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Volumn 84, Issue , 2016, Pages 370-391

Biological function derived from predicted structures in CASP11

Author keywords

CASP11; Missense mutation phenotype prediction; Protein docking; Protein function; Protein structure prediction

Indexed keywords

HOMODIMER; LIGAND; MONOMER; AMIDASE; CYCLIC AMP DEPENDENT PROTEIN KINASE; GLYCOPROTEIN GP 120; GLYCOSYLPHOSPHATIDYLINOSITOL ANCHORED PROTEIN; MACROPHAGE STIMULATING PROTEIN; ONCOPROTEIN; PANTETHEINASE; PROTEIN BINDING; SCATTER FACTOR;

EID: 84978194664     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24997     Document Type: Article
Times cited : (10)

References (101)
  • 2
    • 0013852463 scopus 로고
    • Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution
    • Blake C, Koenig D, Mair G, North A, Phillips D, Sarma V. Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution. Nature 1965;206:757-761.
    • (1965) Nature , vol.206 , pp. 757-761
    • Blake, C.1    Koenig, D.2    Mair, G.3    North, A.4    Phillips, D.5    Sarma, V.6
  • 4
    • 0014693695 scopus 로고
    • A possible three-dimensional structure of bovine a-lactalbumin based on that of hen’s egg-white lysozyme
    • Browne WJ, North A, Phillips D, Brew K, Vanaman TC, Hill RL. A possible three-dimensional structure of bovine a-lactalbumin based on that of hen’s egg-white lysozyme. J Mol Biol 1969;42:65-86.
    • (1969) J Mol Biol , vol.42 , pp. 65-86
    • Browne, W.J.1    North, A.2    Phillips, D.3    Brew, K.4    Vanaman, T.C.5    Hill, R.L.6
  • 5
    • 0019028066 scopus 로고
    • Model for haptoglobin heavy chain based upon structural homology
    • Greer J. Model for haptoglobin heavy chain based upon structural homology. Proc Natl Acad Sci 1980;77:3393-3397.
    • (1980) Proc Natl Acad Sci , vol.77 , pp. 3393-3397
    • Greer, J.1
  • 6
    • 0020656713 scopus 로고
    • Hemoglobin-binding site on haptoglobin probed by selective proteolysis
    • Lustbader J, Arcoleo JP, Birken S, Greer J. Hemoglobin-binding site on haptoglobin probed by selective proteolysis. J Biol Chem 1983; 258:1227-1234.
    • (1983) J Biol Chem , vol.258 , pp. 1227-1234
    • Lustbader, J.1    Arcoleo, J.P.2    Birken, S.3    Greer, J.4
  • 8
    • 0033547273 scopus 로고    scopus 로고
    • The evolutionarily conserved Dim1 protein defines a novel branch of the thioredoxin fold superfamily
    • Zhang YZ, Gould KL, Dunbrack RJ, Cheng H, Roder H, Golemis EA. The evolutionarily conserved Dim1 protein defines a novel branch of the thioredoxin fold superfamily. Physiol Genomics 1999; 1:109-118.
    • (1999) Physiol Genomics , vol.1 , pp. 109-118
    • Zhang, Y.Z.1    Gould, K.L.2    Dunbrack, R.J.3    Cheng, H.4    Roder, H.5    Golemis, E.A.6
  • 9
    • 0035869180 scopus 로고    scopus 로고
    • Mutations in the regulatory domain of cystathionine beta-synthase can functionally suppress patient-derived mutations in cis
    • Shan X, Dunbrack RL, Jr, Christopher SA, Kruger WD. Mutations in the regulatory domain of cystathionine beta-synthase can functionally suppress patient-derived mutations in cis. Hum Mol Genet 2001;10:635-643.
    • (2001) Hum Mol Genet , vol.10 , pp. 635-643
    • Shan, X.1    Dunbrack, R.L.2    Christopher, S.A.3    Kruger, W.D.4
  • 10
    • 0037102412 scopus 로고    scopus 로고
    • Promotion of tumor growth by murine fibroblast activation protein, a serine protease, in an animal model
    • Cheng JD, Dunbrack RL, Jr., Valianou M, Rogatko A, Alpaugh RK, Weiner LM. Promotion of tumor growth by murine fibroblast activation protein, a serine protease, in an animal model. Cancer Res 2002;62:4767-4772.
    • (2002) Cancer Res , vol.62 , pp. 4767-4772
    • Cheng, J.D.1    Dunbrack, R.L.2    Valianou, M.3    Rogatko, A.4    Alpaugh, R.K.5    Weiner, L.M.6
  • 11
    • 0042232046 scopus 로고    scopus 로고
    • A structural basis for half-of-the-sites metal binding revealed in Drosophila melanogaster porphobilinogen synthase
    • Kundrat L, Martins J, Stith L, Dunbrack RL, Jr, Jaffe EK. A structural basis for half-of-the-sites metal binding revealed in Drosophila melanogaster porphobilinogen synthase. J Biol Chem 2003;278: 31325-31330.
    • (2003) J Biol Chem , vol.278 , pp. 31325-31330
    • Kundrat, L.1    Martins, J.2    Stith, L.3    Dunbrack, R.L.4    Jaffe, E.K.5
  • 14
    • 73549102404 scopus 로고    scopus 로고
    • A bifunctional regulatory element in human somatic Wee1 mediates cyclin A/Cdk2 binding and Crm1-dependent nuclear export
    • Li C, Andrake M, Dunbrack R, Enders GH. A bifunctional regulatory element in human somatic Wee1 mediates cyclin A/Cdk2 binding and Crm1-dependent nuclear export. Mol Cell Biol 2010;30: 116-130.
    • (2010) Mol Cell Biol , vol.30 , pp. 116-130
    • Li, C.1    Rake, M.2    Dunbrack, R.3    Enders, G.H.4
  • 16
    • 77649135481 scopus 로고    scopus 로고
    • Numb independently antagonizes Sanpodo membrane targeting and Notch signaling in Drosophila sensory organ precursor cells
    • Tong X, Zitserman D, Serebriiskii I, Andrake M, Dunbrack R, Roegiers F. Numb independently antagonizes Sanpodo membrane targeting and Notch signaling in Drosophila sensory organ precursor cells. Mol Biol Cell 2010;21:802-810.
    • (2010) Mol Biol Cell , vol.21 , pp. 802-810
    • Tong, X.1    Zitserman, D.2    Serebriiskii, I.3    Rake, M.4    Dunbrack, R.5    Roegiers, F.6
  • 18
    • 25144523127 scopus 로고    scopus 로고
    • Loss of protein structure stability as a major causative factor in monogenic disease
    • Yue P, Li Z, Moult J. Loss of protein structure stability as a major causative factor in monogenic disease. J Mol Biol 2005;353:459-473.
    • (2005) J Mol Biol , vol.353 , pp. 459-473
    • Yue, P.1    Li, Z.2    Moult, J.3
  • 19
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • Canutescu AA, Shelenkov AA, Dunbrack RL, Jr. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003; 12:2001-2014.
    • (2003) Protein Sci , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack, R.L.3
  • 20
    • 84903147593 scopus 로고    scopus 로고
    • SuSPect: Enhanced prediction of single amino acid variant (SAV) phenotype using network features
    • Yates CM, Filippis I, Kelley LA, Sternberg MJ. SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features. J Mol Biol 2014;426:2692-2701.
    • (2014) J Mol Biol , vol.426 , pp. 2692-2701
    • Yates, C.M.1    Filippis, I.2    Kelley, L.A.3    Sternberg, M.J.4
  • 23
    • 84871122167 scopus 로고    scopus 로고
    • Using Rosetta ligand for small molecule docking into comparative models
    • Kaufmann KW, Meiler J. Using Rosetta ligand for small molecule docking into comparative models. Plos One 2012;7:e50769.
    • (2012) Plos One , vol.7
    • Kaufmann, K.W.1    Meiler, J.2
  • 24
    • 78649537557 scopus 로고    scopus 로고
    • Predicting the accuracy of protein-ligand docking on homology models
    • Bordogna A, Pandini A, Bonati L. Predicting the accuracy of protein-ligand docking on homology models. J Comput Chem 2011; 32:81-98.
    • (2011) J Comput Chem , vol.32 , pp. 81-98
    • Bordogna, A.1    Pandini, A.2    Bonati, L.3
  • 26
    • 34447095430 scopus 로고    scopus 로고
    • Evaluation of the utility of homology models in high throughput docking
    • Ferrara P, Jacoby E. Evaluation of the utility of homology models in high throughput docking. J Mol Model 2007;13:897-905.
    • (2007) J Mol Model , vol.13 , pp. 897-905
    • Ferrara, P.1    Jacoby, E.2
  • 27
    • 67649518035 scopus 로고    scopus 로고
    • Homology modeling in drug discovery: Current trends and applications
    • Cavasotto CN, Phatak SS. Homology modeling in drug discovery: current trends and applications. Drug Discov Today 2009;14: 676-683.
    • (2009) Drug Discov Today , vol.14 , pp. 676-683
    • Cavasotto, C.N.1    Phatak, S.S.2
  • 28
    • 3242813635 scopus 로고    scopus 로고
    • Utility of homology models in the drug discovery process
    • Hillisch A, Pineda LF, Hilgenfeld R. Utility of homology models in the drug discovery process. Drug Discov Today 2004;9:659-669.
    • (2004) Drug Discov Today , vol.9 , pp. 659-669
    • Hillisch, A.1    Pineda, L.F.2    Hilgenfeld, R.3
  • 29
    • 30344440806 scopus 로고    scopus 로고
    • The prediction of protein function at CASP 6. Proteins: Struct, Funct
    • Soro S, Tramontano A. The prediction of protein function at CASP 6. Proteins: Struct, Funct, Bioinf 2005;61:201-213.
    • (2005) Bioinf , vol.61 , pp. 201-213
    • Soro, S.1    Tramontano, A.2
  • 30
    • 36748998785 scopus 로고    scopus 로고
    • Assessment of predictions submitted for the CASP7 function prediction category
    • Lopez G, Rojas A, Tress M, Valencia A. Assessment of predictions submitted for the CASP7 function prediction category. Proteins: Struct Funct Bioinf 2007;69:165-174.
    • (2007) Proteins: Struct Funct Bioinf , vol.69 , pp. 165-174
    • Lopez, G.1    Rojas, A.2    Tress, M.3    Valencia, A.4
  • 37
    • 78651306870 scopus 로고    scopus 로고
    • The protein common interface database (ProtCID)-a comprehensive database of interactions of homologous proteins in multiple crystal forms
    • Xu Q, Dunbrack RL, Jr. The protein common interface database (ProtCID)-a comprehensive database of interactions of homologous proteins in multiple crystal forms. Nucleic Acids Res 2011;39: D761-D770.
    • (2011) Nucleic Acids Res , vol.39 , pp. D761-D770
    • Xu, Q.1    Dunbrack, R.L.2
  • 38
    • 0001368373 scopus 로고
    • Étude comparative de la distribution florale dans une portion des Alpes et du Jura
    • Jaccard P. Étude comparative de la distribution florale dans une portion des Alpes et du Jura. Bull Soc Vaud Sci Nat 1901;37: 547-549.
    • (1901) Bull Soc Vaud Sci Nat , vol.37 , pp. 547-549
    • Jaccard, P.1
  • 39
    • 84980090975 scopus 로고
    • The distribution of the flora in the alpine zone. 1
    • Jaccard P. The distribution of the flora in the alpine zone. 1. New Phytol 1912;11:37-50.
    • (1912) New Phytol , vol.11 , pp. 37-50
    • Jaccard, P.1
  • 40
    • 79960029361 scopus 로고    scopus 로고
    • SwissDock, a protein-small molecule docking web service based on EADock DSS
    • Grosdidier A, Zoete V, Michielin O. SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res 2011; 39:W270-W277.
    • (2011) Nucleic Acids Res , vol.39 , pp. W270-W277
    • Grosdidier, A.1    Zoete, V.2    Michielin, O.3
  • 41
    • 76149120388 scopus 로고    scopus 로고
    • AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010;31:455-461.
    • (2010) J Comput Chem , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 42
    • 84872531476 scopus 로고    scopus 로고
    • Prediction of phenotypes of missense mutations in human proteins from biological assemblies
    • Wei Q, Xu Q, Dunbrack RL. Prediction of phenotypes of missense mutations in human proteins from biological assemblies. Proteins: Struct Funct Bioinf 2013;81:199-213.
    • (2013) Proteins: Struct Funct Bioinf , vol.81 , pp. 199-213
    • Wei, Q.1    Xu, Q.2    Dunbrack, R.L.3
  • 43
    • 84879987629 scopus 로고    scopus 로고
    • The role of balanced training and testing data sets for binary classifiers in bioinformatics
    • Wei Q, Dunbrack RL, Jr. The role of balanced training and testing data sets for binary classifiers in bioinformatics. Plos One 2013;8: e67863.
    • (2013) Plos One , vol.8
    • Wei, Q.1    Dunbrack, R.L.2
  • 45
    • 34548232365 scopus 로고    scopus 로고
    • Inference of macromolecular assemblies from crystalline state
    • Krissinel E, Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol 2007;372:774-797.
    • (2007) J Mol Biol , vol.372 , pp. 774-797
    • Krissinel, E.1    Henrick, K.2
  • 47
    • 77149167608 scopus 로고    scopus 로고
    • Graphlet kernels for prediction of functional residues in protein structures
    • Vacic V, Iakoucheva LM, Lonardi S, Radivojac P. Graphlet kernels for prediction of functional residues in protein structures. J Comput Biol 2010;17:55-72.
    • (2010) J Comput Biol , vol.17 , pp. 55-72
    • Vacic, V.1    Iakoucheva, L.M.2    Lonardi, S.3    Radivojac, P.4
  • 48
    • 13244291417 scopus 로고    scopus 로고
    • Large scale hierarchical clustering of protein sequences
    • Krause A, Stoye J, Vingron M. Large scale hierarchical clustering of protein sequences. BMC Bioinf 2005;6:15.
    • (2005) BMC Bioinf , vol.6 , pp. 15
    • Krause, A.1    Stoye, J.2    Vingron, M.3
  • 49
    • 0036307493 scopus 로고    scopus 로고
    • Within the twilight zone: A sensitive profileprofile comparison tool based on information theory
    • Yona G, Levitt M. Within the twilight zone: a sensitive profileprofile comparison tool based on information theory. J Mol Biol 2002;315:1257-1275.
    • (2002) J Mol Biol , vol.315 , pp. 1257-1275
    • Yona, G.1    Levitt, M.2
  • 50
    • 84947045999 scopus 로고    scopus 로고
    • Ephrussi A. The crystal structure of the Drosophila germline inducer Oskar identifies two domains with distinct Vasa helicase-and RNA-binding activities
    • Jeske M, Bordi M, Glatt S, Müller S, Rybin V, Müller CW, Ephrussi A. The crystal structure of the Drosophila germline inducer Oskar identifies two domains with distinct Vasa helicase-and RNA-binding activities. Cell Rep 2015;12:587-598.
    • (2015) Cell Rep , vol.12 , pp. 587-598
    • Jeske, M.1    Bordi, M.2    Glatt, S.3    Müller, S.4    Rybin, V.5    Müller, C.W.6
  • 51
    • 84885990516 scopus 로고    scopus 로고
    • LDDT: A local superposition-free score for comparing protein structures and models using distance difference tests
    • Mariani V, Biasini M, Barbato A, Schwede T. lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics 2013;29:2722-2728.
    • (2013) Bioinformatics , vol.29 , pp. 2722-2728
    • Mariani, V.1    Biasini, M.2    Barbato, A.3    Schwede, T.4
  • 52
    • 0042622381 scopus 로고    scopus 로고
    • LGA: A method for finding 3D similarities in protein structures
    • Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 2003;31:3370-3374.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3370-3374
    • Zemla, A.1
  • 53
    • 84868027251 scopus 로고    scopus 로고
    • Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB
    • Xu Q, Dunbrack RL Jr. Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. Bioinformatics 2012;28:2763-2772.
    • (2012) Bioinformatics , vol.28 , pp. 2763-2772
    • Xu, Q.1    Dunbrack, R.L.2
  • 54
    • 0034616960 scopus 로고    scopus 로고
    • Modeling of substrate specificity of the Alzheimer’s disease amyloid precursor protein beta-secretase
    • Sauder JM, Arthur JW, Dunbrack RL, Jr. Modeling of substrate specificity of the Alzheimer’s disease amyloid precursor protein beta-secretase. J Mol Biol 2000;300:241-248.
    • (2000) J Mol Biol , vol.300 , pp. 241-248
    • Sauder, J.M.1    Arthur, J.W.2    Dunbrack, R.L.3
  • 56
    • 84857121123 scopus 로고    scopus 로고
    • Seattle, WA, 2015;05/2015
    • Project NGES. Exome variant server. Seattle, WA (URL: http://evsgswashingtonedu/EVS/) 2015;05/2015.
    • Exome Variant Server
  • 58
    • 84902552584 scopus 로고    scopus 로고
    • A framework for organizing cancer-related variations from existing databases, publications and NGS data using a Highperformance Integrated Virtual Environment (HIVE)
    • bau022
    • Wu T-J, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, Mazumder R. A framework for organizing cancer-related variations from existing databases, publications and NGS data using a Highperformance Integrated Virtual Environment (HIVE). Database 2014;2014:bau022.
    • (2014) Database 2014
    • Wu, T.-J.1    Shamsaddini, A.2    Pan, Y.3    Smith, K.4    Crichton, D.J.5    Simonyan, V.6    Mazumder, R.7
  • 64
    • 84938629859 scopus 로고    scopus 로고
    • Influence of Vanin-1 and catalytic products in liver during normal and oxidative stress conditions
    • Ferreira DW, Naquet P, Manautou JE. Influence of Vanin-1 and catalytic products in liver during normal and oxidative stress conditions. Curr Med Chem 2015;22:2407-2416.
    • (2015) Curr Med Chem , vol.22 , pp. 2407-2416
    • Ferreira, D.W.1    Naquet, P.2    Manautou, J.E.3
  • 65
    • 84898771680 scopus 로고    scopus 로고
    • Molecular prioritization strategies to identify functional genetic variants in the cardiovascular diseaseassociated expression QTL Vanin-1
    • Kaskow BJ, Diepeveen LA, Proffitt JM, Rea AJ, Ulgiati D, Blangero J, Moses EK, Abraham LJ. Molecular prioritization strategies to identify functional genetic variants in the cardiovascular diseaseassociated expression QTL Vanin-1. Eur J Hum Genet 2014;22:688-695.
    • (2014) Eur J Hum Genet , vol.22 , pp. 688-695
    • Kaskow, B.J.1    Diepeveen, L.A.2    Proffitt, J.M.3    Rea, A.J.4    Ulgiati, D.5    Blangero, J.6    Moses, E.K.7    Abraham, L.J.8
  • 68
    • 84903386152 scopus 로고    scopus 로고
    • Bioassemblymodeler (BAM): User-friendly homology modeling of protein homo-and heterooligomers
    • Shapovalov MV, Wang Q, Xu Q, Andrake M, Dunbrack RL Jr. Bioassemblymodeler (BAM): user-friendly homology modeling of protein homo-and heterooligomers. PLOS ONE 2014;9:e98309.
    • (2014) PLOS ONE , vol.9
    • Shapovalov, M.V.1    Wang, Q.2    Xu, Q.3    Rake, M.4    Dunbrack, R.L.5
  • 70
    • 84907185231 scopus 로고    scopus 로고
    • Crystal structure of the cGMP-dependent protein kinase II leucine zipper and Rab11b protein complex reveals molecular details of G-kinase-specific interactions
    • Reger AS, Yang MP, Koide-Yoshida S, Guo E, Mehta S, Yuasa K, Liu A, Casteel DE, Kim C. Crystal structure of the cGMP-dependent protein kinase II leucine zipper and Rab11b protein complex reveals molecular details of G-kinase-specific interactions. J Biol Chem 2014;289:25393-25403.
    • (2014) J Biol Chem , vol.289 , pp. 25393-25403
    • Reger, A.S.1    Yang, M.P.2    Koide-Yoshida, S.3    Guo, E.4    Mehta, S.5    Yuasa, K.6    Liu, A.7    Casteel, D.E.8    Kim, C.9
  • 71
    • 84908152065 scopus 로고    scopus 로고
    • Structural basis for the binding specificity of human recepteur d’Origine Nantais (RON) receptor tyrosine kinase to macrophage-stimulating protein
    • Chao KL, Gorlatova NV, Eisenstein E, Herzberg O. Structural basis for the binding specificity of human recepteur d’Origine Nantais (RON) receptor tyrosine kinase to macrophage-stimulating protein. J Biol Chem 2014;289:29948-29960.
    • (2014) J Biol Chem , vol.289 , pp. 29948-29960
    • Chao, K.L.1    Gorlatova, N.V.2    Eisenstein, E.3    Herzberg, O.4
  • 74
    • 33750437407 scopus 로고    scopus 로고
    • Structural basis for Rab11-mediated recruitment of FIP3 to recycling endosomes
    • Eathiraj S, Mishra A, Prekeris R, Lambright DG. Structural basis for Rab11-mediated recruitment of FIP3 to recycling endosomes. J Mol Biol 2006;364:121-135.
    • (2006) J Mol Biol , vol.364 , pp. 121-135
    • Eathiraj, S.1    Mishra, A.2    Prekeris, R.3    Lambright, D.G.4
  • 76
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: An initial-stage protein-docking algorithm
    • Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
    • (2003) Proteins , vol.52 , pp. 80-87
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 77
    • 3142595278 scopus 로고    scopus 로고
    • Crystal structure of the HGF b-chain in complex with the Sema domain of the Met receptor
    • Stamos J, Lazarus RA, Yao X, Kirchhofer D, Wiesmann C. Crystal structure of the HGF b-chain in complex with the Sema domain of the Met receptor. Embo J 2004;23:2325-2335.
    • (2004) Embo J , vol.23 , pp. 2325-2335
    • Stamos, J.1    Lazarus, R.A.2    Yao, X.3    Kirchhofer, D.4    Wiesmann, C.5
  • 80
    • 33845663050 scopus 로고    scopus 로고
    • Structural basis for protein recognition by B30. 2/SPRY domains
    • Woo J-S, Suh H-Y, Park S-Y, Oh B-H. Structural basis for protein recognition by B30. 2/SPRY domains. Mol Cell 2006;24:967-976.
    • (2006) Mol Cell , vol.24 , pp. 967-976
    • Woo, J.-S.1    Suh, H.-Y.2    Park, S.-Y.3    Oh, B.-H.4
  • 84
    • 0035702809 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP): Round IV
    • Moult J, Fidelis K, Zemla A, Hubbard T. Critical assessment of methods of protein structure prediction (CASP): round IV. Proteins 2001; Suppl 5:2-7.
    • (2001) Proteins , pp. 2-7
    • Moult, J.1    Fidelis, K.2    Zemla, A.3    Hubbard, T.4
  • 86
    • 84892957566 scopus 로고    scopus 로고
    • Evaluation of predictions in the CASP10 model refinement category
    • Nugent T, Cozzetto D, Jones DT. Evaluation of predictions in the CASP10 model refinement category. Proteins: Struct Funct Bioinf 2014;82:98-111.
    • (2014) Proteins: Struct Funct Bioinf , vol.82 , pp. 98-111
    • Nugent, T.1    Cozzetto, D.2    Jones, D.T.3
  • 88
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 89
    • 0031307019 scopus 로고    scopus 로고
    • Evaluation of comparative protein structure modeling byMODELLER-3
    • Sanchez R, Sali A. Evaluation of comparative protein structure modeling byMODELLER-3. Proteins: Struct Funct Genet 1997;Suppl 1:50-58.
    • (1997) Proteins: Struct Funct Genet , pp. 50-58
    • Sanchez, R.1    Sali, A.2
  • 91
    • 0031576989 scopus 로고    scopus 로고
    • Prediction of protein sidechain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
    • Bower MJ, Cohen FE, Dunbrack RL, Jr. Prediction of protein sidechain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997;267:1268-1282.
    • (1997) J Mol Biol , vol.267 , pp. 1268-1282
    • Bower, M.J.1    Cohen, F.E.2    Dunbrack, R.L.3
  • 92
    • 70450106216 scopus 로고    scopus 로고
    • Improved prediction of protein side-chain conformations with SCWRL 4
    • Krivov GG, Shapovalov MV, Dunbrack RL, Jr. Improved prediction of protein side-chain conformations with SCWRL 4. Proteins 2009; 77:778-795.
    • (2009) Proteins , vol.77 , pp. 778-795
    • Krivov, G.G.1    Shapovalov, M.V.2    Dunbrack, R.L.3
  • 93
    • 30344488120 scopus 로고    scopus 로고
    • TASSER: An automated method for the prediction of protein tertiary structures in CASP 6
    • Zhang Y, Arakaki AK, Skolnick J. TASSER: an automated method for the prediction of protein tertiary structures in CASP 6. Proteins: Struct Funct Genet 2005;61:91-98.
    • (2005) Proteins: Struct Funct Genet , vol.61 , pp. 91-98
    • Zhang, Y.1    Arakaki, A.K.2    Skolnick, J.3
  • 94
    • 39449115394 scopus 로고    scopus 로고
    • I-TASSER server for protein 3D structure prediction
    • Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinf. 2008;9:40.
    • (2008) BMC Bioinf , vol.9 , pp. 40
    • Zhang, Y.1
  • 95
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005;33:W244-W248.
    • (2005) Nucleic Acids Res , vol.33 , pp. W244-W248
    • Soding, J.1    Biegert, A.2    Lupas, A.N.3
  • 96
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997;18:2714-2723.
    • (1997) Electrophoresis , vol.18 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 97
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 2003; 31:3381-3385.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 98
    • 84858126537 scopus 로고    scopus 로고
    • Automated protein structure modeling with SWISS-MODEL workspace and the protein model portal
    • Bordoli L, Schwede T. Automated protein structure modeling with SWISS-MODEL workspace and the protein model portal. Methods Mol Biol 2012;857:107-136.
    • (2012) Methods Mol Biol , vol.857 , pp. 107-136
    • Bordoli, L.1    Schwede, T.2
  • 100
    • 84865149772 scopus 로고    scopus 로고
    • Optimal simultaneous superpositioning of multiple structures with missing data
    • Theobald DL, Steindel PA. Optimal simultaneous superpositioning of multiple structures with missing data. Bioinformatics 2012;28: 1972-1979.
    • (2012) Bioinformatics , vol.28 , pp. 1972-1979
    • Theobald, D.L.1    Steindel, P.A.2
  • 101
    • 33748663254 scopus 로고    scopus 로고
    • THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures
    • Theobald DL, Wuttke DS. THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures. Bioinformatics 2006;22:2171-2172.
    • (2006) Bioinformatics , vol.22 , pp. 2171-2172
    • Theobald, D.L.1    Wuttke, D.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.