76.
    • (1968) Acta Crystallogr. Sect.B , vol.24 , pp. 63-76
    • Schomaker, V.1    Trueblood, K.N.2
  • 37
    • 0029967362 scopus 로고    scopus 로고
    • SRS: Information retrieval system for molecular biology data banks
    • DOI 10.1016/S0076-6879(96)66010-8
    • Etzold, T., Ulyanov, A. and Argos, P. (1996) SRS: information retrieval system for molecular biology data banks. Meth. Enzymol., 266, 114-128. (Pubitemid 26165864)
    • (1996) Methods in Enzymology , vol.266 , pp. 114-128
    • Etzold, T.1    Ulyanov, A.2    Argos, P.3
  • 39
    • 23144440938 scopus 로고    scopus 로고
    • MRS: A fast and compact retrieval system for biological data
    • Hekkelman, M.L. and Vriend, G. (2005) MRS: A fast and compact retrieval system for biological data. Nucleic Acids Res., 33, W766-W769.
    • (2005) Nucleic Acids Res. , vol.33
    • Hekkelman, M.L.1    Vriend, G.2
  • 40
    • 0030461976 scopus 로고    scopus 로고
    • The PDBFINDER database: A summary of PDB, DSSP and HSSP information with added value
    • Hooft, R.W., Sander, C., Scharf, M. and Vriend, G. (1996) The PDBFINDER database: A summary of PDB, DSSP and HSSP information with added value. Comput. Appl. Biosci., 12, 525-529.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 525-529
    • Hooft, R.W.1    Sander, C.2    Scharf, M.3    Vriend, G.4
  • 41
    • 0001554681 scopus 로고
    • Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin
    • Teeter, M.M. (1984) Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin. Proc. Natl Acad. Sci. USA, 81, 6014-6018.
    • (1984) Proc. Natl Acad. Sci. USA , vol.81 , pp. 6014-6018
    • Teeter, M.M.1
  • 42
    • 0037093644 scopus 로고    scopus 로고
    • Increasing the precision of comparative models with YASARA NOVA-A self-parameterizing force field
    • Krieger, E., Koraimann, G. and Vriend, G. (2002) Increasing the precision of comparative models with YASARA NOVA-a self-parameterizing force field. Proteins, 47, 393-402.
    • (2002) Proteins , vol.47 , pp. 393-402
    • Krieger, E.1    Koraimann, G.2    Vriend, G.3
  • 43
    • 0001141858 scopus 로고
    • On the disordered activation domain in trypsinogen: Chemical labelling and low-temperature crystallography
    • Walter, J., Steigemann, W., Singh, T.P., Bartunik, H., Bode, W. and Huber, R. (1982) On the disordered activation domain in trypsinogen: chemical labelling and low-temperature crystallography. Acta Cryst. Sect. B, 38, 1462-1472.
    • (1982) Acta Cryst. Sect. B , vol.38 , pp. 1462-1472
    • Walter, J.1    Steigemann, W.2    Singh, T.P.3    Bartunik, H.4    Bode, W.5    Huber, R.6
  • 44
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J. App. Crystallogr., 26, 283-291.
    • (1993) J. App. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 45
  • 46
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • Hobohm, U. and Sander, C. (1994) Enlarged representative set of protein structures. Protein Sci., 3, 522-524.
    • (1994) Protein Sci. , vol.3 , pp. 522-524
    • Hobohm, U.1    Sander, C.2
  • 47
    • 75549084424 scopus 로고    scopus 로고
    • PDBselect 1992-2009 and PDBfilter-select
    • Griep, S. and Hobohm, U. (2010) PDBselect 1992-2009 and PDBfilter-select. Nucleic Acids Res., 38, D318-D319.
    • (2010) Nucleic Acids Res. , vol.38
    • Griep, S.1    Hobohm, U.2
  • 48
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • Wang, G. and Dunbrack, R.L. (2003) PISCES: A protein sequence culling server. Bioinformatics, 19, 1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack, R.L.2
  • 50
    • 0035172128 scopus 로고    scopus 로고
    • PDB-REPRDB: A database of representative protein chains from the protein data bank (PDB)
    • Noguchi, T., Matsuda, H. and Akiyama, Y. (2001) PDB-REPRDB: A database of representative protein chains from the Protein Data Bank (PDB). Nucleic Acids Res., 29, 219-220.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 219-220
    • Noguchi, T.1    Matsuda, H.2    Akiyama, Y.3
  • 51
    • 0037250308 scopus 로고    scopus 로고
    • PDB-REPRDB: A database of representative protein chains from the protein data bank (PDB) in 2003
    • Noguchi, T. and Akiyama, Y. (2003) PDB-REPRDB: A database of representative protein chains from the Protein Data Bank (PDB) in 2003. Nucleic Acids Res., 31, 492-493.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 492-493
    • Noguchi, T.1    Akiyama, Y.2
  • 52
    • 2542554197 scopus 로고    scopus 로고
    • Verification of protein structures: Side-chain planarity
    • Hooft, R.W.W., Sander, C. and Vriend, G. (1996) Verification of protein structures: side-chain planarity. J. App. Crystallogr., 29, 714-716.
    • (1996) J. App. Crystallogr. , vol.29 , pp. 714-716
    • Hooft, R.W.W.1    Sander, C.2    Vriend, G.3
  • 54
    • 0022433369 scopus 로고
    • Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA
    • Brown, R.S., Dewan, J.C. and Klug, A. (1985) Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA. Biochemistry, 24, 4785-4801.
    • (1985) Biochemistry , vol.24 , pp. 4785-4801
    • Brown, R.S.1    Dewan, J.C.2    Klug, A.3
  • 55
    • 84944816485 scopus 로고
    • The use of molecular-replacement phases for the refinement of the human rhinovirus 14 structure
    • Arnold, E. and Rossmann, M.G. (1988) The use of molecular-replacement phases for the refinement of the human rhinovirus 14 structure. Acta Crystallogr., A, Found. Crystallogr., 44(Pt 3), 270-282.
    • (1988) Acta Crystallogr., A, Found. Crystallogr. , vol.44 , Issue.PART 3 , pp. 270-282
    • Arnold, E.1    Rossmann, M.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.