{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T13:25:04Z","timestamp":1742995504859,"version":"3.40.3"},"publisher-location":"Cham","reference-count":79,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319340982"},{"type":"electronic","value":"9783319340999"}],"license":[{"start":{"date-parts":[[2016,1,1]],"date-time":"2016-01-01T00:00:00Z","timestamp":1451606400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016]]},"DOI":"10.1007\/978-3-319-34099-9_32","type":"book-chapter","created":{"date-parts":[[2016,4,27]],"date-time":"2016-04-27T14:40:35Z","timestamp":1461768035000},"page":"419-433","source":"Crossref","is-referenced-by-count":7,"title":["eQuant - A Server for Fast Protein Model Quality Assessment by Integrating High-Dimensional Data and Machine Learning"],"prefix":"10.1007","author":[{"given":"Sebastian","family":"Bittrich","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florian","family":"Heinke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dirk","family":"Labudde","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,4,28]]},"reference":[{"issue":"17","key":"32_CR1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"S Altschul","year":"1997","unstructured":"Altschul, S.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17), 3389\u20133402 (1997)","journal-title":"Nucleic Acids Res."},{"issue":"4","key":"32_CR2","first-page":"725","volume":"5","author":"R Ambrish","year":"2010","unstructured":"Ambrish, R., Kucukural, A., Zhang, Y.: I-TASSER: a unified platform for automated protein structure and function prediction. Nucleic Acids Res. 5(4), 725\u2013738 (2010)","journal-title":"Nucleic Acids Res."},{"issue":"4096","key":"32_CR3","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1126\/science.181.4096.223","volume":"181","author":"CB Anfinsen","year":"1973","unstructured":"Anfinsen, C.B.: Principles that govern the folding of protein chains. Science 181(4096), 223\u2013230 (1973)","journal-title":"Science"},{"issue":"2","key":"32_CR4","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1093\/bioinformatics\/bti770","volume":"22","author":"K Arnold","year":"2006","unstructured":"Arnold, K., Bordoli, L., Kopp, J., Schwede, T.: The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22(2), 195\u2013201 (2006)","journal-title":"Bioinformatics"},{"issue":"5","key":"32_CR5","first-page":"586","volume":"15","author":"I Bahar","year":"2005","unstructured":"Bahar, I., Rader, A.J.: Coarse-grained normal mode analysis in structural biology. Bioinformatics 15(5), 586\u2013592 (2005)","journal-title":"Bioinformatics"},{"issue":"1","key":"32_CR6","first-page":"291","volume":"4","author":"U Bastolla","year":"2014","unstructured":"Bastolla, U.: Detecting selection on protein stability through statistical mechanical models of folding and evolution. Bioinformatics 4(1), 291\u2013314 (2014)","journal-title":"Bioinformatics"},{"issue":"3","key":"32_CR7","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1093\/bioinformatics\/btq662","volume":"27","author":"P Benkert","year":"2011","unstructured":"Benkert, P., Biasini, M., Schwede, T.: Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 27(3), 343\u2013350 (2011)","journal-title":"Bioinformatics"},{"issue":"Web Server","key":"32_CR8","doi-asserted-by":"crossref","first-page":"W510","DOI":"10.1093\/nar\/gkp322","volume":"37","author":"P Benkert","year":"2009","unstructured":"Benkert, P., Kunzli, M., Schwede, T.: QMEAN server for protein model quality estimation. Nucleic Acids Res. 37(Web Server), W510\u2013W514 (2009)","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"32_CR9","first-page":"35","volume":"9","author":"P Benkert","year":"2009","unstructured":"Benkert, P., Schwede, T., Tosatto, S.: QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. Bioinformatics 9(1), 35 (2009)","journal-title":"Bioinformatics"},{"issue":"1","key":"32_CR10","first-page":"261","volume":"71","author":"P Benkert","year":"2008","unstructured":"Benkert, P., Tosatto, S.E., Schomburg, D.: QMEAN: a comprehensive scoring function for model quality assessment. Bioinformatics 71(1), 261\u2013277 (2008)","journal-title":"Bioinformatics"},{"issue":"Web Server","key":"32_CR11","doi-asserted-by":"crossref","first-page":"W633","DOI":"10.1093\/nar\/gkq375","volume":"38","author":"M Berjanskii","year":"2010","unstructured":"Berjanskii, M., Liang, Y., Zhou, J., Tang, P., Stothard, P., Zhou, Y., Cruz, J., MacDonell, C., Lin, G., Lu, P., et al.: PROSESS: a protein structure evaluation suite and server. Nucleic Acids Res. 38(Web Server), W633\u2013W640 (2010)","journal-title":"Nucleic Acids Res."},{"issue":"4","key":"32_CR12","first-page":"778","volume":"66","author":"A Bhattacharya","year":"2006","unstructured":"Bhattacharya, A., Tejero, R., Montelione, G.T.: Evaluating protein structures determined by structural genomics consortia. Bioinformatics 66(4), 778\u2013795 (2006)","journal-title":"Bioinformatics"},{"key":"32_CR13","unstructured":"Biasini, M.: Pv-WebGL-based protein viewer (2014)"},{"issue":"W1","key":"32_CR14","doi-asserted-by":"crossref","first-page":"W252","DOI":"10.1093\/nar\/gku340","volume":"42","author":"M Biasini","year":"2014","unstructured":"Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T.G., Bertoni, M., Bordoli, L., Schwede, T.: SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 42(W1), W252\u2013W258 (2014)","journal-title":"Nucleic Acids Res."},{"issue":"1467","key":"32_CR15","first-page":"413","volume":"361","author":"T Blundell","year":"2006","unstructured":"Blundell, T., et al.: Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery. Bioinformatics 361(1467), 413\u2013423 (2006)","journal-title":"Bioinformatics"},{"issue":"5016","key":"32_CR16","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1126\/science.1853201","volume":"253","author":"J Bowie","year":"1991","unstructured":"Bowie, J., Luthy, R., Eisenberg, D.: A method to identify protein sequences that fold into a known three-dimensional structure. Science 253(5016), 164\u2013170 (1991)","journal-title":"Science"},{"issue":"S7","key":"32_CR17","first-page":"128","volume":"61","author":"P Bradley","year":"2005","unstructured":"Bradley, P., Malmstr\u00f6m, L., Qian, B., Schonbrun, J., Chivian, D., Kim, D., Meiler, J., Misura, K., Baker, D.: Free modeling with Rosetta in CASP6. Science 61(S7), 128\u2013134 (2005)","journal-title":"Science"},{"issue":"6","key":"32_CR18","first-page":"1291","volume":"36","author":"R Bryll","year":"2003","unstructured":"Bryll, R., Gutierrez-Osuna, R., Quek, F.: Attribute bagging: improving accuracy of classifier ensembles by using random feature subsets. Science 36(6), 1291\u20131302 (2003)","journal-title":"Science"},{"issue":"4","key":"32_CR19","first-page":"1003","volume":"297","author":"F Domingues","year":"2000","unstructured":"Domingues, F., Lackner, P., Andreeva, A., Sippl, M.J.: Structure-based evaluation of sequence comparison and fold recognition alignment accuracy. Science 297(4), 1003\u20131013 (2000)","journal-title":"Science"},{"key":"32_CR20","unstructured":"Dressel, F., Marsico, A., Tuukkanen, A., Schroeder, M., Labudde, D.: Understanding of SMFS barriers by means of energy profiles. In: Proceedings of German Conference on Bioinformatics, pp. 90\u201399 (2007)"},{"key":"32_CR21","first-page":"396","volume":"277","author":"D Eisenberg","year":"1997","unstructured":"Eisenberg, D., L\u00fcthy, R., Bowie, J.U.: Verify3D: assessment of protein models with three-dimensional profiles. Science 277, 396\u2013404 (1997)","journal-title":"Science"},{"issue":"1","key":"32_CR22","first-page":"73","volume":"23","author":"A Elofsson","year":"1995","unstructured":"Elofsson, A., Le Grand, S.M., Eisenberg, D.: Local moves: an efficient algorithm for simulation of protein folding. Science 23(1), 73\u201382 (1995)","journal-title":"Science"},{"issue":"4","key":"32_CR23","first-page":"392","volume":"47","author":"RA Engh","year":"1991","unstructured":"Engh, R.A., Huber, R.: Accurate bond and angle parameters for x-ray protein structure refinement. Science 47(4), 392\u2013400 (1991)","journal-title":"Science"},{"key":"32_CR24","volume-title":"Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding","author":"A Fersht","year":"1995","unstructured":"Fersht, A.: Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, 3rd edn. W H Freeman & Co, New York (1995)","edition":"3"},{"issue":"4","key":"32_CR25","first-page":"365","volume":"33","author":"MJ Forster","year":"2002","unstructured":"Forster, M.J.: Molecular modelling in structural biology. Science 33(4), 365\u2013384 (2002)","journal-title":"Science"},{"issue":"15","key":"32_CR26","doi-asserted-by":"crossref","first-page":"2479","DOI":"10.1093\/bioinformatics\/bth261","volume":"20","author":"E Frank","year":"2004","unstructured":"Frank, E., Hall, M., Trigg, L., Holmes, G., Witten, I.H.: Data mining in bioinformatics using Weka. Bioinformatics 20(15), 2479\u20132481 (2004)","journal-title":"Bioinformatics"},{"issue":"10","key":"32_CR27","first-page":"2836","volume":"16","author":"TM Fujiwara","year":"2005","unstructured":"Fujiwara, T.M., Bichet, D.G.: Molecular biology of hereditary diabetes insipidus. Bioinformatics 16(10), 2836\u20132846 (2005)","journal-title":"Bioinformatics"},{"issue":"12","key":"32_CR28","first-page":"3696","volume":"80","author":"N Go","year":"1983","unstructured":"Go, N., Noguti, T., Nishikawa, T.: Dynamics of a small globular protein in terms of low-frequency vibrational modes. Bioinformatics 80(12), 3696\u20133700 (1983)","journal-title":"Bioinformatics"},{"issue":"5","key":"32_CR29","first-page":"459","volume":"9","author":"M Grabowski","year":"2009","unstructured":"Grabowski, M., Chruszcz, M., Zimmerman, M.D., Kirillova, O., Minor, W.: Benefits of structural genomics for drug discovery research. Bioinformatics 9(5), 459\u2013474 (2009)","journal-title":"Bioinformatics"},{"issue":"S1","key":"32_CR30","first-page":"S162","volume":"30","author":"N Guex","year":"2009","unstructured":"Guex, N., Peitsch, M.C., Schwede, T.: Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Bioinformatics 30(S1), S162\u2013S173 (2009)","journal-title":"Bioinformatics"},{"key":"32_CR31","doi-asserted-by":"crossref","first-page":"bat031","DOI":"10.1093\/database\/bat031","volume":"2013","author":"J Haas","year":"2013","unstructured":"Haas, J., Roth, S., Arnold, K., Kiefer, F., Schmidt, T., Bordoli, L., Schwede, T.: The protein model portal \u2013 a comprehensive resource for protein structure and model information. Database 2013, bat031 (2013)","journal-title":"Database"},{"issue":"1","key":"32_CR32","first-page":"10","volume":"11","author":"M Hall","year":"2009","unstructured":"Hall, M., Frank, E., Holmes, G., Pfahringer, B., Reutemann, P., Witten, I.H.: The Weka data mining software. Bioinformatics 11(1), 10 (2009)","journal-title":"Bioinformatics"},{"key":"32_CR33","first-page":"1","volume":"2012","author":"F Heinke","year":"2012","unstructured":"Heinke, F., Labudde, D.: Membrane protein stability analyses by means of protein energy profiles in case of nephrogenic diabetes insipidus. Bioinformatics 2012, 1\u201311 (2012)","journal-title":"Bioinformatics"},{"issue":"D1","key":"32_CR34","first-page":"D320","volume":"41","author":"F Heinke","year":"2013","unstructured":"Heinke, F., Schildbach, S., Stockmann, D., Labudde, D.: eProS-a database and toolbox for investigating protein sequence-structure-function relationships through energy profiles. Bioinformatics 41(D1), D320\u2013D326 (2013)","journal-title":"Bioinformatics"},{"key":"32_CR35","unstructured":"A Highsoft Solutions: Highcharts JS (2012)"},{"issue":"18","key":"32_CR36","doi-asserted-by":"crossref","first-page":"2096","DOI":"10.1093\/bioinformatics\/btn397","volume":"24","author":"RCG Holland","year":"2008","unstructured":"Holland, R.C.G., Down, T.A., Pocock, M., Prlic, A., Huen, D., James, K., Foisy, S., Drager, A., Yates, A., Heuer, M., et al.: BioJava: an open-source framework for bioinformatics. Bioinformatics 24(18), 2096\u20132097 (2008)","journal-title":"Bioinformatics"},{"key":"32_CR37","doi-asserted-by":"crossref","unstructured":"Holmes, G., Donkin, A., Witten, I.: Weka: a machine learning workbench. In: Proceedings of ANZIIS 94 - Australian New Zealand Intelligent Information Systems Conference, pp. 357\u2013361 (1994)","DOI":"10.1109\/ANZIIS.1994.396988"},{"issue":"6381","key":"32_CR38","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1038\/358086a0","volume":"358","author":"DT Jones","year":"1992","unstructured":"Jones, D.T., Taylort, W.R., Thornton, J.M.: A new approach to protein fold recognition. Nature 358(6381), 86\u201389 (1992)","journal-title":"Nature"},{"issue":"5","key":"32_CR39","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1093\/bioinformatics\/btv637","volume":"32","author":"F Kaiser","year":"2015","unstructured":"Kaiser, F., Eisold, A., Bittrich, S., Labudde, D.: Fit3D - a web application for highly accurate screening of spatial residue patterns in protein structure data. Bioinformatics 32(5), 792\u2013794 (2015)","journal-title":"Bioinformatics"},{"issue":"7","key":"32_CR40","first-page":"698","volume":"22","author":"F Kaiser","year":"2015","unstructured":"Kaiser, F., Eisold, A., Labudde, D.: A novel algorithm for enhanced structural motif matching in proteins. Nature 22(7), 698\u2013713 (2015)","journal-title":"Nature"},{"issue":"8","key":"32_CR41","first-page":"832","volume":"20","author":"TK Ho","year":"1998","unstructured":"Ho, T.K.: The random subspace method for constructing decision forests. Nature 20(8), 832\u2013844 (1998)","journal-title":"Nature"},{"issue":"6106","key":"32_CR42","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1038\/325733a0","volume":"325","author":"J Kang","year":"1987","unstructured":"Kang, J., Lemaire, H., Unterbeck, A., Salbaum, J.M., Masters, C.L., Grzeschik, K.H., Multhaup, G., Beyreuther, K., M\u00fcller-Hill, B.: The precursor of Alzheimer\u2019s disease amyloid A4 protein resembles a cell-surface receptor. Nature 325(6106), 733\u2013736 (1987)","journal-title":"Nature"},{"issue":"4610","key":"32_CR43","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1038\/181662a0","volume":"181","author":"JC Kendrew","year":"1958","unstructured":"Kendrew, J.C., Bodo, G., Dintzis, H.M., Parrish, R.G., Wyckoff, H., Phillips, D.C.: A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature 181(4610), 662\u2013666 (1958)","journal-title":"Nature"},{"key":"32_CR44","first-page":"112","volume":"82","author":"A Kryshtafovych","year":"2014","unstructured":"Kryshtafovych, A., Barbato, A., Fidelis, K., Monastyrskyy, B., Schwede, T., Tramontano, A.: Assessment of the assessment: evaluation of the model quality estimates in CASP10. Nature 82, 112\u2013126 (2014)","journal-title":"Nature"},{"key":"32_CR45","first-page":"7","volume":"82","author":"A Kryshtafovych","year":"2014","unstructured":"Kryshtafovych, A., Monastyrskyy, B., Fidelis, K.: CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL. Nature 82, 7\u201313 (2014)","journal-title":"Nature"},{"issue":"5073","key":"32_CR46","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1126\/science.257.5073.1078","volume":"257","author":"ID Kuntz","year":"1992","unstructured":"Kuntz, I.D.: Structure-based strategies for drug design and discovery. Science 257(5073), 1078\u20131082 (1992)","journal-title":"Science"},{"issue":"4","key":"32_CR47","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1007\/BF00228148","volume":"8","author":"R Laskowski","year":"1996","unstructured":"Laskowski, R., Rullmann, J., MacArthur, M., Kaptein, R., Thornton, J.M.: AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8(4), 477\u2013486 (1996)","journal-title":"J. Biomol. NMR"},{"issue":"2","key":"32_CR48","first-page":"283","volume":"26","author":"RA Laskowski","year":"1993","unstructured":"Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M.: PROCHECK: a program to check the stereochemical quality of protein structures. Science 26(2), 283\u2013291 (1993)","journal-title":"Science"},{"issue":"6364","key":"32_CR49","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/356083a0","volume":"356","author":"R L\u00fcthy","year":"1992","unstructured":"L\u00fcthy, R., Bowie, J.U., Eisenberg, D.: Assessment of protein models with three-dimensional profiles. Nature 356(6364), 83\u201385 (1992)","journal-title":"Nature"},{"key":"32_CR50","unstructured":"Marrin, C.: WebGL Specification. Khronos WebGL Working Group (2011)"},{"issue":"W1","key":"32_CR51","first-page":"W368","volume":"41","author":"LJ McGuffin","year":"2013","unstructured":"McGuffin, L.J., Buenavista, M.T., Roche, D.B.: The ModFOLD4 server for the quality assessment of 3D protein models. Nature 41(W1), W368\u2013W372 (2013)","journal-title":"Nature"},{"key":"32_CR52","first-page":"187","volume":"5","author":"F Melo","year":"1997","unstructured":"Melo, F., Devos, D., Depiereux, E., Feytmans, E.: ANOLEA: a WWW server to assess protein structures. Nature 5, 187\u2013190 (1997)","journal-title":"Nature"},{"issue":"1","key":"32_CR53","first-page":"207","volume":"267","author":"F Melo","year":"1997","unstructured":"Melo, F., Feytmans, E.: Novel knowledge-based mean force potential at atomic level. Nature 267(1), 207\u2013222 (1997)","journal-title":"Nature"},{"issue":"5","key":"32_CR54","first-page":"1141","volume":"277","author":"F Melo","year":"1998","unstructured":"Melo, F., Feytmans, E.: Assessing protein structures with a non-local atomic interaction energy. Nature 277(5), 1141\u20131152 (1998)","journal-title":"Nature"},{"issue":"1","key":"32_CR55","first-page":"219","volume":"29","author":"T Noguchi","year":"2001","unstructured":"Noguchi, T.: PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB). Nature 29(1), 219\u2013220 (2001)","journal-title":"Nature"},{"issue":"13","key":"32_CR56","first-page":"1656","volume":"25","author":"C Oostenbrink","year":"2004","unstructured":"Oostenbrink, C., Villa, A., Mark, A.E., van Gunsteren, W.F.: A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. Nature 25(13), 1656\u20131676 (2004)","journal-title":"Nature"},{"key":"32_CR57","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1007\/978-3-540-74825-0_11","volume-title":"Advances in Intelligent Data Analysis VII","author":"P Panov","year":"2007","unstructured":"Panov, P., Dzeroski, S.: Combining bagging and random subspaces to create better ensembles. In: Berthold, M., Shawe-Taylor, J., Lavra\u010d, N. (eds.) IDA 2007. LNCS, vol. 4723, pp. 118\u2013129. Springer, Heidelberg (2007)"},{"issue":"20","key":"32_CR58","doi-asserted-by":"crossref","first-page":"2693","DOI":"10.1093\/bioinformatics\/bts494","volume":"28","author":"A Prlic","year":"2012","unstructured":"Prlic, A., et al.: BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics 28(20), 2693\u20132695 (2012)","journal-title":"Bioinformatics"},{"issue":"1","key":"32_CR59","first-page":"95","volume":"7","author":"G Ramachandran","year":"1963","unstructured":"Ramachandran, G., Ramakrishnan, C., Sasisekharan, V.: Stereochemistry of polypeptide chain configurations. Bioinformatics 7(1), 95\u201399 (1963)","journal-title":"Bioinformatics"},{"issue":"1","key":"32_CR60","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1186\/1471-2105-13-224","volume":"13","author":"A Ray","year":"2012","unstructured":"Ray, A., Lindahl, E., Wallner, B.: Improved model quality assessment using ProQ2. BMC Bioinform. 13(1), 224 (2012)","journal-title":"BMC Bioinform."},{"issue":"Database issue","key":"32_CR61","doi-asserted-by":"crossref","first-page":"D475","DOI":"10.1093\/nar\/gks1200","volume":"41","author":"PW Rose","year":"2013","unstructured":"Rose, P.W., et al.: The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res. 41(Database issue), D475\u2013D482 (2013)","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"32_CR62","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1002\/prot.21531","volume":"69","author":"MI Sadowski","year":"2007","unstructured":"Sadowski, M.I., Jones, D.T.: Benchmarking template selection and model quality assessment for high-resolution comparative modeling. Proteins: Struct. Funct. Bioinform. 69(3), 476\u2013485 (2007)","journal-title":"Proteins: Struct. Funct. Bioinform."},{"issue":"3","key":"32_CR63","first-page":"779","volume":"234","author":"A Sali","year":"1993","unstructured":"Sali, A., Blundell, T.L.: Comparative protein modelling by satisfaction of spatial restraints. BMC Bioinform. 234(3), 779\u2013815 (1993)","journal-title":"BMC Bioinform."},{"key":"32_CR64","volume-title":"Principles of Protein Structure","author":"GE Schulz","year":"1984","unstructured":"Schulz, G.E., Schirmer, R.H.: Principles of Protein Structure, 5th edn. Springer, New York (1984)","edition":"5"},{"issue":"2","key":"32_CR65","first-page":"151","volume":"17","author":"T Schwede","year":"2009","unstructured":"Schwede, T., et al.: Outcome of a workshop on applications of protein models in biomedical research. BMC Bioinform. 17(2), 151\u2013159 (2009)","journal-title":"BMC Bioinform."},{"issue":"4","key":"32_CR66","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1007\/BF02337562","volume":"7","author":"MJ Sippl","year":"1993","unstructured":"Sippl, M.J.: Boltzmann\u2019s principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J. Comput.-Aided Mol. Des. 7(4), 473\u2013501 (1993)","journal-title":"J. Comput.-Aided Mol. Des."},{"issue":"4","key":"32_CR67","first-page":"355","volume":"17","author":"MJ Sippl","year":"1993","unstructured":"Sippl, M.J.: Recognition of errors in three-dimensional structures of proteins. BMC Bioinform. 17(4), 355\u2013362 (1993)","journal-title":"BMC Bioinform."},{"issue":"2","key":"32_CR68","first-page":"229","volume":"5","author":"MJ Sippl","year":"1995","unstructured":"Sippl, M.J.: Knowledge-based potentials for proteins. BMC Bioinform. 5(2), 229\u2013235 (1995)","journal-title":"BMC Bioinform."},{"issue":"1","key":"32_CR69","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.jmb.2009.05.087","volume":"392","author":"B Strandberg","year":"2009","unstructured":"Strandberg, B.: Chapter 1: building the ground for the first two protein structures: myoglobin and haemoglobin. J. Mol. Biol. 392(1), 2\u201310 (2009)","journal-title":"J. Mol. Biol."},{"issue":"1","key":"32_CR70","first-page":"42","volume":"19","author":"S Surade","year":"2012","unstructured":"Surade, S., Blundell, T.L.: Structural biology and drug discovery of difficult targets: the limits of ligandability. BMC Bioinform. 19(1), 42\u201350 (2012)","journal-title":"BMC Bioinform."},{"issue":"Database issue","key":"32_CR71","first-page":"D191","volume":"42","author":"The UniProt Consortium","year":"2014","unstructured":"The UniProt Consortium: Activities at the universal protein resource (UniProt). Nucleic Acids Res. 42(Database issue), D191\u2013D198 (2014)","journal-title":"Nucleic Acids Res."},{"issue":"7","key":"32_CR72","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1093\/protein\/8.7.677","volume":"8","author":"G Verkhivker","year":"1995","unstructured":"Verkhivker, G., Appelt, K., Freer, S., Villafranca, J.: Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. Protein Eng. Des. Sel. 8(7), 677\u2013691 (1995)","journal-title":"Protein Eng. Des. Sel."},{"key":"32_CR73","first-page":"1","volume":"1137","author":"B Webb","year":"2014","unstructured":"Webb, B., Sali, A.: Protein structure modeling with modeller. BMC Bioinform. 1137, 1\u201315 (2014)","journal-title":"BMC Bioinform."},{"key":"32_CR74","first-page":"349","volume":"23","author":"PJ Whittle","year":"1994","unstructured":"Whittle, P.J., Blundell, T.L.: Protein structure-based drug design. BMC Bioinform. 23, 349\u2013375 (1994)","journal-title":"BMC Bioinform."},{"issue":"Web Server","key":"32_CR75","doi-asserted-by":"crossref","first-page":"W407","DOI":"10.1093\/nar\/gkm290","volume":"35","author":"M Wiederstein","year":"2007","unstructured":"Wiederstein, M., Sippl, M.J.: ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 35(Web Server), W407\u2013W410 (2007)","journal-title":"Nucleic Acids Res."},{"issue":"13","key":"32_CR76","first-page":"3316","volume":"31","author":"L Willard","year":"2003","unstructured":"Willard, L.: VADAR: a web server for quantitative evaluation of protein structure quality. BMC Bioinform. 31(13), 3316\u20133319 (2003)","journal-title":"BMC Bioinform."},{"issue":"36","key":"32_CR77","first-page":"22059","volume":"265","author":"K W\u00fcthrich","year":"1990","unstructured":"W\u00fcthrich, K.: Protein structure determination in solution by nmr spectroscopy. BMC Bioinform. 265(36), 22059\u201322062 (1990)","journal-title":"BMC Bioinform."},{"issue":"13","key":"32_CR78","first-page":"3370","volume":"31","author":"A Zemla","year":"2003","unstructured":"Zemla, A.: LGA: a method for finding 3D similarities in protein structures. BMC Bioinform. 31(13), 3370\u20133374 (2003)","journal-title":"BMC Bioinform."},{"issue":"5","key":"32_CR79","doi-asserted-by":"crossref","first-page":"e1003592","DOI":"10.1371\/journal.pcbi.1003592","volume":"10","author":"N Zhao","year":"2014","unstructured":"Zhao, N., Han, J.G., Shyu, C., Korkin, D.: Determining effects of non-synonymous SNPs on protein-protein interactions using supervised and semi-supervised learning. PLoS Comput. Biol. 10(5), e1003592 (2014)","journal-title":"PLoS Comput. Biol."}],"container-title":["Communications in Computer and Information Science","Beyond Databases, Architectures and Structures. Advanced Technologies for Data Mining and Knowledge Discovery"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-34099-9_32","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,24]],"date-time":"2017-06-24T07:56:01Z","timestamp":1498290961000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-34099-9_32"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016]]},"ISBN":["9783319340982","9783319340999"],"references-count":79,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-34099-9_32","relation":{},"ISSN":["1865-0929","1865-0937"],"issn-type":[{"type":"print","value":"1865-0929"},{"type":"electronic","value":"1865-0937"}],"subject":[],"published":{"date-parts":[[2016]]}}}