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Found 482 Documents (Results 1–100)

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Peng, Chunxiang; Zhou, Xiaogen; Zhang, Guijun
Multi-subpopulation algorithm with ensemble mutation strategies for protein structure prediction. (English) Zbl 07239986
Pan, Linqiang (ed.) et al., Bio-inspired computing: theories and applications. 14th international conference, BIC-TA 2019, Zhengzhou, China, November 22–25, 2019. Revised selected papers. Part I. Singapore: Springer (ISBN 978-981-15-3424-9/pbk; 978-981-15-3425-6/ebook). Communications in Computer and Information Science 1159, 255-268 (2020).
MSC:  68Q07
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\textit{C. Peng} et al., Commun. Comput. Inf. Sci. 1159, 255--268 (2020; Zbl 07239986)
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Goundaroulis, Dimos; Dorier, Julien; Stasiak, Andrzej
Knotoids and protein structure. (English) Zbl 1447.92302
Flapan, Erica (ed.) et al., Topology and geometry of biopolymers. AMS special session on topology of biopolymers, Northeastern University, Boston, MA, USA, April 21–22, 2018. Providence, RI: American Mathematical Society (AMS). Contemp. Math. 746, 185-199 (2020).
MSC:  92D20 57K10 57Z10 92-02
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\textit{D. Goundaroulis} et al., Contemp. Math. 746, 185--199 (2020; Zbl 1447.92302)
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Nunes, Ana; Faísca, Patrícia F. N.
Knotted proteins: Tie etiquette in structural biology. (English) Zbl 1451.57005
Flapan, Erica (ed.) et al., Topology and geometry of biopolymers. AMS special session on topology of biopolymers, Northeastern University, Boston, MA, USA, April 21–22, 2018. Providence, RI: American Mathematical Society (AMS). Contemp. Math. 746, 155-184 (2020).
Reviewer: Pengyu Liu (Burnaby)
MSC:  57K10 92-00
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\textit{A. Nunes} and \textit{P. F. N. Faísca}, Contemp. Math. 746, 155--184 (2020; Zbl 1451.57005)
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Flapan, Erica (ed.); Wong, Helen (ed.)
Topology and geometry of biopolymers. AMS special session on topology of biopolymers, Northeastern University, Boston, MA, USA, April 21–22, 2018. (English) Zbl 1435.57001
Contemporary Mathematics 746. Providence, RI: American Mathematical Society (AMS) (ISBN 978-1-4704-4840-0/pbk; 978-1-4704-5456-2/ebook). ix, 234 p. (2020).
MSC:  57-06 82-06 92-06 57Kxx 05C10 92C05 92C40 92D20 92E10 82D60 82B41 65C05 00B25
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\textit{E. Flapan} (ed.) and \textit{H. Wong} (ed.), Topology and geometry of biopolymers. AMS special session on topology of biopolymers, Northeastern University, Boston, MA, USA, April 21--22, 2018. Providence, RI: American Mathematical Society (AMS) (2020; Zbl 1435.57001)
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Davies, Robin; Ghosh-Dastidar, Urmi; Knisley, Jeff; Samyono, Widodo
Toward revealing protein function: identifying biologically relevant clusters with graph spectral methods. (English) Zbl 1409.92181
Robeva, Raina (ed.) et al., Algebraic and combinatorial computational biology. Amsterdam: Elsevier/Academic Press. Math. Sci. Eng., 375-418 (2019).
MSC:  92D20 05C90
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\textit{R. Davies} et al., in: Algebraic and combinatorial computational biology. Amsterdam: Elsevier/Academic Press. 375--418 (2019; Zbl 1409.92181)
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Liberti, Leo; Lavor, Carlile
Open research areas in distance geometry. (English) Zbl 1420.51011
Pardalos, Panos M. (ed.) et al., Open problems in optimization and data analysis. Based on the summer school on challenges and open problems in optimization and data science, Deucalion Summer Institute for Advanced Studies in Optimization, Mathematics, and Data Science, Greece, August 2016. Cham: Springer. Springer Optim. Appl. 141, 183-223 (2018).
MSC:  51K05
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\textit{L. Liberti} and \textit{C. Lavor}, Springer Optim. Appl. 141, 183--223 (2018; Zbl 1420.51011)
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Mrozek, Dariusz
Scalable big data analytics for protein bioinformatics. Efficient computational solutions for protein structures. (English) Zbl 1411.92002
Computational Biology 28. Cham: Springer (ISBN 978-3-319-98838-2/hbk; 978-3-319-98839-9/ebook). xxvi, 315 p. (2018).
Reviewer: Jasbir Kaur (Chennai)
MSC:  92-02 92D20 62P10 68M11
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\textit{D. Mrozek}, Scalable big data analytics for protein bioinformatics. Efficient computational solutions for protein structures. Cham: Springer (2018; Zbl 1411.92002)
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Jana, Nanda Dulal; Das, Swagatam; Sil, Jaya
A metaheuristic approach to protein structure prediction. Algorithms and insights from fitness landscape analysis. (English) Zbl 1387.92003
Emergence, Complexity and Computation 31. Cham: Springer (ISBN 978-3-319-74774-3/hbk; 978-3-319-74775-0/ebook). xxix, 220 p. (2018).
MSC:  92-02 92D20
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\textit{N. D. Jana} et al., A metaheuristic approach to protein structure prediction. Algorithms and insights from fitness landscape analysis. Cham: Springer (2018; Zbl 1387.92003)
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Archilla, Juan F. R. (ed.); Palmero, Faustino (ed.); Lemos, M. Carmen (ed.); Sánchez-Rey, Bernardo (ed.); Casado-Pascual, Jesús (ed.)
Nonlinear systems. Vol. 2. Nonlinear phenomena in biology, optics and condensed matter. (English) Zbl 1382.92005
Understanding Complex Systems; Springer: Complexity. Cham: Springer (ISBN 978-3-319-72217-7/hbk; 978-3-319-72218-4/ebook). xix, 340 p. (2018).
MSC:  92-06 78-06 82-06 81-06 92D20 92E10 00B15
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\textit{J. F. R. Archilla} (ed.) et al., Nonlinear systems. Vol. 2. Nonlinear phenomena in biology, optics and condensed matter. Cham: Springer (2018; Zbl 1382.92005)
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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
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\textit{H. Jabbari} et al., LIPIcs -- Leibniz Int. Proc. Inform. 88, Article 12, 13 p. (2017; Zbl 1443.92140)
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Bayegan, Amir H.; Clote, Peter
An IP algorithm for RNA folding trajectories. (English) Zbl 1443.92135
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 6, 16 p. (2017).
MSC:  92D20 90C10 92-04
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\textit{A. H. Bayegan} and \textit{P. Clote}, LIPIcs -- Leibniz Int. Proc. Inform. 88, Article 6, 16 p. (2017; Zbl 1443.92135)
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Wegner, Michael; Taubert, Oskar; Schug, Alexander; Meyerhenke, Henning
Maxent-stress optimization of 3D biomolecular models. (English) Zbl 1442.68253
Pruhs, Kirk (ed.) et al., 25th European symposium on algorithms, ESA 2017, Vienna, Austria, September 4–6, 2017. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 87, Article 70, 15 p. (2017).
MSC:  68U05 68R10 92C40 92E10
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\textit{M. Wegner} et al., LIPIcs -- Leibniz Int. Proc. Inform. 87, Article 70, 15 p. (2017; Zbl 1442.68253)
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Lavor, Carlile; Maculan, Nelson; Souza, Michael; Alves, Rafael
Algebra and geometry in the calculation of molecular structure. Paper from the 31st Brazilian mathematics colloquium – 31\(^{\text o}\) Colóquio Brasileiro de Matemática, IMPA, Rio de Janeiro, Brazil, July 30 – August 5, 2017. (Álgebra e geometria no cálculo de estrutura molecular.) (Portuguese) Zbl 1431.92002
Publicações Matemáticas do IMPA. Rio de Janeiro: Instituto Nacional de Matemática Pura e Aplicada (IMPA) (ISBN 978-85-244-0432-0 /pbk). v, 110 p., open access (2017).
Reviewer: Stefanie Sonner (Nijmegen)
MSC:  92-01 92D20 92E10 51K05 51N35 51-01
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\textit{C. Lavor} et al., Álgebra e geometria no cálculo de estrutura molecular (Portuguese). Rio de Janeiro: Instituto Nacional de Matemática Pura e Aplicada (IMPA) (2017; Zbl 1431.92002)
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Li, Zhicheng; Lin, Shirong; Li, Yang; Lei, Qiang; Zhao, Qing
Protein structure estimation from incomplete NMR data. (English) Zbl 1395.92104
Mondaini, Rubem P. (ed.), Mathematical biology and biological physics. Selected papers based on the presentations at the 16th international symposium on mathematical and computational biology, BIOMAT 2016, Nankai University, Tianjin, China, October 30 – November 4, 2016. Hackensack, NJ: World Scientific (ISBN 978-981-3227-87-3/hbk; 978-981-3227-89-7/ebook). 224-238 (2017).
MSC:  92D20
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\textit{Z. Li} et al., in: Mathematical biology and biological physics. Selected papers based on the presentations at the 16th international symposium on mathematical and computational biology, BIOMAT 2016, Nankai University, Tianjin, China, October 30 -- November 4, 2016. Hackensack, NJ: World Scientific. 224--238 (2017; Zbl 1395.92104)
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Scherer, Philipp O. J.; Fischer, Sighart F.
Theoretical molecular biophysics. 2nd edition. (English) Zbl 1395.92001
Biological and Medical Physics, Biomedical Engineering. Berlin: Springer (ISBN 978-3-662-55670-2/hbk; 978-3-662-55671-9/ebook). xvi, 513 p. (2017).
Reviewer: Eugene Kryachko (Liège)
MSC:  92-01 92C05 92E10 81-01 81V55 92E20 92D20
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\textit{P. O. J. Scherer} and \textit{S. F. Fischer}, Theoretical molecular biophysics. 2nd edition. Berlin: Springer (2017; Zbl 1395.92001)
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Drellich, Elizabeth; Gainer-Dewar, Andrew; Harrington, Heather A.; He, Qijun; Heitsch, Christine; Poznanović, Svetlana
Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences. (English) Zbl 1360.92080
Harrington, Heather A. (ed.) et al., Algebraic and geometric methods in discrete mathematics. AMS special session on algebraic and geometric methods in applied discrete mathematics, San Antonio, TX, USA, January 11, 2015. Proceedings. Providence, RI: American Mathematical Society (AMS) (ISBN 978-1-4704-2321-6/pbk; 978-1-4704-3743-5/ebook). Contemporary Mathematics 685, 137-153 (2017).
MSC:  92D20
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\textit{E. Drellich} et al., Contemp. Math. 685, 137--153 (2017; Zbl 1360.92080)
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Mneimneh, Saad; Ahmed, Syed Ali
Gibbs/MCMC sampling for multiple RNA interaction with sub-optimal solutions. (English) Zbl 1346.92050
Botón-Fernández, María (ed.) et al., Algorithms for computational biology. Third international conference, AlCoB 2016, Trujillo, Spain, June 21–22, 2016. Proceedings. Cham: Springer (ISBN 978-3-319-38826-7/pbk; 978-3-319-38827-4/ebook). Lecture Notes in Computer Science 9702. Lecture Notes in Bioinformatics, 78-90 (2016).
MSC:  92D20 92C40 90C39
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\textit{S. Mneimneh} and \textit{S. A. Ahmed}, Lect. Notes Comput. Sci. 9702, 78--90 (2016; Zbl 1346.92050)
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Chauve, Cedric; Courtiel, Julien; Ponty, Yann
Counting, generating and sampling tree alignments. (English) Zbl 1346.92048
Botón-Fernández, María (ed.) et al., Algorithms for computational biology. Third international conference, AlCoB 2016, Trujillo, Spain, June 21–22, 2016. Proceedings. Cham: Springer (ISBN 978-3-319-38826-7/pbk; 978-3-319-38827-4/ebook). Lecture Notes in Computer Science 9702. Lecture Notes in Bioinformatics, 53-64 (2016).
MSC:  92D20 05C90
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\textit{C. Chauve} et al., Lect. Notes Comput. Sci. 9702, 53--64 (2016; Zbl 1346.92048)
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Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.)
Data mining techniques for the life sciences. 2nd edition. (English) Zbl 1353.92002
Methods in Molecular Biology 1415. New York, NY: Humana Press/Springer (ISBN 978-1-4939-3570-3/hbk; 978-1-4939-3572-7/ebook). xiii, 552 p. (2016).
Reviewer: Irina Ioana Mohorianu (Norwich)
MSC:  92-01 62-01 62-07 92B15 62P10 92C40
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\textit{O. Carugo} (ed.) and \textit{F. Eisenhaber} (ed.), Data mining techniques for the life sciences. 2nd edition. New York, NY: Humana Press/Springer (2016; Zbl 1353.92002)
Full Text: DOI
Shepard, Ron (ed.); Pitzer, Russell M. (ed.); Dunning, Thom (ed.)
Isaiah Shavitt. A memorial Festschrift from theoretical chemistry accounts. Reprinted from the journal Theoretical Chemistry Accounts 133 (2014). (English) Zbl 1323.92005
Highlights in Theoretical Chemistry 9. Berlin: Springer (ISBN 978-3-662-48147-9/hbk; 978-3-662-48148-6/ebook). vii, 359 p. (2016).
MSC:  92-06 92E10 92D20 92E99 82C10 82C20 00B30 00B15
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\textit{R. Shepard} (ed.) et al., Isaiah Shavitt. A memorial Festschrift from theoretical chemistry accounts. Reprinted from the journal Theoretical Chemistry Accounts 133 (2014). Berlin: Springer (2016; Zbl 1323.92005)
Full Text: DOI
Orenstein, Yaron; Berger, Bonnie
Efficient design of compact unstructured RNA libraries covering all \(k\)-mers. (English) Zbl 1367.92089
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, 308-325 (2015).
MSC:  92D20 92-08 68W25 68Q25
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\textit{Y. Orenstein} and \textit{B. Berger}, Lect. Notes Comput. Sci. 9289, 308--325 (2015; Zbl 1367.92089)
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