{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T15:22:34Z","timestamp":1725895354383},"publisher-location":"Berlin, Heidelberg","reference-count":37,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642335570"},{"type":"electronic","value":"9783642335587"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012]]},"DOI":"10.1007\/978-3-642-33558-7_61","type":"book-chapter","created":{"date-parts":[[2012,10,2]],"date-time":"2012-10-02T22:32:47Z","timestamp":1349217167000},"page":"850-866","source":"Crossref","is-referenced-by-count":0,"title":["A Filtering Technique for Fragment Assembly- Based Proteins Loop Modeling with Constraints"],"prefix":"10.1007","author":[{"given":"Federico","family":"Campeotto","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandro","family":"Dal Pal\u00f9","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Agostino","family":"Dovier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ferdinando","family":"Fioretto","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Enrico","family":"Pontelli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"issue":"1","key":"61_CR1","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1007\/s10601-006-6848-8","volume":"11","author":"R. Backofen","year":"2006","unstructured":"Backofen, R., Will, S.: A Constraint-Based Approach to Fast and Exact Structure Prediction in 3-Dimensional Protein Models. Constraints\u00a011(1), 5\u201330 (2006)","journal-title":"Constraints"},{"issue":"1-2","key":"61_CR2","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/s10601-007-9036-6","volume":"13","author":"P. Barahona","year":"2008","unstructured":"Barahona, P., Krippahl, L.: Constraint programming in structural bioinformatics. Constraints\u00a013(1-2), 3\u201320 (2008)","journal-title":"Constraints"},{"key":"61_CR3","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1002\/prot.22591","volume":"77","author":"M. Ben-David","year":"2009","unstructured":"Ben-David, M., Noivirt-Brik, O., Paz, A., Prilusky, J., Sussman, J.L., Levy, Y.: Assessment of CASP8 structure predictions for template free targets. Proteins\u00a077, 50\u201365 (2009)","journal-title":"Proteins"},{"key":"61_CR4","unstructured":"Best, M., Bhattarai, K., Campeotto, F., Dal Pal\u2019u, A., Dang, H., Dovier, A., Fioretto, F., Fogolari, F., Le, T., Pontelli, E.: Introducing FIASCO: Fragment-based Interactive Assembly for protein Structure prediction with COnstraints. In: Proc. of Workshop on Constraint Based Methods for Bioinformatics (2011), http:\/\/www.dmi.unipg.it\/WCB11\/wcb11proc.pdf"},{"issue":"11","key":"61_CR5","doi-asserted-by":"publisher","first-page":"1364","DOI":"10.1002\/jcc.10245","volume":"24","author":"S. Cahill","year":"2003","unstructured":"Cahill, S., Cahill, M., Cahill, K.: On the kinematics of protein folding. Journal of Computational Chemistry\u00a024(11), 1364\u20131370 (2003)","journal-title":"Journal of Computational Chemistry"},{"key":"61_CR6","doi-asserted-by":"publisher","first-page":"963","DOI":"10.1110\/ps.0242703","volume":"12","author":"A. Canutescu","year":"2003","unstructured":"Canutescu, A., Dunbrack, R.: Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci.\u00a012, 963\u2013972 (2003)","journal-title":"Protein Sci."},{"issue":"6","key":"61_CR7","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1002\/prot.22658","volume":"78","author":"Y. Choi","year":"2010","unstructured":"Choi, Y., Deane, C.M.: FREAD revisited: Accurate loop structure prediction using a database search algorithm. Proteins\u00a078(6), 1431\u20131440 (2010)","journal-title":"Proteins"},{"key":"61_CR8","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1186\/1471-2105-5-186","volume":"5","author":"A. Pal\u00f9 Dal","year":"2004","unstructured":"Dal Pal\u00f9, A., Dovier, A., Fogolari, F.: Constraint logic programming approach to protein structure prediction. BMC Bioinformatics\u00a05, 186 (2004)","journal-title":"BMC Bioinformatics"},{"issue":"4-6","key":"61_CR9","first-page":"709","volume":"10","author":"A. Pal\u00f9 Dal","year":"2010","unstructured":"Dal Pal\u00f9, A., Dovier, A., Fogolari, F., Pontelli, E.: CLP-based protein fragment assembly. TPLP\u00a010(4-6), 709\u2013724 (2010)","journal-title":"TPLP"},{"key":"61_CR10","unstructured":"Dal Pal\u00f9, A., Dovier, A., Fogolari, F., Pontelli, E.: Exploring Protein Fragment Assembly Using CLP. In: Walsh, T. (ed.) IJCAI, pp. 2590\u20132595. IJCAI\/AAAI (2011)"},{"issue":"13","key":"61_CR11","doi-asserted-by":"publisher","first-page":"1405","DOI":"10.1002\/spe.810","volume":"37","author":"A. Pal\u00f9 Dal","year":"2007","unstructured":"Dal Pal\u00f9, A., Dovier, A., Pontelli, E.: A constraint solver for discrete lattices, its parallelization, and application to protein structure prediction. Softw., Pract. Exper.\u00a037(13), 1405\u20131449 (2007)","journal-title":"Softw., Pract. Exper."},{"issue":"1","key":"61_CR12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1504\/IJDMB.2010.030964","volume":"4","author":"A. Pal\u00f9 Dal","year":"2010","unstructured":"Dal Pal\u00f9, A., Dovier, A., Pontelli, E.: Computing approximate solutions of the protein structure determination problem using global constraints on discrete crystal lattices. IJDMB\u00a04(1), 1\u201320 (2010)","journal-title":"IJDMB"},{"key":"61_CR13","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1016\/j.ejmech.2012.01.003","volume":"49","author":"A. Pal\u00f9 Dal","year":"2012","unstructured":"Dal Pal\u00f9, A., Spyrakis, F., Cozzini, P.: A new approach for investigating protein flexibility based on Constraint Logic Programming: The first application in the case of the estrogen receptor. European Journal of Medicinal Chemistry\u00a049, 127\u2013140 (2012)","journal-title":"European Journal of Medicinal Chemistry"},{"key":"61_CR14","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1110\/ps.37601","volume":"10","author":"C. Deane","year":"2001","unstructured":"Deane, C., Blundell, T.: CODA. A combined algorithm for predicting the structurally variable regions of protein models. Protein Sci.\u00a010, 599\u2013612 (2001)","journal-title":"Protein Sci."},{"issue":"6","key":"61_CR15","doi-asserted-by":"publisher","first-page":"1620","DOI":"10.1109\/TCBB.2011.41","volume":"8","author":"I. Dot\u00fa","year":"2011","unstructured":"Dot\u00fa, I., Cebri\u00e1n, M., Van Hentenryck, P., Clote, P.: On Lattice Protein Structure Prediction Revisited. IEEE\/ACM Trans. Comput. Biology Bioinform.\u00a08(6), 1620\u20131632 (2011)","journal-title":"IEEE\/ACM Trans. Comput. Biology Bioinform."},{"key":"61_CR16","doi-asserted-by":"publisher","first-page":"855","DOI":"10.1021\/ct800051k","volume":"4","author":"A. Felts","year":"2008","unstructured":"Felts, A., Gallicchio, E., Chekmarev, D., Paris, K., Friesner, R., Levy, R.: Prediction of protein loop conformations using AGBNP implicit solvent model and torsion angle sampling. J. Chem. Theory Comput.\u00a04, 855\u2013868 (2008)","journal-title":"J. Chem. Theory Comput."},{"key":"61_CR17","doi-asserted-by":"publisher","first-page":"1753","DOI":"10.1110\/ps.9.9.1753","volume":"9","author":"A. Fiser","year":"2000","unstructured":"Fiser, A., Do, R., Sali, A.: Modeling of loops in protein structures. Protein Sci.\u00a09, 1753\u20131773 (2000)","journal-title":"Protein Sci."},{"issue":"15","key":"61_CR18","first-page":"1","volume":"7","author":"F. Fogolari","year":"2007","unstructured":"Fogolari, F., Pieri, L., Dovier, A., Bortolussi, L., Giugliarelli, G., Corazza, A., Esposito, G., Viglino, P.: Scoring predictive models using a reduced representation of proteins: model and energy definition. BMC Structural Biology\u00a07(15), 1\u201317 (2007)","journal-title":"BMC Structural Biology"},{"key":"61_CR19","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1002\/prot.20748","volume":"62","author":"Y. Fujitsuka","year":"2006","unstructured":"Fujitsuka, Y., Chikenji, G., Takada, S.: SimFold energy function for de novo protein structure prediction: consensus with Rosetta. Proteins\u00a062, 381\u2013398 (2006)","journal-title":"Proteins"},{"key":"61_CR20","first-page":"215","volume":"77","author":"R. Hartenberg","year":"1995","unstructured":"Hartenberg, R., Denavit, J.: A kinematic notation for lower pair mechanisms based on matrices. Journal of Applied Mechanics\u00a077, 215\u2013221 (1995)","journal-title":"Journal of Applied Mechanics"},{"key":"61_CR21","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1002\/prot.10613","volume":"55","author":"M. Jacobson","year":"2004","unstructured":"Jacobson, M., Pincus, D., Rapp, C., Day, T., Honig, B., Shaw, D., Friesner, R.: A hierarchical approach to all-atom protein loop prediction. Proteins\u00a055, 351\u2013367 (2004)","journal-title":"Proteins"},{"key":"61_CR22","doi-asserted-by":"crossref","unstructured":"Jamroz, M., Kolinski, A.: Modeling of loops in proteins: a multi-method approach. BMC Struct. Biol. 10(5) (2010)","DOI":"10.1186\/1472-6807-10-5"},{"key":"61_CR23","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1002\/prot.21771","volume":"69","author":"R. Jauch","year":"2007","unstructured":"Jauch, R., Yeo, H., Kolatkar, P.R., Clarke, N.D.: Assessment of CASP7 structure predictions for template free targets. Proteins\u00a069, 57\u201367 (2007)","journal-title":"Proteins"},{"key":"61_CR24","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1002\/prot.1171","volume":"45","author":"D. Jones","year":"2006","unstructured":"Jones, D.: Predicting novel protein folds by using FRAGFOLD. Proteins\u00a045, 127\u2013132 (2006)","journal-title":"Proteins"},{"issue":"6","key":"61_CR25","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1002\/prot.10540","volume":"53","author":"K. Karplus","year":"2003","unstructured":"Karplus, K., Karchin, R., Draper, J., Casper, J., Mandel-Gutfreund, Y., Diekhans, M., Source, R.H.: Combining local structure, fold-recognition, and new fold methods for protein structure prediction. Proteins\u00a053(6), 491\u2013497 (2003)","journal-title":"Proteins"},{"key":"61_CR26","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1002\/prot.23181","volume":"79","author":"L. Kinch","year":"2011","unstructured":"Kinch, L., Yong Shi, S., Cong, Q., Cheng, H., Liao, Y., Grishin, N.V.: CASP9 assessment of free modeling target predictions. Proteins\u00a079, 59\u201373 (2011)","journal-title":"Proteins"},{"key":"61_CR27","doi-asserted-by":"crossref","unstructured":"LaValle, S.: Planning Algorithms. Cambridge University Press (2006)","DOI":"10.1017\/CBO9780511546877"},{"issue":"4","key":"61_CR28","doi-asserted-by":"publisher","first-page":"704","DOI":"10.1002\/prot.20150","volume":"56","author":"J. Lee","year":"2004","unstructured":"Lee, J., Kim, S., Joo, K., Kim, I., Lee, J.: Prediction of protein tertiary structure using profesy, a novel method based on fragment assembly and conformational space annealing. Proteins\u00a056(4), 704\u2013714 (2004)","journal-title":"Proteins"},{"issue":"16","key":"61_CR29","doi-asserted-by":"publisher","first-page":"3428","DOI":"10.1002\/prot.22849","volume":"78","author":"J. Lee","year":"2010","unstructured":"Lee, J., Lee, D., Park, H., Coutsias, E., Seok, C.: Protein Loop Modeling by Using Fragment Assembly and Analytical Loop Closure. Proteins\u00a078(16), 3428\u20133436 (2010)","journal-title":"Proteins"},{"key":"61_CR30","doi-asserted-by":"crossref","unstructured":"Liu, P., Zhu, F., Rassokhin, D., Agrafiotis, D.: A self-organizing algorithm for modeling protein loops. PLOS Comput. Biol. 5(8) (2009)","DOI":"10.1371\/journal.pcbi.1000478"},{"key":"61_CR31","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1002\/(SICI)1097-0134(19990501)35:2<173::AID-PROT4>3.0.CO;2-2","volume":"35","author":"C.S. Rapp","year":"1999","unstructured":"Rapp, C.S., Friesner, R.A.: Prediction of loop geometries using a generalized born model of solvation effects. Proteins\u00a035, 173\u2013183 (1999)","journal-title":"Proteins"},{"key":"61_CR32","doi-asserted-by":"publisher","first-page":"2507","DOI":"10.1110\/ps.062416606","volume":"15","author":"M. Shen","year":"2006","unstructured":"Shen, M., Sali, A.: Statistical potential for assessment and prediction of protein structures. Protein Sci.\u00a015, 2507\u20132524 (2006)","journal-title":"Protein Sci."},{"key":"61_CR33","doi-asserted-by":"crossref","unstructured":"Shmygelska, A., Hoos, H.: An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem. BMC Bioinformatics 6 (2005)","DOI":"10.1186\/1471-2105-6-30"},{"key":"61_CR34","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1006\/jmbi.1997.0959","volume":"268","author":"K. Simons","year":"1997","unstructured":"Simons, K., Kooperberg, C., Huang, E., Baker, D.: Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions. J. Mol. Biol.\u00a0268, 209\u2013225 (1997)","journal-title":"J. Mol. Biol."},{"key":"61_CR35","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1093\/protein\/gzm083","volume":"21","author":"V. Spassov","year":"2008","unstructured":"Spassov, V., Flook, P., Yan, L.: LOOPER: a molecular mechanics-based algorithm for protein loop prediction. Protein Eng.\u00a021, 91\u2013100 (2008)","journal-title":"Protein Eng."},{"key":"61_CR36","doi-asserted-by":"publisher","first-page":"7432","DOI":"10.1073\/pnas.102179699","volume":"99","author":"Z. Xiang","year":"2002","unstructured":"Xiang, Z., Soto, C., Honig, B.: Evaluating conformal energies: the colony energy and its application to the problem of loop prediction. PNAS\u00a099, 7432\u20137437 (2002)","journal-title":"PNAS"},{"key":"61_CR37","doi-asserted-by":"publisher","first-page":"2714","DOI":"10.1110\/ps.0217002","volume":"11","author":"H. Zhou","year":"2002","unstructured":"Zhou, H., Zhou, Y.: Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci.\u00a011, 2714\u20132726 (2002)","journal-title":"Protein Sci."}],"container-title":["Lecture Notes in Computer Science","Principles and Practice of Constraint Programming"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-33558-7_61","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,29]],"date-time":"2022-01-29T17:46:19Z","timestamp":1643478379000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-33558-7_61"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012]]},"ISBN":["9783642335570","9783642335587"],"references-count":37,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-33558-7_61","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2012]]}}}