Chen, Ye; Yuan, Xiaoping; Cang, Xiaohui Population-based incremental learning for the prediction of Homo sapiens’ protein secondary structure. (English) Zbl 1416.92128 Int. J. Biomath. 12, No. 3, Article ID 1950017, 21 p. (2019). MSC: 92D20 68T05 PDF BibTeX XML Cite \textit{Y. Chen} et al., Int. J. Biomath. 12, No. 3, Article ID 1950017, 21 p. (2019; Zbl 1416.92128) Full Text: DOI
Doluca, Osman G4Catchall: A G-quadruplex prediction approach considering atypical features. (English) Zbl 1406.92453 J. Theor. Biol. 463, 92-98 (2019). MSC: 92D20 62P10 PDF BibTeX XML Cite \textit{O. Doluca}, J. Theor. Biol. 463, 92--98 (2019; Zbl 1406.92453) Full Text: DOI
Jabbari, Hosna; Wark, Ian; Montemagno, Carlo; Will, Sebastian Sparsification enables predicting kissing hairpin pseudoknot structures of long RNAs in practice. (English) Zbl 1443.92140 Schwartz, Russell (ed.) et al., 17th international workshop on algorithms in bioinformatics, WABI 2017, Boston, MA, USA, August 21–23, 2017. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 88, Article 12, 13 p. (2017). MSC: 92D20 92-08 PDF BibTeX XML Cite \textit{H. Jabbari} et al., LIPIcs -- Leibniz Int. Proc. Inform. 88, Article 12, 13 p. (2017; Zbl 1443.92140) Full Text: DOI
Riechert, Maik; Höner zu Siederdissen, Christian; Stadler, Peter F. Algebraic dynamic programming for multiple context-free grammars. (English) Zbl 1344.68112 Theor. Comput. Sci. 639, 91-109 (2016). MSC: 68Q42 90C39 92D20 PDF BibTeX XML Cite \textit{M. Riechert} et al., Theor. Comput. Sci. 639, 91--109 (2016; Zbl 1344.68112) Full Text: DOI
Frid, Yelena; Gusfield, Dan A sparsified Four-Russian algorithm for RNA folding. (English) Zbl 1367.92088 Pop, Mihai (ed.) et al., Algorithms in bioinformatics. 15th international workshop, WABI 2015, Atlanta, GA, USA, September 10–12, 2015. Proceedings. Berlin: Springer (ISBN 978-3-662-48220-9/pbk; 978-3-662-48221-6/ebook). Lecture Notes in Computer Science 9289. Lecture Notes in Bioinformatics, 271-285 (2015). MSC: 92D20 92-08 68Q17 68W25 PDF BibTeX XML Cite \textit{Y. Frid} and \textit{D. Gusfield}, Lect. Notes Comput. Sci. 9289, 271--285 (2015; Zbl 1367.92088) Full Text: DOI
Will, Sebastian; Jabbari, Hosna Sparse RNA folding revisited: space-efficient minimum free energy prediction. (English) Zbl 1367.92090 Pop, Mihai (ed.) et al., Algorithms in bioinformatics. 15th international workshop, WABI 2015, Atlanta, GA, USA, September 10–12, 2015. Proceedings. Berlin: Springer (ISBN 978-3-662-48220-9/pbk; 978-3-662-48221-6/ebook). Lecture Notes in Computer Science 9289. Lecture Notes in Bioinformatics, 257-270 (2015). MSC: 92D20 92-08 PDF BibTeX XML Cite \textit{S. Will} and \textit{H. Jabbari}, Lect. Notes Comput. Sci. 9289, 257--270 (2015; Zbl 1367.92090) Full Text: DOI
Tran, Van Du T.; Chassignet, Philippe; Steyaert, Jean-Marc On permuted super-secondary structures of transmembrane \(\beta\)-barrel proteins. (English) Zbl 1422.92108 Theor. Comput. Sci. 540-541, 133-142 (2014). MSC: 92D20 PDF BibTeX XML Cite \textit{V. D. T. Tran} et al., Theor. Comput. Sci. 540--541, 133--142 (2014; Zbl 1422.92108) Full Text: DOI Link
Weinberg, Frank; Nebel, Markus E. Applying length-dependent stochastic context-free grammars to RNA secondary structure prediction. (English) Zbl 07042106 Algorithms (Basel) 4, No. 4, 223-238 (2011). MSC: 68 03 PDF BibTeX XML Cite \textit{F. Weinberg} and \textit{M. E. Nebel}, Algorithms (Basel) 4, No. 4, 223--238 (2011; Zbl 07042106) Full Text: DOI
Liu, Tian; Jia, Cangzhi A high-accuracy protein structural class prediction algorithm using predicted secondary structural information. (English) Zbl 1410.92087 J. Theor. Biol. 267, No. 3, 272-275 (2010). MSC: 92D20 68T05 PDF BibTeX XML Cite \textit{T. Liu} and \textit{C. Jia}, J. Theor. Biol. 267, No. 3, 272--275 (2010; Zbl 1410.92087) Full Text: DOI
Huang, Chen; Zhang, Ruijie; Chen, Zhiqiang; Jiang, Yongshuai; Shang, Zhenwei; Sun, Peng; Zhang, Xuehong; Li, Xia Predict potential drug targets from the ion channel proteins based on SVM. (English) Zbl 1403.92205 J. Theor. Biol. 262, No. 4, 750-756 (2010). MSC: 92D20 92C40 68T05 PDF BibTeX XML Cite \textit{C. Huang} et al., J. Theor. Biol. 262, No. 4, 750--756 (2010; Zbl 1403.92205) Full Text: DOI
Yang, Bingru; Zhou, Zhun; Hou, Wei An association multi-classification algorithm based on the secondary structure sequence of proteins. (Chinese. English summary) Zbl 1240.68225 Syst. Eng. Electron. 32, No. 6, 1318-1324 (2010). MSC: 68T05 68T10 92D20 PDF BibTeX XML Cite \textit{B. Yang} et al., Syst. Eng. Electron. 32, No. 6, 1318--1324 (2010; Zbl 1240.68225) Full Text: DOI
Xia, Fei; Dou, Yong; Zhou, Dan; Li, Xin Fine-grained parallel RNA secondary structure prediction using SCFGs on FPGA. (English) Zbl 1204.68269 Parallel Comput. 36, No. 9, 516-530 (2010). MSC: 68W10 68M99 PDF BibTeX XML Cite \textit{F. Xia} et al., Parallel Comput. 36, No. 9, 516--530 (2010; Zbl 1204.68269) Full Text: DOI
Malekpour, Seyed Amir; Naghizadeh, Sima; Pezeshk, Hamid; Sadeghi, Mehdi; Eslahchi, Changiz A segmental semi Markov model for protein secondary structure prediction. (English) Zbl 1175.92015 Math. Biosci. 221, No. 2, 130-135 (2009). MSC: 92C40 62P10 60J99 60J20 PDF BibTeX XML Cite \textit{S. A. Malekpour} et al., Math. Biosci. 221, No. 2, 130--135 (2009; Zbl 1175.92015) Full Text: DOI
Condon, Anne; Jabbari, Hosna Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges. (English) Zbl 1162.68806 Theor. Comput. Sci. 410, No. 4-5, 294-301 (2009). MSC: 68W05 PDF BibTeX XML Cite \textit{A. Condon} and \textit{H. Jabbari}, Theor. Comput. Sci. 410, No. 4--5, 294--301 (2009; Zbl 1162.68806) Full Text: DOI
Raghuraj, Rao; Lakshminarayanan, S. Variable predictive model based classification algorithm for effective separation of protein structural classes. (English) Zbl 1158.62081 Comput. Biol. Chem. 32, No. 4, 302-306 (2008). MSC: 62P10 92C40 62H30 PDF BibTeX XML Cite \textit{R. Raghuraj} and \textit{S. Lakshminarayanan}, Comput. Biol. Chem. 32, No. 4, 302--306 (2008; Zbl 1158.62081) Full Text: DOI
Zhao, Jizhen; Malmberg, Russell L.; Cai, Liming Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition. (English) Zbl 1143.92016 J. Math. Biol. 56, No. 1-2, 145-159 (2008). MSC: 92C40 05C90 90C90 92-08 PDF BibTeX XML Cite \textit{J. Zhao} et al., J. Math. Biol. 56, No. 1--2, 145--159 (2008; Zbl 1143.92016) Full Text: DOI
Machado-Lima, Ariane; del Portillo, Hernando A.; Durham, Alan Mitchell Computational methods in noncoding RNA research. (English) Zbl 1143.92010 J. Math. Biol. 56, No. 1-2, 15-49 (2008). MSC: 92C40 92-08 PDF BibTeX XML Cite \textit{A. Machado-Lima} et al., J. Math. Biol. 56, No. 1--2, 15--49 (2008; Zbl 1143.92010) Full Text: DOI
Crochemore, Maxime; Hermelin, Danny; Landau, Gad M.; Rawitz, Dror; Vialette, Stéphane Approximating the 2-interval pattern problem. (English) Zbl 1142.68070 Theor. Comput. Sci. 395, No. 2-3, 283-297 (2008). MSC: 68W20 PDF BibTeX XML Cite \textit{M. Crochemore} et al., Theor. Comput. Sci. 395, No. 2--3, 283--297 (2008; Zbl 1142.68070) Full Text: DOI
Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M. PreSSAPro: a software for the prediction of secondary structure by amino acid properties. (English) Zbl 1142.92320 Comput. Biol. Chem. 31, No. 5-6, 389-392 (2007). MSC: 92C40 92-04 PDF BibTeX XML Cite \textit{S. Costantini} et al., Comput. Biol. Chem. 31, No. 5--6, 389--392 (2007; Zbl 1142.92320) Full Text: DOI
Yoon, Sukjoon; Welsh, William J.; Jung, Heeyoung; Yoo, Young Do CSSP2: an improved method for predicting contact-dependent secondary structure propensity. (English) Zbl 1141.92320 Comput. Biol. Chem. 31, No. 5-6, 373-377 (2007). MSC: 92C40 68T05 92-08 PDF BibTeX XML Cite \textit{S. Yoon} et al., Comput. Biol. Chem. 31, No. 5--6, 373--377 (2007; Zbl 1141.92320) Full Text: DOI
Jiang, Minghui A 2-approximation for the preceding-and-crossing structured 2-interval pattern problem. (English) Zbl 1123.68146 J. Comb. Optim. 13, No. 3, 217-221 (2007). MSC: 68W25 92D20 PDF BibTeX XML Cite \textit{M. Jiang}, J. Comb. Optim. 13, No. 3, 217--221 (2007; Zbl 1123.68146) Full Text: DOI
Gubbi, Jayavardhana; Lai, Daniel T. H.; Palaniswami, Marimuthu; Parker, Michael Protein secondary structure prediction using support vector machines and a new feature representation. (English) Zbl 1143.68541 Int. J. Comput. Intell. Appl. 6, No. 4, 551-567 (2006). MSC: 68T05 92-08 92C40 PDF BibTeX XML Cite \textit{J. Gubbi} et al., Int. J. Comput. Intell. Appl. 6, No. 4, 551--567 (2006; Zbl 1143.68541) Full Text: DOI
Kurgan, Lukasz A.; Homaeian, Leila Prediction of structural classes for protein sequences and domains–impact of prediction algorithms, sequence representation and homology, and test procedures on accuracy. (English) Zbl 1103.68767 Pattern Recognition 39, No. 12, 2323-2343 (2006). MSC: 68T10 68T05 PDF BibTeX XML Cite \textit{L. A. Kurgan} and \textit{L. Homaeian}, Pattern Recognition 39, No. 12, 2323--2343 (2006; Zbl 1103.68767) Full Text: DOI
Taneda, Akito Cofolga: a genetic algorithm for finding the common folding of two RNAs. (English) Zbl 1096.92019 Comput. Biol. Chem. 29, No. 2, 111-119 (2005). MSC: 92C40 90C59 PDF BibTeX XML Cite \textit{A. Taneda}, Comput. Biol. Chem. 29, No. 2, 111--119 (2005; Zbl 1096.92019) Full Text: DOI
Simossis, V. A.; Heringa, J. The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods. (English) Zbl 1089.92017 Comput. Biol. Chem. 28, No. 5-6, 351-366 (2004). MSC: 92C40 90C39 90C90 PDF BibTeX XML Cite \textit{V. A. Simossis} and \textit{J. Heringa}, Comput. Biol. Chem. 28, No. 5--6, 351--366 (2004; Zbl 1089.92017) Full Text: DOI
Klepeis, J. L.; Floudas, C. A. Ab initio tertiary structure prediction of proteins. (English) Zbl 1045.92018 J. Glob. Optim. 25, No. 1, 113-140 (2003). MSC: 92C40 90C26 PDF BibTeX XML Cite \textit{J. L. Klepeis} and \textit{C. A. Floudas}, J. Glob. Optim. 25, No. 1, 113--140 (2003; Zbl 1045.92018) Full Text: DOI
Siermala, Markku; Juhola, Martti Behaviour of protein secondary structure types in the sequence space of a certain length. (English) Zbl 1085.68666 Intell. Data Anal. 6, No. 5, 411-427 (2002). MSC: 68T10 68T05 PDF BibTeX XML Cite \textit{M. Siermala} and \textit{M. Juhola}, Intell. Data Anal. 6, No. 5, 411--427 (2002; Zbl 1085.68666) Full Text: Link
Wang, Longhui; Shi, Feng Protein secondary structure prediction based on PM genetic Meira network. (Chinese. English summary) Zbl 1028.92012 J. Math., Wuhan Univ. 22, No. 2, 179-184 (2002). MSC: 92C40 PDF BibTeX XML Cite \textit{L. Wang} and \textit{F. Shi}, J. Math., Wuhan Univ. 22, No. 2, 179--184 (2002; Zbl 1028.92012)
Elloumi, M. Algorithm for the prediction of RNA secondary structures. (English. Russian summary) Zbl 0986.92012 Vychisl. Tekhnol. 6, No. 5, 3-23 (2001). Reviewer: V.Grebenev (Novosibirsk) MSC: 92C40 90C39 90C30 PDF BibTeX XML Cite \textit{M. Elloumi}, Vychisl. Tekhnol. 6, No. 5, 3--23 (2001; Zbl 0986.92012)
Akutsu, Tatsuya Approximation and exact algorithms for RNA secondary structure prediction and recognition of stochastic context-free languages. (English) Zbl 0972.92012 J. Comb. Optim. 3, No. 2-3, 321-336 (1999). MSC: 92C40 90C90 92-08 65Y20 PDF BibTeX XML Cite \textit{T. Akutsu}, J. Comb. Optim. 3, No. 2--3, 321--336 (1999; Zbl 0972.92012) Full Text: DOI
Uemura, Yasuo; Hasegawa, Aki; Kobayashi, Satoshi; Yokomori, Takashi Tree adjoining grammars for RNA structure prediction. (English) Zbl 0912.68121 Theor. Comput. Sci. 210, No. 2, 277-303 (1999). MSC: 68Q42 68N20 PDF BibTeX XML Cite \textit{Y. Uemura} et al., Theor. Comput. Sci. 210, No. 2, 277--303 (1999; Zbl 0912.68121) Full Text: DOI
Tchoumatchenko, I.; Ganascia, J.-G. Mixture modeling to incorporate meaningful constraints into learning. (English) Zbl 0886.62013 Hanson, Kenneth M. (ed.) et al., Maximum entropy and Bayesian methods. Proceedings of the 15th international workshop, Santa Fe, NM, USA, July 31–August 4, 1995. Dordrecht: Kluwer Academic Publishers. Fundam. Theor. Phys. 79, 85-92 (1996). MSC: 62B10 62F15 PDF BibTeX XML Cite \textit{I. Tchoumatchenko} and \textit{J. G. Ganascia}, Fundam. Theor. Phys. 79, 85--92 (1996; Zbl 0886.62013)
Hu, Xiche; Xu, Dong; Hamer, Kenneth; Schulten, Klaus; Koepke, Juergen; Michel, Hartmut Knowledge based structure prediction of the light-harvesting complex II of Rhodospirillum molischianum. (English) Zbl 0836.92010 Pardalos, P. M. (ed.) et al., Global minimization of nonconvex energy functions: molecular conformation and protein folding. Papers selected from a DIMACS workshop held on March 20-21, 1995. Providence, RI: American Mathematical Society. DIMACS, Ser. Discrete Math. Theor. Comput. Sci. 23, 97-122 (1996). MSC: 92C40 92C05 92-08 PDF BibTeX XML Cite \textit{X. Hu} et al., DIMACS, Ser. Discrete Math. Theor. Comput. Sci. 23, 97--122 (1996; Zbl 0836.92010)
Eppstein, David; Galil, Zvi; Giancarlo, Raffaele; Italiano, Giuseppe F. Sparse dynamic programming I: Linear cost functions. (English) Zbl 0807.90120 J. Assoc. Comput. Mach. 39, No. 3, 519-545 (1992). MSC: 90C39 92D20 90C90 90C60 PDF BibTeX XML Cite \textit{D. Eppstein} et al., J. Assoc. Comput. Mach. 39, No. 3, 519--545 (1992; Zbl 0807.90120) Full Text: DOI
Fu, Yun-Xin; Curnow, R. N. Maximum likelihood estimation of multiple change points. (English) Zbl 0724.62025 Biometrika 77, No. 3, 563-573 (1990). Reviewer: S.Penev (Sofia) MSC: 62F10 62F99 62P10 92C40 PDF BibTeX XML Cite \textit{Y.-X. Fu} and \textit{R. N. Curnow}, Biometrika 77, No. 3, 563--573 (1990; Zbl 0724.62025) Full Text: DOI
Waterman, Michael S.; Smith, Temple F. Rapid dynamic programming algorithms for RNA secondary structure. (English) Zbl 0607.92012 Adv. Appl. Math. 7, 455-464 (1986). MSC: 92Cxx 68Q25 90C39 PDF BibTeX XML Cite \textit{M. S. Waterman} and \textit{T. F. Smith}, Adv. Appl. Math. 7, 455--464 (1986; Zbl 0607.92012) Full Text: DOI
Kanehisa, Minoru; DeLisi, Charles The prediction of a protein and nucleic acid structure: Problems and prospects. (English) Zbl 0568.92011 Acta Appl. Math. 4, 115-137 (1985). MSC: 92Cxx 92-08 90C90 82B99 90C39 PDF BibTeX XML Cite \textit{M. Kanehisa} and \textit{C. DeLisi}, Acta Appl. Math. 4, 115--137 (1985; Zbl 0568.92011) Full Text: DOI
Zuker, Michael; Sankoff, David RNA secondary structures and their prediction. (English) Zbl 0548.92007 Bull. Math. Biol. 46, 591-621 (1984). MSC: 92Cxx 90C90 90C39 92-04 PDF BibTeX XML Cite \textit{M. Zuker} and \textit{D. Sankoff}, Bull. Math. Biol. 46, 591--621 (1984; Zbl 0548.92007) Full Text: DOI