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Volumn , Issue , 2008, Pages 309-326

The state of the art of membrane protein structure prediction: From sequence to 3D structure

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EID: 84920160782     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-211-75123-7_15     Document Type: Chapter
Times cited : (2)

References (33)
  • 1
    • 2942532202 scopus 로고    scopus 로고
    • Functional characterization of a second porin isoform in drosophila melanogster: DmPorin2 forms voltage-independent cation selective pores
    • Aiello R, Messina A, Schiffler B, Benz R, Tasco G, Casadio R, De Pinto V (2004) Functional characterization of a second porin isoform in drosophila melanogster: DmPorin2 forms voltage-independent cation selective pores. J Biol Chem 279:25364-25373
    • (2004) J Biol Chem , vol.279 , pp. 25364-25373
    • Aiello, R.1    Messina, A.2    Schiffler, B.3    Benz, R.4    Tasco, G.5    Casadio, R.6    De Pinto, V.7
  • 3
    • 13244259253 scopus 로고    scopus 로고
    • Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method
    • Bagos PG, Liakopoulos TD, Hamodrakas SJ (2005) Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. BMC Bioinformatics 6:7
    • (2005) BMC Bioinformatics , vol.6 , pp. 7
    • Bagos, P.G.1    Liakopoulos, T.D.2    Hamodrakas, S.J.3
  • 4
    • 2642581701 scopus 로고    scopus 로고
    • Predicting disease using genomics
    • Bell J (2004) Predicting disease using genomics. Nature 429:453-456
    • (2004) Nature , vol.429 , pp. 453-456
    • Bell, J.1
  • 5
    • 22244451035 scopus 로고    scopus 로고
    • Improved membrane protein topology prediction by domain assignments
    • Bernsel A, Von Heijne G (2005) Improved membrane protein topology prediction by domain assignments. Protein Sci 14:1723-1728
    • (2005) Protein Sci , vol.14 , pp. 1723-1728
    • Bernsel, A.1    Von Heijne, G.2
  • 6
    • 33751013750 scopus 로고    scopus 로고
    • Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information
    • Capriotti E, Calabrese R, Casadio R (2006) Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics 22:2729-2734
    • (2006) Bioinformatics , vol.22 , pp. 2729-2734
    • Capriotti, E.1    Calabrese, R.2    Casadio, R.3
  • 7
    • 0037024368 scopus 로고    scopus 로고
    • A 3D model of the voltage-dependent anion channel (VDAC)
    • Casadio R, Jacoboni I, Messina A, De Pinto V (2002) A 3D model of the voltage-dependent anion channel (VDAC). FEBS Lett 520:1-7
    • (2002) FEBS Lett , vol.520 , pp. 1-7
    • Casadio, R.1    Jacoboni, I.2    Messina, A.3    De Pinto, V.4
  • 8
    • 0037569526 scopus 로고    scopus 로고
    • Fishing new proteins in the twilight zone of genomes: The test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria
    • Casadio R, Fariselli P, Finocchiaro G, Martelli PL (2003a) Fishing new proteins in the twilight zone of genomes: The test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria. Protein Sci 11:1158-1168
    • (2003) Protein Sci , vol.11 , pp. 1158-1168
    • Casadio, R.1    Fariselli, P.2    Finocchiaro, G.3    Martelli, P.L.4
  • 9
    • 4143066779 scopus 로고    scopus 로고
    • In silico prediction of the structure of membrane proteins: Is it feasible?
    • Casadio R, Fariselli P, Martelli PL (2003b) In silico prediction of the structure of membrane proteins: is it feasible? Brief Bioinf 4:341-348
    • (2003) Brief Bioinf , vol.4 , pp. 341-348
    • Casadio, R.1    Fariselli, P.2    Martelli, P.L.3
  • 10
    • 39049189646 scopus 로고    scopus 로고
    • Thinking the impossible: How to solve the protein folding problem with and without homologous structures and more
    • Casadio R, Fariselli P, Martelli PL, Tasco G (2006) Thinking the impossible: how to solve the protein folding problem with and without homologous structures and more. Methods Mol Biol 350:305-320
    • (2006) Methods Mol Biol , vol.350 , pp. 305-320
    • Casadio, R.1    Fariselli, P.2    Martelli, P.L.3    Tasco, G.4
  • 11
    • 0032429154 scopus 로고    scopus 로고
    • A DNA polymorphism discovery resource for research on human genetic variation
    • Collins FS, Brooks LD, Chakravarti A (1998) A DNA polymorphism discovery resource for research on human genetic variation. Genome Res 8:1229-1231
    • (1998) Genome Res , vol.8 , pp. 1229-1231
    • Collins, F.S.1    Brooks, L.D.2    Chakravarti, A.3
  • 12
    • 19744376674 scopus 로고    scopus 로고
    • Global topology analysis of the Escherichia coli inner membrane proteome
    • Daley DO, Rapp M, Granseth E, Melen K, Drew D, Von Heijne G (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 27:1321-1323
    • (2005) Science , vol.27 , pp. 1321-1323
    • Daley, D.O.1    Rapp, M.2    Granseth, E.3    Melen, K.4    Drew, D.5    Von Heijne, G.6
  • 13
    • 0021755973 scopus 로고
    • X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis
    • Deisenhofer J, Epp O, Miki K, Huber R, Michel H (1984) X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis. J Mol Biol 180:385-398
    • (1984) J Mol Biol , vol.180 , pp. 385-398
    • Deisenhofer, J.1    Epp, O.2    Miki, K.3    Huber, R.4    Michel, H.5
  • 14
    • 34249683488 scopus 로고    scopus 로고
    • Membrane protein structure: Prediction versus reality
    • Elofsson A, Von Heijne G (2007) Membrane protein structure: prediction versus reality. Annu Rev Biochem 76:125-140
    • (2007) Annu Rev Biochem , vol.76 , pp. 125-140
    • Elofsson, A.1    Von Heijne, G.2
  • 15
    • 0037339488 scopus 로고    scopus 로고
    • MaxSubSeq: An algorithm for segment-length optimization. The case study of the transmembrane spanning segments
    • Fariselli P, Finelli M, Marchignoli D, Martelli PL, Rossi I, Casadio R (2003a) MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments. Bioinformatics 19:500-505
    • (2003) Bioinformatics , vol.19 , pp. 500-505
    • Fariselli, P.1    Finelli, M.2    Marchignoli, D.3    Martelli, P.L.4    Rossi, I.5    Casadio, R.6
  • 16
    • 0348143178 scopus 로고    scopus 로고
    • SPEPlip: The detection of signal peptide and lipoprotein cleavage sites
    • Fariselli P, Finocchiaro G, Casadio R (2003b) SPEPlip: the detection of signal peptide and lipoprotein cleavage sites. Bioinformatics 19:2498-2499
    • (2003) Bioinformatics , vol.19 , pp. 2498-2499
    • Fariselli, P.1    Finocchiaro, G.2    Casadio, R.3
  • 17
    • 33947417295 scopus 로고    scopus 로고
    • A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins
    • Fariselli P, Martelli PL, Casadio R (2005a) A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics 6(Suppl 4):S12
    • (2005) BMC Bioinformatics , vol.6 , pp. S12
    • Fariselli, P.1    Martelli, P.L.2    Casadio, R.3
  • 20
    • 34047151404 scopus 로고    scopus 로고
    • Improving the accuracy of transmembrane protein topology prediction using evolutionary information
    • Jones DT (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics 23:538-544
    • (2007) Bioinformatics , vol.23 , pp. 538-544
    • Jones, D.T.1
  • 21
    • 0028211273 scopus 로고
    • A model recognition approach to the prediction of allhelical membrane protein structure and topology
    • Jones DT, Taylor WR, Thornton JM (1994) A model recognition approach to the prediction of allhelical membrane protein structure and topology. Biochemistry 33:3038-3049
    • (1994) Biochemistry , vol.33 , pp. 3038-3049
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 22
    • 34547584314 scopus 로고    scopus 로고
    • Advantages of combined transmembrane topology and signal peptide prediction - The Phobius web server
    • Kall L, Krogh A, Sonnhammer EL (2007) Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. Nucleic Acids Res 35:W429-W432
    • (2007) Nucleic Acids Res , vol.35 , pp. W429-W432
    • Kall, L.1    Krogh, A.2    Sonnhammer, E.L.3
  • 23
    • 33746616385 scopus 로고    scopus 로고
    • A global topology map of the Saccharomyces cerevisiae membrane proteome
    • Kim H, Melen K, Osterberg M, Von Heijne G (2006) A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc Natl Acad Sci USA 103:11142-11147
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 11142-11147
    • Kim, H.1    Melen, K.2    Osterberg, M.3    Von Heijne, G.4
  • 24
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh A, Larsson B, Von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567-580
    • (2001) J Mol Biol , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Von Heijne, G.3    Sonnhammer, E.L.4
  • 26
    • 4243671284 scopus 로고    scopus 로고
    • A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins
    • Martelli PL, Fariselli P, Krogh A, Casadio R (2002) A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics 18:S46-S53
    • (2002) Bioinformatics , vol.18 , pp. S46-S53
    • Martelli, P.L.1    Fariselli, P.2    Krogh, A.3    Casadio, R.4
  • 27
    • 4944242989 scopus 로고    scopus 로고
    • An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins
    • Martelli PL, Fariselli P, Casadio R (2003) An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. Bioinformatics 19:I205-I211
    • (2003) Bioinformatics , vol.19 , pp. I205-I211
    • Martelli, P.L.1    Fariselli, P.2    Casadio, R.3
  • 29
    • 0036119504 scopus 로고    scopus 로고
    • Accounting for human polymorphisms predicted to affect protein function
    • Ng PC, Henikoff S (2002) Accounting for human polymorphisms predicted to affect protein function. Genome Res 12:436-434
    • (2002) Genome Res , vol.12 , pp. 436-434
    • Ng, P.C.1    Henikoff, S.2
  • 30
    • 24644490119 scopus 로고    scopus 로고
    • Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes
    • Nilsson J, Persson B, Von Heijne G (2005) Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes. Proteins 60:606-616
    • (2005) Proteins , vol.60 , pp. 606-616
    • Nilsson, J.1    Persson, B.2    Von Heijne, G.3
  • 32
    • 0036713510 scopus 로고    scopus 로고
    • Human non-synonymous SNPs: Server and survey
    • Ramensky V, Bork P, Sunyaev S (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30:3894-8900
    • (2002) Nucleic Acids Res , vol.30 , pp. 3894-8900
    • Ramensky, V.1    Bork, P.2    Sunyaev, S.3
  • 33
    • 3042579686 scopus 로고    scopus 로고
    • Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information
    • Viklund H, Elofsson A (2004) Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci 13:1908-1917
    • (2004) Protein Sci , vol.13 , pp. 1908-1917
    • Viklund, H.1    Elofsson, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.