{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,2,2]],"date-time":"2024-02-02T00:17:02Z","timestamp":1706833022137},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,9,5]],"date-time":"2016-09-05T00:00:00Z","timestamp":1473033600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,9,5]],"date-time":"2016-09-05T00:00:00Z","timestamp":1473033600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>According to structure-dependent function of proteins, two main challenging problems called Protein Structure Prediction (PSP) and Inverse Protein Folding (IPF) are investigated. In spite of IPF essential applications, it has not been investigated as much as PSP problem.<\/jats:p>\n                <jats:p>In fact, the ultimate goal of IPF problem or protein design is to create proteins with enhanced properties or even novel functions. One of the major computational challenges in protein design is its large sequence space, namely searching through all plausible sequences is impossible. Inasmuch as, protein secondary structure represents an appropriate primary scaffold of the protein conformation, undoubtedly studying the Protein Secondary Structure Inverse Folding (PSSIF) problem is a quantum leap forward in protein design, as it can reduce the search space.<\/jats:p>\n                <jats:p>In this paper, a novel genetic algorithm which uses native secondary sub-structures is proposed to solve PSSIF problem. In essence, evolutionary information can lead the algorithm to design appropriate amino acid sequences respective to the target secondary structures. Furthermore, they can be folded to tertiary structures almost similar to their reference 3D structures.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The proposed algorithm called <jats:italic>GA<\/jats:italic>PSSIF benefits from evolutionary information obtained by solved proteins in the PDB. Therefore, we construct a repository of protein secondary sub-structures to accelerate convergence of the algorithm.<\/jats:p>\n                <jats:p>The secondary structure of designed sequences by GAPSSIF is comparable with those obtained by Evolver and EvoDesign. Although we do not explicitly consider tertiary structure features through the algorithm, the structural similarity of native and designed sequences declares acceptable values.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Using the evolutionary information of native structures can significantly improve the quality of designed sequences. In fact, the combination of this information and effective features such as solvent accessibility and torsion angles leads IPF problem to an efficient solution. GAPSSIF can be downloaded at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/bioinformatics.aut.ac.ir\/GAPSSIF\/\">http:\/\/bioinformatics.aut.ac.ir\/GAPSSIF\/<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-016-1199-y","type":"journal-article","created":{"date-parts":[[2016,9,5]],"date-time":"2016-09-05T12:57:08Z","timestamp":1473080228000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Evaluating the accuracy of protein design using native secondary sub-structures"],"prefix":"10.1186","volume":"17","author":[{"given":"Marziyeh","family":"Movahedi","sequence":"first","affiliation":[]},{"given":"Fatemeh","family":"Zare-Mirakabad","sequence":"additional","affiliation":[]},{"given":"Seyed Shahriar","family":"Arab","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,9,5]]},"reference":[{"issue":"7","key":"1199_CR1","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1016\/0968-0004(89)90070-4","volume":"14","author":"J Richardson","year":"1989","unstructured":"Richardson J, Richardson D. The de novo design of protein structures. Trends Biochem Sci. 1989;14(7):304\u20139.","journal-title":"Trends Biochem Sci"},{"issue":"9","key":"1199_CR2","doi-asserted-by":"publisher","first-page":"4163","DOI":"10.1073\/pnas.89.9.4163","volume":"89","author":"K Yue","year":"1992","unstructured":"Yue K, Dill K. Inverse Protein Folding Problem: designing polymer sequences. Proc Natl Acad Sci U S A. 1992;89(9):4163\u20137.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"W1","key":"1199_CR3","doi-asserted-by":"publisher","first-page":"W273","DOI":"10.1093\/nar\/gkt384","volume":"41","author":"P Mitra","year":"2013","unstructured":"Mitra P, Shultis D, Zhang Y. EvoDesign: de novo protein design based on structural and evolutionary profiles. Nucl Acids Res. 2013;41(W1):W273\u201380.","journal-title":"Nucl Acids Res"},{"issue":"10","key":"1199_CR4","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1093\/protein\/15.10.779","volume":"15","author":"N Pierce","year":"2002","unstructured":"Pierce N, Winfree E. Protein Design in NP-hard. Protein Eng. 2002;15(10):779\u201382.","journal-title":"Protein Eng"},{"issue":"4868","key":"1199_CR5","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1126\/science.3043666","volume":"241","author":"L Regan","year":"1988","unstructured":"Regan L, Degrado W. Characterization of a helical protein designed from first principles. Science. 1988;241(4868):976\u20138.","journal-title":"Science"},{"issue":"04","key":"1199_CR6","first-page":"244","volume":"3109","author":"P Berman","year":"2004","unstructured":"Berman P, DasGupta B, Mubayi D, Sloan R, Turan G, Zhang Y. The protein sequence design problem in canonical model on 2D and 3D lattices. Proc CPM. 2004;3109(04):244\u201353.","journal-title":"Proc CPM"},{"issue":"3","key":"1199_CR7","doi-asserted-by":"publisher","first-page":"R45","DOI":"10.1016\/S1359-0278(98)00021-2","volume":"3","author":"E Shakhnovich","year":"1998","unstructured":"Shakhnovich E. Protein design: a perspective from simple tractable models. Fold Des. 1998;3(3):R45\u201358.","journal-title":"Fold Des"},{"issue":"4","key":"1199_CR8","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1002\/pro.5560030405","volume":"3","author":"D Jones","year":"1994","unstructured":"Jones D. De novo protein design using pairwise potentials and a genetic algorithm. Protein Sci. 1994;3(4):567\u201374.","journal-title":"Protein Sci"},{"issue":"3","key":"1199_CR9","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1006\/jmbi.2000.3984","volume":"301","author":"L Wernisch","year":"2000","unstructured":"Wernisch L, Hery S, Wodak S. Automatic protein design with all-atom force fields by exact and heuristic. J Mol Biol. 2000;301(3):713\u201336.","journal-title":"J Mol Biol"},{"issue":"4","key":"1199_CR10","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1016\/S0959-440X(99)80072-4","volume":"9","author":"D Gordon","year":"1999","unstructured":"Gordon D, Marshall S, Mayot S. Energy functions for protein design. Curr Opin Struct Biol. 1999;9(4):509\u201313.","journal-title":"Curr Opin Struct Biol"},{"issue":"suppl 2","key":"1199_CR11","doi-asserted-by":"publisher","first-page":"W382","DOI":"10.1093\/nar\/gki387","volume":"33","author":"J Schymkowitz","year":"2005","unstructured":"Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L. The FoldX web server: an online force field. Nucl Acids Res. 2005;33 suppl 2:W382\u20138.","journal-title":"Nucl Acids Res"},{"issue":"4","key":"1199_CR12","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1016\/S0959-440X(02)00344-5","volume":"12","author":"R Dunbrack","year":"2002","unstructured":"Dunbrack R. Rotamer Libraries in the 21st century. Curr Opin Struct Biol. 2002;12(4):431\u201340.","journal-title":"Curr Opin Struct Biol"},{"issue":"suppl 2","key":"1199_CR13","doi-asserted-by":"publisher","first-page":"W235","DOI":"10.1093\/nar\/gkl163","volume":"34","author":"Y Liu","year":"2006","unstructured":"Liu Y, Kuhlman B. RosettaDesign server for protein design. Nucl Acids Res. 2006;34 suppl 2:W235\u20138.","journal-title":"Nucl Acids Res"},{"key":"1199_CR14","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1016\/B978-0-12-394292-0.00005-9","volume":"523","author":"P Gainza","year":"2013","unstructured":"Gainza P, Roberts K, Georhiev I, Lilien R, Keedy D, Chen C. OSPREY: protein design with ensembles, flexibility, and provable algorithms. Methods Enzymol. 2013;523:87\u2013107.","journal-title":"Methods Enzymol"},{"issue":"10","key":"1199_CR15","doi-asserted-by":"publisher","first-page":"e1003298","DOI":"10.1371\/journal.pcbi.1003298","volume":"9","author":"P Mitra","year":"2013","unstructured":"Mitra P, Shultis D, Brender J, Czajka J, Marsh D, Gray F, Zhang Y. An evolution-based approach to de novo protein designd and case study on Mycobacterium tuberculosis. PLoS Comput Biol. 2013;9(10):e1003298.","journal-title":"PLoS Comput Biol"},{"key":"1199_CR16","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/j.jtbi.2013.03.018","volume":"328","author":"M Brylinski","year":"2013","unstructured":"Brylinski M. The utility of artificially evolved sequences in protein threading and fold recognition. J Theor Biol. 2013;328:77\u201388.","journal-title":"J Theor Biol"},{"issue":"1","key":"1199_CR17","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1186\/1756-0500-6-303","volume":"6","author":"M Brylinski","year":"2013","unstructured":"Brylinski M. eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures. BMC Res Notes. 2013;6(1):303.","journal-title":"BMC Res Notes"},{"issue":"2","key":"1199_CR18","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1007\/BF00175354","volume":"4","author":"D Whitley","year":"1994","unstructured":"Whitley D. A genetic algorithm tutorial. Stat Comput. 1994;4(2):65\u201385.","journal-title":"Stat Comput"},{"issue":"12","key":"1199_CR19","doi-asserted-by":"publisher","first-page":"2577","DOI":"10.1002\/bip.360221211","volume":"22","author":"W Kabsch","year":"1983","unstructured":"Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983;22(12):2577\u2013637.","journal-title":"Biopolymers"},{"key":"1199_CR20","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1146\/annurev.bi.47.070178.001343","volume":"47.1","author":"PY Chou","year":"1978","unstructured":"Chou PY, Fasman GD. Empirical predictions of protein conformation. Annu Rev Biochem. 1978;47.1:251\u201376.","journal-title":"Annu Rev Biochem"},{"issue":"1","key":"1199_CR21","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1002\/prot.340190108","volume":"19","author":"B Rost","year":"1994","unstructured":"Rost B, Sander C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins Struct Funct Bioinf. 1994;19(1):55\u201372.","journal-title":"Proteins Struct Funct Bioinf"},{"issue":"Suppl 1","key":"1199_CR22","first-page":"D419","volume":"36","author":"A Andreeva","year":"2008","unstructured":"Andreeva A, Howorth D, Chandonia J, Brenner S, Hubbard T, Chothia C. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 2008;36 Suppl 1:D419\u201325.","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"1199_CR23","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1002\/(SICI)1097-0134(19990201)34:2<220::AID-PROT7>3.0.CO;2-K","volume":"34","author":"A Zemla","year":"1999","unstructured":"Zemla A, Venclovas \u010c, Fidelis K, Rost B. A modified definition of Sov, a segment\u2010based measure for protein secondary structure prediction assessment. Proteins Struct Funct Bionf. 1999;34(2):220\u20133.","journal-title":"Proteins Struct Funct Bionf"},{"issue":"1","key":"1199_CR24","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1038\/nmeth.3213","volume":"12","author":"J Yang","year":"2015","unstructured":"Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER Suite: protein structure and function prediction. Nat Methods. 2015;12(1):7\u20138.","journal-title":"Nat Methods"},{"issue":"4","key":"1199_CR25","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1093\/bioinformatics\/16.4.404","volume":"16","author":"L McGuffin","year":"2000","unstructured":"McGuffin L, Bryson K, Jones D. The PSIPRED protein structure prediction server. Bioinformatics. 2000;16(4):404\u20135.","journal-title":"Bioinformatics"},{"key":"1199_CR26","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1073\/pnas.0407152101","volume":"102","author":"Y Zhang","year":"2005","unstructured":"Zhang Y, Skolnick J. The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci. 2005;102:1029\u201334.","journal-title":"Proc Natl Acad Sci"},{"key":"1199_CR27","doi-asserted-by":"publisher","first-page":"2605","DOI":"10.1073\/pnas.0509379103","volume":"103","author":"Y Zhang","year":"2006","unstructured":"Zhang Y, Hubner I, Arakaki A, Shakhnovich E, Skolnick J. On the origin and completeness of highly likely single. Proc Natl Acad Sci U S A. 2006;103:2605\u201310.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1199_CR28","doi-asserted-by":"publisher","first-page":"6654","DOI":"10.1021\/jp211052j","volume":"116","author":"J Skolnick","year":"2012","unstructured":"Skolnick J, Zhou H, Brylinski M. Further evidence for the likely completeness of the library of solved single domain protein structures. J Phys Chem B. 2012;116:6654\u201364.","journal-title":"J Phys Chem B"},{"key":"1199_CR29","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1186\/1471-2105-9-40","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics. 2008;9:40.","journal-title":"BMC Bioinformatics"},{"issue":"7","key":"1199_CR30","doi-asserted-by":"publisher","first-page":"2302","DOI":"10.1093\/nar\/gki524","volume":"33","author":"Y Zhang","year":"2005","unstructured":"Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 2005;33(7):2302\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"1199_CR31","doi-asserted-by":"publisher","first-page":"702","DOI":"10.1002\/prot.20264","volume":"57","author":"Y Zhang","year":"2004","unstructured":"Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins Struct Funct Bioinf. 2004;57(4):702\u201310.","journal-title":"Proteins Struct Funct Bioinf"},{"issue":"34","key":"1199_CR32","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1107\/S0567739478001680","volume":"A","author":"W Kabsch","year":"1978","unstructured":"Kabsch W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr. 1978;A(34):827\u20138.","journal-title":"Acta Crystallogr"},{"issue":"3","key":"1199_CR33","first-page":"301","volume":"64","author":"H Schmidt","year":"2000","unstructured":"Schmidt H. A proposed measure for psi-induced bunching of randomly spaced events. J Parapsychol. 2000;64(3):301.","journal-title":"J Parapsychol"},{"key":"1199_CR34","volume-title":"A guide to chi-squared testing","author":"PE Greenwood","year":"1996","unstructured":"Greenwood PE, Nikulin MS. A guide to chi-squared testing, vol. 280. Hoboken: Wiley; 1996."},{"key":"1199_CR35","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1007\/978-1-59745-535-0_4","volume-title":"Plant Bioinformatics: Methods and Protocols","author":"E Boutet","year":"2007","unstructured":"Boutet E, et al. \u201cUniprotkb\/swiss-prot.\u201d. In: Plant Bioinformatics: Methods and Protocols. 2007. p. 89\u2013112."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1199-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-016-1199-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1199-y","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1199-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T18:23:10Z","timestamp":1706811790000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1199-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,9,5]]},"references-count":35,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12]]}},"alternative-id":["1199"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1199-y","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,9,5]]},"assertion":[{"value":"23 March 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 August 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 September 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"353"}}