메뉴 건너뛰기




Volumn 29, Issue 5, 2015, Pages 413-420

Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions

Author keywords

Conserved interactions; G protein coupled receptors; Homology modeling; Multiple templates

Indexed keywords

BIOINFORMATICS;

EID: 84939962097     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-014-9823-2     Document Type: Article
Times cited : (10)

References (39)
  • 1
    • 84881232356 scopus 로고    scopus 로고
    • G-protein-coupled receptors and their (Bio) chemical significance win 2012 Nobel Prize in Chemistry
    • Lin HH (2013) G-protein-coupled receptors and their (Bio) chemical significance win 2012 Nobel Prize in Chemistry. Biomed J 36:118-124
    • (2013) Biomed J , vol.36 , pp. 118-124
    • Lin, H.H.1
  • 4
    • 42149181885 scopus 로고    scopus 로고
    • Structural diversity of G protein-coupled receptors and significance for drug discovery
    • Lagerstrom MC, Schioth HB (2008) Structural diversity of G protein-coupled receptors and significance for drug discovery. Nat Rev Drug Discov 7:339-357
    • (2008) Nat Rev Drug Discov , vol.7 , pp. 339-357
    • Lagerstrom, M.C.1    Schioth, H.B.2
  • 9
    • 84865201339 scopus 로고    scopus 로고
    • Homology model-assisted elucidation of binding sites in GPCRs
    • 1:CAS:528:DC%2BC3sXitlWgsrY%3D
    • Levit A, Barak D, Behrens M, Meyerhof W, Niv MY (2012) Homology model-assisted elucidation of binding sites in GPCRs. Methods Mol Biol 914:179-205
    • (2012) Methods Mol Biol , vol.914 , pp. 179-205
    • Levit, A.1    Barak, D.2    Behrens, M.3    Meyerhof, W.4    Niv, M.Y.5
  • 10
    • 77649196223 scopus 로고    scopus 로고
    • GPCR 3D homology models for ligand screening: Lessons learned from blind predictions of adenosine A2a receptor complex
    • 1:CAS:528:DC%2BD1MXhsFWrsb7L
    • Katritch V, Rueda M, Lam PC, Yeager M, Abagyan R (2010) GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. Proteins 78:197-211
    • (2010) Proteins , vol.78 , pp. 197-211
    • Katritch, V.1    Rueda, M.2    Lam, P.C.3    Yeager, M.4    Abagyan, R.5
  • 11
    • 0031565726 scopus 로고    scopus 로고
    • An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors
    • 1:CAS:528:DyaK2sXmt1Wgt74%3D
    • Baldwin JM, Schertler GF, Unger VM (1997) An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. J Mol Biol 272:144-164
    • (1997) J Mol Biol , vol.272 , pp. 144-164
    • Baldwin, J.M.1    Schertler, G.F.2    Unger, V.M.3
  • 12
    • 0034948696 scopus 로고    scopus 로고
    • Structural mimicry in G protein-coupled receptors: Implications of the high-resolution structure of rhodopsin for structure-function analysis of rhodopsin-like receptors
    • 1:CAS:528:DC%2BD3MXks1Crt70%3D
    • Ballesteros JA, Shi L, Javitch JA (2001) Structural mimicry in G protein-coupled receptors: implications of the high-resolution structure of rhodopsin for structure-function analysis of rhodopsin-like receptors. Mol Pharmacol 60:1-19
    • (2001) Mol Pharmacol , vol.60 , pp. 1-19
    • Ballesteros, J.A.1    Shi, L.2    Javitch, J.A.3
  • 13
    • 77957963878 scopus 로고    scopus 로고
    • Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations
    • 1:CAS:528:DC%2BC3cXhtFCrtrnP
    • Subbotina J, Yarov-Yarovoy V, Lees-Miller J, Durdagi S, Guo J, Duff HJ, Noskov SY (2010) Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations. Proteins 78:2922-2934
    • (2010) Proteins , vol.78 , pp. 2922-2934
    • Subbotina, J.1    Yarov-Yarovoy, V.2    Lees-Miller, J.3    Durdagi, S.4    Guo, J.5    Duff, H.J.6    Noskov, S.Y.7
  • 14
    • 84855710159 scopus 로고    scopus 로고
    • Bihelix: Towards de novo structure prediction of an ensemble of G-protein coupled receptor conformations
    • Abrol R, Bray JK, Goddard WA 3rd (2011) Bihelix: towards de novo structure prediction of an ensemble of G-protein coupled receptor conformations. Proteins 80:505-518
    • (2011) Proteins , vol.80 , pp. 505-518
    • Abrol, R.1    Bray, J.K.2    Goddard, W.A.3
  • 16
    • 84885667789 scopus 로고    scopus 로고
    • High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling
    • 1:CAS:528:DC%2BC3sXhsFOmsbfM
    • Yang J, Jang R, Zhang Y, Shen HB (2013) High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling. Bioinformatics 29:2579-2587
    • (2013) Bioinformatics , vol.29 , pp. 2579-2587
    • Yang, J.1    Jang, R.2    Zhang, Y.3    Shen, H.B.4
  • 17
    • 78149236789 scopus 로고    scopus 로고
    • MEDELLER: Homology-based coordinate generation for membrane proteins
    • 1:CAS:528:DC%2BC3cXhsVSltL7E
    • Kelm S, Shi J, Deane CM (2010) MEDELLER: homology-based coordinate generation for membrane proteins. Bioinformatics 26:2833-2840
    • (2010) Bioinformatics , vol.26 , pp. 2833-2840
    • Kelm, S.1    Shi, J.2    Deane, C.M.3
  • 18
    • 77955803232 scopus 로고    scopus 로고
    • FoldGPCR: Structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A
    • 1:CAS:528:DC%2BC3cXnsVWlsr4%3D
    • Michino M, Chen J, Stevens RC, Brooks CL 3rd (2010) FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A. Proteins 78:2189-2201
    • (2010) Proteins , vol.78 , pp. 2189-2201
    • Michino, M.1    Chen, J.2    Stevens, R.C.3    Brooks, C.L.4
  • 19
    • 84875862125 scopus 로고    scopus 로고
    • Critical analysis of the successes and failures of homology models of G protein-coupled receptors
    • 1:CAS:528:DC%2BC3sXisVSlu7g%3D
    • Bhattacharya S, Lam AR, Li H, Balaraman G, Niesen MJ, Vaidehi N (2013) Critical analysis of the successes and failures of homology models of G protein-coupled receptors. Proteins 81:729-739
    • (2013) Proteins , vol.81 , pp. 729-739
    • Bhattacharya, S.1    Lam, A.R.2    Li, H.3    Balaraman, G.4    Niesen, M.J.5    Vaidehi, N.6
  • 20
    • 79955721878 scopus 로고    scopus 로고
    • Progress in the structural prediction of G protein-coupled receptors: D3 receptor in complex with eticlopride
    • 1:CAS:528:DC%2BC3MXlvVCgtrc%3D
    • Obiol-Pardo C, Lopez L, Pastor M, Selent J (2011) Progress in the structural prediction of G protein-coupled receptors: D3 receptor in complex with eticlopride. Proteins 79:1695-1703
    • (2011) Proteins , vol.79 , pp. 1695-1703
    • Obiol-Pardo, C.1    Lopez, L.2    Pastor, M.3    Selent, J.4
  • 21
    • 84880696788 scopus 로고    scopus 로고
    • Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: Application to the agonist interaction of the human dopamine D2 receptor
    • 1:CAS:528:DC%2BC3sXmslaksro%3D
    • Malo M, Persson R, Svensson P, Luthman K, Brive L (2013) Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor. J Comput Aided Mol Des 27:277-291
    • (2013) J Comput Aided Mol des , vol.27 , pp. 277-291
    • Malo, M.1    Persson, R.2    Svensson, P.3    Luthman, K.4    Brive, L.5
  • 22
    • 67349088738 scopus 로고    scopus 로고
    • Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008
    • GPCR Dock 2008 Participants 1:CAS:528:DC%2BD1MXmt1Skt7k%3D
    • Michino M, Abola E, GPCR Dock 2008 Participants, Brooks CL 3rd, Dixon JS, Moult J, Stevens RC (2009) Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat Rev Drug Discov 8:455-463
    • (2009) Nat Rev Drug Discov , vol.8 , pp. 455-463
    • Michino, M.1    Abola, E.2    Brooks, C.L.3    Dixon, J.S.4    Moult, J.5    Stevens, R.C.6
  • 23
    • 80051521545 scopus 로고    scopus 로고
    • Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment
    • GPCR Dock 2010 Participants
    • Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R, GPCR Dock 2010 Participants (2010) Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure 19:1108-1126
    • (2010) Structure , vol.19 , pp. 1108-1126
    • Kufareva, I.1    Rueda, M.2    Katritch, V.3    Stevens, R.C.4    Abagyan, R.5
  • 25
    • 44349091007 scopus 로고    scopus 로고
    • Using multiple templates to improve quality of homology models in automated homology modeling
    • 1:CAS:528:DC%2BD1cXmvFKhtL4%3D
    • Larsson P, Wallner B, Lindahl E, Elofsson A (2008) Using multiple templates to improve quality of homology models in automated homology modeling. Protein Sci 17:990-1002
    • (2008) Protein Sci , vol.17 , pp. 990-1002
    • Larsson, P.1    Wallner, B.2    Lindahl, E.3    Elofsson, A.4
  • 26
    • 77957055780 scopus 로고
    • Integrated methods for the construction of three dimensional models and computational probing of structure function relations in G protein-coupled receptors
    • S.C. Sealfon M. Conn (eds) Academic Press San Diego
    • Ballesteros JA, Weinstein H (1995) Integrated methods for the construction of three dimensional models and computational probing of structure function relations in G protein-coupled receptors. In: Sealfon SC, Conn PM (eds) Methods in neurosciences. Academic Press, San Diego, p 428
    • (1995) Methods in Neurosciences , pp. 428
    • Ballesteros, J.A.1    Weinstein, H.2
  • 27
    • 84874677954 scopus 로고    scopus 로고
    • PDBTM: Protein data bank of transmembrane proteins after 8 years
    • 1:CAS:528:DC%2BC38XhvV2ksbrK
    • Kozma D, Simon I, Tusnady GE (2013) PDBTM: protein data bank of transmembrane proteins after 8 years. Nucleic Acids Res 41:D524-D529
    • (2013) Nucleic Acids Res , vol.41 , pp. 524-D529
    • Kozma, D.1    Simon, I.2    Tusnady, G.E.3
  • 28
    • 84941107270 scopus 로고    scopus 로고
    • Protein structure modeling with MODELLER
    • Webb B, Sali A (2014) Protein structure modeling with MODELLER. Methods Mol Biol 1137:1-15
    • (2014) Methods Mol Biol , vol.1137 , pp. 1-15
    • Webb, B.1    Sali, A.2
  • 29
    • 84905732337 scopus 로고    scopus 로고
    • Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: Meeting new challenges
    • Participants of GPCR Dock
    • Kufareva I, Katritch V, Participants of GPCR Dock, Stevens RC, Abagyan R (2013) Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure 22:1120-1139
    • (2013) Structure , vol.22 , pp. 1120-1139
    • Kufareva, I.1    Katritch, V.2    Stevens, R.C.3    Abagyan, R.4
  • 31
    • 33748207211 scopus 로고    scopus 로고
    • Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non-enzyme families
    • del Sol A, Fujihashi H, Amoros D, Nussinov R (2006) Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Sci 15:2120-2128
    • (2006) Protein Sci , vol.15 , pp. 2120-2128
    • Del Sol, A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 32
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • 1:CAS:528:DyaK2sXlvFyhu7w%3D
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res 25(17):3389-3402
    • (1997) Nucleic Acid 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
  • 33
    • 84863104506 scopus 로고    scopus 로고
    • Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions
    • 1:CAS:528:DC%2BC38XltFOqsr4%3D
    • Heim AJ, Li Z (2012) Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions. J Comput Aided Mol Des 26:301-309
    • (2012) J Comput Aided Mol des , vol.26 , pp. 301-309
    • Heim, A.J.1    Li, Z.2
  • 34
    • 84901660029 scopus 로고    scopus 로고
    • High-resolution modeling of transmembrane helical protein structures from distant homologues
    • Chen K-YM, Sun J, Salvo JS, Baker D, Barth P (2014) High-resolution modeling of transmembrane helical protein structures from distant homologues. PLoS Comput Biol 10(5):e1003636
    • (2014) PLoS Comput Biol , vol.10 , Issue.5 , pp. 1003636
    • Chen, K.-Y.1    Sun, J.2    Salvo, J.S.3    Baker, D.4    Barth, P.5
  • 35
    • 0242362175 scopus 로고    scopus 로고
    • Comparative modeling in CASP5: Progress is evident, but alignment errors remain a significant hindrance
    • 1:CAS:528:DC%2BD3sXptVygt7g%3D
    • Venclovas C (2003) Comparative modeling in CASP5: progress is evident, but alignment errors remain a significant hindrance. Proteins 53(Suppl 6):380-388
    • (2003) Proteins , vol.53 , pp. 380-388
    • Venclovas, C.1
  • 36
    • 84892429575 scopus 로고    scopus 로고
    • Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks
    • Kukic P, Mirabello C, Tradigo G, Walsh I, Veltri P, Pollastri G (2014) Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks. BMC Bioinformatics 15:6
    • (2014) BMC Bioinformatics , vol.15 , pp. 6
    • Kukic, P.1    Mirabello, C.2    Tradigo, G.3    Walsh, I.4    Veltri, P.5    Pollastri, G.6
  • 37
    • 84898812971 scopus 로고    scopus 로고
    • Computational prediction of kink properties of helices in membrane proteins
    • 1:CAS:528:DC%2BC2cXivFCjtLs%3D
    • Mai TL, Chen CM (2014) Computational prediction of kink properties of helices in membrane proteins. J Comput Aided Mol Des 28:99-109
    • (2014) J Comput Aided Mol des , vol.28 , pp. 99-109
    • Mai, T.L.1    Chen, C.M.2
  • 38
    • 79951747486 scopus 로고    scopus 로고
    • Model quality assessment for membrane proteins
    • 1:CAS:528:DC%2BC3cXhsFamtr7F
    • Ray A, Lindahl E, Wallner B (2010) Model quality assessment for membrane proteins. Bioinformatics 26:3067-3074
    • (2010) Bioinformatics , vol.26 , pp. 3067-3074
    • Ray, A.1    Lindahl, E.2    Wallner, B.3
  • 39
    • 0036681416 scopus 로고    scopus 로고
    • Scoring residue conservation
    • 1:CAS:528:DC%2BD38Xlt1Wqu7k%3D
    • Valdar WS (2002) Scoring residue conservation. Proteins 48:227-241
    • (2002) Proteins , vol.48 , pp. 227-241
    • Valdar, W.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.