IDEAS home Printed from https://ideas.repec.org/a/spr/annopr/v175y2010i1p9-3510.1007-s10479-009-0652-y.html
   My bibliography  Save this article

Some operations research methods for analyzing protein sequences and structures

Author

Listed:
  • Piotr Łukasiak
  • Jacek Błażewicz
  • Maciej Miłostan

Abstract

The operations research is probably one of the most successful field of applied mathematics used in economics, physics, chemistry, almost everywhere where one has to analyze huge amounts of data. Lately, these techniques of operations research were introduced in biology, especially in the protein analysis area to support biologists. The fast growth of protein data makes operations research an important issue in bioinformatics, a science which lays on the border between computer science and biology. This paper gives a short overview of the operations research techniques currently used to support structural and functional analysis of proteins. Copyright Springer Science+Business Media, LLC 2010

Suggested Citation

  • Piotr Łukasiak & Jacek Błażewicz & Maciej Miłostan, 2010. "Some operations research methods for analyzing protein sequences and structures," Annals of Operations Research, Springer, vol. 175(1), pages 9-35, March.
    • Handle: RePEc:spr:annopr:v:175:y:2010:i:1:p:9-35:10.1007/s10479-009-0652-y
    DOI: 10.1007/s10479-009-0652-y
    as

    Download full text from publisher

    File URL: http://hdl.handle.net/10.1007/s10479-009-0652-y
    Download Restriction: Access to full text is restricted to subscribers.
    File URL: https://libkey.io/10.1007/s10479-009-0652-y?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Jinbo Xu & Ming Li & Ying Xu, 2004. "Protein Threading by Linear Programming: Theoretical Analysis and Computational Results," Journal of Combinatorial Optimization, Springer, vol. 8(4), pages 403-418, December.
    2. Harvey J. Greenberg & William E. Hart & Giuseppe Lancia, 2004. "Opportunities for Combinatorial Optimization in Computational Biology," INFORMS Journal on Computing, INFORMS, vol. 16(3), pages 211-231, August.
    3. Blazewicz, Jacek & Formanowicz, Piotr & Kasprzak, Marta, 2005. "Selected combinatorial problems of computational biology," European Journal of Operational Research, Elsevier, vol. 161(3), pages 585-597, March.
    4. Rumen Andonov & Stefan Balev & Nicola Yanev, 2004. "Protein Threading: From Mathematical Models to Parallel Implementations," INFORMS Journal on Computing, INFORMS, vol. 16(4), pages 393-405, November.
    5. Stephen Johnson, 1967. "Hierarchical clustering schemes," Psychometrika, Springer;The Psychometric Society, vol. 32(3), pages 241-254, September.
    6. Bernard Chazelle & Carl Kingsford & Mona Singh, 2004. "A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies," INFORMS Journal on Computing, INFORMS, vol. 16(4), pages 380-392, November.
    7. Dawn M. Strickland & Earl Barnes & Joel S. Sokol, 2005. "Optimal Protein Structure Alignment Using Maximum Cliques," Operations Research, INFORMS, vol. 53(3), pages 389-402, June.
    8. Jonathan P. K. Doye & Robert H. Leary & Marco Locatelli & Fabio Schoen, 2004. "Global Optimization of Morse Clusters by Potential Energy Transformations," INFORMS Journal on Computing, INFORMS, vol. 16(4), pages 371-379, November.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Blazewicz, Jacek & Burke, Edmund K. & Kasprzak, Marta & Kovalev, Alexandr & Kovalyov, Mikhail Y., 2011. "The simplified partial digest problem: Approximation and a graph-theoretic model," European Journal of Operational Research, Elsevier, vol. 208(2), pages 142-152, January.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Butenko, S. & Wilhelm, W.E., 2006. "Clique-detection models in computational biochemistry and genomics," European Journal of Operational Research, Elsevier, vol. 173(1), pages 1-17, August.
    2. Claudia Quinteros-Cartaya & Guillermo Solorio-Magaña & Francisco Javier Núñez-Cornú & Felipe de Jesús Escalona-Alcázar & Diana Núñez, 2023. "Microearthquakes in the Guadalajara Metropolitan Zone, Mexico: evidence from buried active faults in Tesistán Valley, Zapopan," Natural Hazards: Journal of the International Society for the Prevention and Mitigation of Natural Hazards, Springer;International Society for the Prevention and Mitigation of Natural Hazards, vol. 116(3), pages 2797-2818, April.
    3. repec:ers:journl:v:xxiv:y:2021:i:4b:p:659-667 is not listed on IDEAS
    4. Kim, Junyung & Shah, Asad Ullah Amin & Kang, Hyun Gook, 2020. "Dynamic risk assessment with bayesian network and clustering analysis," Reliability Engineering and System Safety, Elsevier, vol. 201(C).
    5. Marco Baioletti & Valentino Santucci & Marco Tomassini, 2024. "A performance analysis of Basin hopping compared to established metaheuristics for global optimization," Journal of Global Optimization, Springer, vol. 89(3), pages 803-832, July.
    6. Roberts, Leigh, 2014. "Consistent estimation of breakpoints in time series, with application to wavelet analysis of Citigroup returns," Working Paper Series 18815, Victoria University of Wellington, School of Economics and Finance.
    7. David G Mets & Michael S Brainard, 2018. "An automated approach to the quantitation of vocalizations and vocal learning in the songbird," PLOS Computational Biology, Public Library of Science, vol. 14(8), pages 1-29, August.
    8. Michael Brusco & J Dennis Cradit & Douglas Steinley, 2021. "A comparison of 71 binary similarity coefficients: The effect of base rates," PLOS ONE, Public Library of Science, vol. 16(4), pages 1-19, April.
    9. Noah E. Friedkin, 1984. "Structural Cohesion and Equivalence Explanations of Social Homogeneity," Sociological Methods & Research, , vol. 12(3), pages 235-261, February.
    10. Locatelli, Marco & Schoen, Fabio, 2012. "Local search based heuristics for global optimization: Atomic clusters and beyond," European Journal of Operational Research, Elsevier, vol. 222(1), pages 1-9.
    11. David Matesanz Gomez & Guillermo J. Ortega & Benno Torgler, 2011. "Measuring globalization: A hierarchical network approach," CREMA Working Paper Series 2011-11, Center for Research in Economics, Management and the Arts (CREMA).
    12. Balepur, Prashant Narayan, 1998. "Impacts of Computer-Mediated Communication on Travel and Communication Patterns: The Davis Community Network Study," Institute of Transportation Studies, Research Reports, Working Papers, Proceedings qt6cb1f85c, Institute of Transportation Studies, UC Berkeley.
    13. İsmail Güzel & Atabey Kaygun, 2022. "A new non-archimedean metric on persistent homology," Computational Statistics, Springer, vol. 37(4), pages 1963-1983, September.
    14. Lisa Price, 2001. "Demystifying farmers' entomological and pest management knowledge: A methodology for assessing the impacts on knowledge from IPM-FFS and NES interventions," Agriculture and Human Values, Springer;The Agriculture, Food, & Human Values Society (AFHVS), vol. 18(2), pages 153-176, June.
    15. Elisa Frutos-Bernal & Ángel Martín del Rey & Irene Mariñas-Collado & María Teresa Santos-Martín, 2022. "An Analysis of Travel Patterns in Barcelona Metro Using Tucker3 Decomposition," Mathematics, MDPI, vol. 10(7), pages 1-17, March.
    16. Geert Soete & Wayne DeSarbo & J. Carroll, 1985. "Optimal variable weighting for hierarchical clustering: An alternating least-squares algorithm," Journal of Classification, Springer;The Classification Society, vol. 2(1), pages 173-192, December.
    17. Silvia Blasi & Edoardo Gobbo & Silvia Rita Sedita, 2022. "Big Data for smart cities and citizen engagement: evidence from Twitter data analysis on Italian municipalities," Working Papers - Business wp2022_01.rdf, Universita' degli Studi di Firenze, Dipartimento di Scienze per l'Economia e l'Impresa.
    18. Teh, Boon Kin & Goo, Yik Wen & Lian, Tong Wei & Ong, Wei Guang & Choi, Wen Ting & Damodaran, Mridula & Cheong, Siew Ann, 2015. "The Chinese Correction of February 2007: How financial hierarchies change in a market crash," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 424(C), pages 225-241.
    19. Dalila B. M. M. Fontes & Seyed Mahdi Homayouni, 2019. "Joint production and transportation scheduling in flexible manufacturing systems," Journal of Global Optimization, Springer, vol. 74(4), pages 879-908, August.
    20. Yoshio Takane & Forrest Young & Jan Leeuw, 1977. "Nonmetric individual differences multidimensional scaling: An alternating least squares method with optimal scaling features," Psychometrika, Springer;The Psychometric Society, vol. 42(1), pages 7-67, March.
    21. Fernández, D. & Arnold, R. & Pledger, S., 2016. "Mixture-based clustering for the ordered stereotype model," Computational Statistics & Data Analysis, Elsevier, vol. 93(C), pages 46-75.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:spr:annopr:v:175:y:2010:i:1:p:9-35:10.1007/s10479-009-0652-y. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.