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Volumn 12, Issue 6, 2014, Pages

PRIGSA: Protein repeat identification by graph spectral analysis

Author keywords

graph theory; protein contact network; Protein structural repeat

Indexed keywords

SOLENOIDEA;

EID: 84930015767     PISSN: 02197200     EISSN: 17576334     Source Type: Journal    
DOI: 10.1142/S0219720014420098     Document Type: Conference Paper
Times cited : (17)

References (42)
  • 2
    • 78649389313 scopus 로고    scopus 로고
    • The role of leucine-rich repeat kinase 2 (LRRK2) in Parkinson's disease
    • Cookson MR, The role of leucine-rich repeat kinase 2 (LRRK2) in Parkinson's disease, Nat Rev Neurosci 11:791-797, 2010.
    • (2010) Nat Rev Neurosci , vol.11 , pp. 791-797
    • Cookson, M.R.1
  • 3
    • 84899513558 scopus 로고    scopus 로고
    • Deep conservation of human protein tandem repeats within the eukaryotes
    • Schaper E, Gascuel O, Anisimova M, Deep conservation of human protein tandem repeats within the eukaryotes, Mol Biol Evol 31:1132-1148, 2014.
    • (2014) Mol Biol Evol , vol.31 , pp. 1132-1148
    • Schaper, E.1    Gascuel, O.2    Anisimova, M.3
  • 4
    • 84865174088 scopus 로고    scopus 로고
    • Tandem repeats in proteins: From sequence to structure
    • Kajava AV, Tandem repeats in proteins: From sequence to structure, J Struct Biol 179:279-288, 2012.
    • (2012) J Struct Biol , vol.179 , pp. 279-288
    • Kajava, A.V.1
  • 6
    • 84878552115 scopus 로고    scopus 로고
    • DARPin-targeting of measles virus: Unique bispecicity e ective oncolysis, and enhanced safety
    • Friedrich K et al., DARPin-targeting of measles virus: Unique bispecicity, e ective oncolysis, and enhanced safety, Mol Ther 21:849-859, 2013.
    • (2013) Mol Ther , vol.21 , pp. 849-859
    • Friedrich, K.1
  • 7
    • 84874020669 scopus 로고    scopus 로고
    • Conformation-dependent recognition of HIV gp120 by designed ankyrin repeat proteins provides access to novel HIV entry inhibitors
    • Mann A et al., Conformation-dependent recognition of HIV gp120 by designed ankyrin repeat proteins provides access to novel HIV entry inhibitors, J Virol 87:5868-5881, 2013.
    • (2013) J Virol , vol.87 , pp. 5868-5881
    • Mann, A.1
  • 8
    • 0017136639 scopus 로고
    • The 14-fold periodicity in alpha-tropomyosin and the interaction with actin
    • McLachlan AD, Stewart M, The 14-fold periodicity in alpha-tropomyosin and the interaction with actin, J Mol Biol 103:271-298, 1976.
    • (1976) J Mol Biol , vol.103 , pp. 271-298
    • McLachlan, A.D.1    Stewart, M.2
  • 9
    • 0031692720 scopus 로고    scopus 로고
    • Detecting periodic patterns in biological sequences
    • Coward E, Drabløs F, Detecting periodic patterns in biological sequences, Bioinformatics 14:498-507, 1998.
    • (1998) Bioinformatics , vol.14 , pp. 498-507
    • Coward, E.1    Drabløs, F.2
  • 10
    • 23144450570 scopus 로고    scopus 로고
    • REPPER-repeats and their periodicities in brous proteins
    • Gruber M, Soding J, Lupas AN, REPPER-repeats and their periodicities in brous proteins, Nucleic Acids Res 33:W239-W243, 2005.
    • (2005) Nucleic Acids Res , vol.33 , pp. W239-W243
    • Gruber, M.1    Soding, J.2    Lupas, A.N.3
  • 11
    • 66349088076 scopus 로고    scopus 로고
    • REPETITA: Detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform
    • Marsella L, Sirocco F, Trovato A, Seno F, Tosatto SCE, REPETITA: Detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform, Bioinformatics 25:i289-i295, 2009.
    • (2009) Bioinformatics , vol.25 , pp. i289-i295
    • Marsella, L.1    Sirocco, F.2    Trovato, A.3    Seno, F.4    Tosatto, S.C.E.5
  • 12
    • 40749102414 scopus 로고    scopus 로고
    • XSTREAM: A practical algorithm for identication and architecture modeling of tandem repeats in protein sequences
    • Newman AM, Cooper JB, XSTREAM: A practical algorithm for identication and architecture modeling of tandem repeats in protein sequences, BMC Bioinform 8:382, 2007.
    • (2007) BMC Bioinform , vol.8 , pp. 382
    • Newman, A.M.1    Cooper, J.B.2
  • 13
    • 70349989506 scopus 로고    scopus 로고
    • T-REKS: Identication of Tandem REpeats in sequences with a K-meanS based algorithm
    • Jorda J, Kajava AV, T-REKS: Identication of Tandem REpeats in sequences with a K-meanS based algorithm, Bioinformatics 25:2632-2638, 2009.
    • (2009) Bioinformatics , vol.25 , pp. 2632-2638
    • Jorda, J.1    Kajava, A.V.2
  • 14
    • 0033151949 scopus 로고    scopus 로고
    • A fast algorithm for genome-wide analysis of proteins with repeated sequences
    • Pellegrini M, Marcotte EM, Yeates TO, A fast algorithm for genome-wide analysis of proteins with repeated sequences, Proteins 35:440-446, 1999.
    • (1999) Proteins , vol.35 , pp. 440-446
    • Pellegrini, M.1    Marcotte, E.M.2    Yeates, T.O.3
  • 15
    • 0034333196 scopus 로고    scopus 로고
    • Rapid automatic detection and alignment of repeats in protein sequences
    • Heger A, Holm L, Rapid automatic detection and alignment of repeats in protein sequences, Proteins 41:224-237, 2000.
    • (2000) Proteins , vol.41 , pp. 224-237
    • Heger, A.1    Holm, L.2
  • 16
    • 20444451594 scopus 로고    scopus 로고
    • Tracking repeats using signicance and transitivity
    • Szklarczyk R, Heringa J, Tracking repeats using signicance and transitivity, Bioinformatics 20(Suppl 1):i311-i317, 2004.
    • (2004) Bioinformatics , vol.20 , pp. 1311-1317
    • Szklarczyk, R.1    Heringa, J.2
  • 17
    • 40749144066 scopus 로고    scopus 로고
    • De novo identication of highly diverged protein repeats by probabilistic consistency
    • Biegert A, Soding J, De novo identication of highly diverged protein repeats by probabilistic consistency, Bioinformatics 24:807-814, 2008.
    • (2008) Bioinformatics , vol.24 , pp. 807-814
    • Biegert, A.1    Soding, J.2
  • 19
    • 0030093114 scopus 로고    scopus 로고
    • A °exible motif search technique based on generalized proles
    • Bucher P, Karplus K, Moeri N, Hofmann K, A °exible motif search technique based on generalized proles, Comput Chem 20:3-23, 1996.
    • (1996) Comput Chem , vol.20 , pp. 3-23
    • Bucher, P.1    Karplus, K.2    Moeri, N.3    Hofmann, K.4
  • 20
    • 77953211283 scopus 로고    scopus 로고
    • Protein tandem repeats the more perfect the less structured
    • Jorda J, Xue B, Uversky VN, Kajava AV, Protein tandem repeats---The more perfect, the less structured, FEBS J 277:2673-2682, 2010.
    • (2010) FEBS J , vol.277 , pp. 2673-2682
    • Jorda, J.1    Xue, B.2    Uversky, V.N.3    Kajava, A.V.4
  • 21
    • 0019332167 scopus 로고
    • How di erent amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
    • Lesk AM, Chothia C, How di erent amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins, J Mol Biol 136:225-270, 1980.
    • (1980) J Mol Biol , vol.136 , pp. 225-270
    • Lesk, A.M.1    Chothia, C.2
  • 22
    • 4544298192 scopus 로고    scopus 로고
    • Toward the detection and validation of repeats in protein structure
    • Murray KB, Taylor WR, Thornton JM, Toward the detection and validation of repeats in protein structure, Proteins 57:365-380, 2004.
    • (2004) Proteins , vol.57 , pp. 365-380
    • Murray, K.B.1    Taylor, W.R.2    Thornton, J.M.3
  • 24
    • 46249097882 scopus 로고    scopus 로고
    • Swelfe: A detector of internal repeats in sequences and structures
    • Abraham A-L, Rocha EPC, Pothier J, Swelfe: A detector of internal repeats in sequences and structures, Bioinformatics 24:1536-1537, 2008.
    • (2008) Bioinformatics , vol.24 , pp. 1536-1537
    • Abraham, A.-L.1    Epc, R.2    Pothier, J.3
  • 25
    • 77953285175 scopus 로고    scopus 로고
    • ProSTRIP: A method to nd similar structural repeats in three-dimensional protein structures
    • Sabarinathan R, Basu R, Sekar K, ProSTRIP: A method to nd similar structural repeats in three-dimensional protein structures, Comput Biol Chem 34:126-130, 2010.
    • (2010) Comput Biol Chem , vol.34 , pp. 126-130
    • Sabarinathan, R.1    Basu, R.2    Sekar, K.3
  • 26
    • 84870806739 scopus 로고    scopus 로고
    • RAPHAEL: Recognition periodicity and insertion assignment of solenoid protein structures
    • Walsh I et al., RAPHAEL: Recognition, periodicity and insertion assignment of solenoid protein structures, Bioinformatics 28:3257-3264, 2012.
    • (2012) Bioinformatics , vol.28 , pp. 3257-3264
    • Walsh, I.1
  • 27
    • 84900302422 scopus 로고    scopus 로고
    • ConSole: Using modularity of Contact maps to locate Solenoid domains in protein structures
    • Hrabe T, Godzik A, ConSole: Using modularity of Contact maps to locate Solenoid domains in protein structures, BMC Bioinform 15:119, 2014.
    • (2014) BMC Bioinform , vol.15 , pp. 119
    • Hrabe, T.1    Godzik, A.2
  • 28
    • 84881115632 scopus 로고    scopus 로고
    • Tandem-repeat proteins: Regularity plus modularity equals designability
    • Javadi Y, Itzhaki LS, Tandem-repeat proteins: Regularity plus modularity equals designability, Curr Opin Struct Biol 23:622-631, 2013.
    • (2013) Curr Opin Struct Biol , vol.23 , pp. 622-631
    • Javadi, Y.1    Itzhaki, L.S.2
  • 29
    • 2442706456 scopus 로고    scopus 로고
    • The ankyrin repeat as molecular architecture for protein recognition
    • Mosavi LK, Cammett TJ, Desrosiers DC, Peng Z, The ankyrin repeat as molecular architecture for protein recognition, Protein Sci 13:1435-1448, 2004.
    • (2004) Protein Sci , vol.13 , pp. 1435-1448
    • Mosavi, L.K.1    Cammett, T.J.2    Desrosiers, D.C.3    Peng, Z.4
  • 30
    • 0032473425 scopus 로고    scopus 로고
    • The structure of the tetratricopeptide repeats of protein phosphatase 5: Implications for TPR-mediated protein-protein interactions
    • Das AK, Cohen PW, Barford D, The structure of the tetratricopeptide repeats of protein phosphatase 5: Implications for TPR-mediated protein-protein interactions, EMBO J 17:1192-1199, 1998.
    • (1998) EMBO J , vol.17 , pp. 1192-1199
    • Das, A.K.1    Cohen, P.W.2    Barford, D.3
  • 31
    • 0035783062 scopus 로고    scopus 로고
    • Review: Proteins with repeated sequence-structural prediction and modeling
    • Kajava AV, Review: Proteins with repeated sequence-structural prediction and modeling, J Struct Biol 134:132-144, 2001.
    • (2001) J Struct Biol , vol.134 , pp. 132-144
    • Kajava, A.V.1
  • 33
    • 84875170915 scopus 로고    scopus 로고
    • Protein contact networks: An emerging paradigm in chemistry
    • Di Paola L, De Ruvo M, Paci P, Santoni D, Giuliani A, Protein contact networks: An emerging paradigm in chemistry, Chem Rev 113:1598-1613, 2013.
    • (2013) Chem Rev , vol.113 , pp. 1598-1613
    • Di Paola, L.1    De Ruvo, M.2    Paci, P.3    Santoni, D.4    Giuliani, A.5
  • 34
    • 0033578690 scopus 로고    scopus 로고
    • Identication of side-chain clusters in protein structures by a graph spectral method
    • Kannan N, Vishveshwara S, Identication of side-chain clusters in protein structures by a graph spectral method, J Mol Biol 292:441-464, 1999.
    • (1999) J Mol Biol , vol.292 , pp. 441-464
    • Kannan, N.1    Vishveshwara, S.2
  • 35
    • 0033955344 scopus 로고    scopus 로고
    • Backbone cluster identication in proteins by a graph theoretical method
    • Patra SM, Vishveshwara S, Backbone cluster identication in proteins by a graph theoretical method, Biophys Chem 84:13-25, 2000.
    • (2000) Biophys Chem , vol.84 , pp. 13-25
    • Patra, S.M.1    Vishveshwara, S.2
  • 37
    • 84930020579 scopus 로고    scopus 로고
    • Graph centrality analysis of structural ankyrin repeats
    • Chakrabarty B, Parekh N, Graph centrality analysis of structural ankyrin repeats, IJCISIM 6:305-314, 2014.
    • (2014) IJCISIM , vol.6 , pp. 305-314
    • Chakrabarty, B.1    Parekh, N.2
  • 38
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D, Argos P, Knowledge-based protein secondary structure assignment, Proteins 23:566-579, 1995.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 39
    • 84891766568 scopus 로고    scopus 로고
    • RepeatsDB: A database of tandem repeat protein structures
    • Di Domenico T et al., RepeatsDB: A database of tandem repeat protein structures, Nucleic Acids Res 42:D352-D357, 2014.
    • (2014) Nucleic Acids Res , vol.42 , pp. D352-D357
    • Di Domenico, T.1
  • 40
    • 75849153303 scopus 로고    scopus 로고
    • The universal protein resource (UniProt) in 2010
    • UniProt Consortium
    • UniProt Consortium, The Universal Protein Resource (UniProt) in 2010, Nucleic Acids Res 38:D142-D148, 2010.
    • (2010) Nucleic Acids Res , vol.38 , pp. D142-D148
  • 41
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman HM et al., The Protein Data Bank, Nucleic Acids Res 28:235-242, 2000.
    • (2000) Nucleic Acids Res , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 42
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: A comprehensive database of protein domain families based on seed alignments
    • Sonnhammer EL, Eddy SR, Durbin R, Pfam: A comprehensive database of protein domain families based on seed alignments, Proteins 28:405-420, 1997.
    • (1997) Proteins , vol.28 , pp. 405-420
    • Sonnhammer, E.L.1    Eddy, S.R.2    Durbin, R.3


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