Skip to main content

Contact Map Overlap Maximization Problem, CMO

  • Reference work entry
Encyclopedia of Optimization
  • 250 Accesses

Article Outline

Introduction

Definition

Methods

  Exact algorithms

  Approximate Algorithms

Conclusions

References

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 2,500.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 2,499.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Agarwal PK, Mustafa NH, Wang Y (2007) Fast molecular shape matching using contact maps. J Comput Biol 14(2):131–143

    Article  MathSciNet  Google Scholar 

  2. Caprara A, Carr R, Istrail S, Lancia G, Walenz B (2004) 1001 optimal PDB structure alignments: Integer programming methods for finding the maximum contact map overlap. J Comput Biol 11(1):27–52

    Article  Google Scholar 

  3. Caprara A, Lancia G (2002) Structural alignment of large-size proteins via Lagrangian relaxation. In: Proceedings of International Conference on Computational Biology (RECOMB), Washington, April 2002. pp 100–108

    Google Scholar 

  4. Carr B, Hart WE, Krasnogor N, Burke EK, Hirst JD, Smith JE (2002) Alignment of protein structures with a memetic evolutionary algorithm. In: Proceedings of the Genetic and Evolutionary Computation Conference, New York, July 2002. Morgan Kaufmann Publishers, pp 1027–1034

    Google Scholar 

  5. Carr RD, Lancia G, Istrail S (2000) Branch-and-cut algorithms for independent set problems: Integrality gap and an application to protein structural alignment, Technical report. Sandia National laboratories

    Google Scholar 

  6. Godzik A, Skolnick J (1994) Flexible algorithm for direct multiple alignment of protein structures and sequences. Comput Appl Biosci 10(6):587–596

    Google Scholar 

  7. Goldman D, Papadimitriou C, Istrail S (1999) Algorithmic aspects of protein structure similarity. In: Proceedings of the 40th Annual Symposium on Foundations of Computer Science (FOCS), New York, October 1999. IEEE Computer societypages, pp 512–522

    Google Scholar 

  8. Krasnogor N, Lancia G, Zemla A, Hart WE, Carr RD, Hirst JD, Burke EK (2005) A comparison of computational methods for the maximum contact map overlap of protein pairs. http://citeseer.ist.psu.edu/659931.html. Accessed 30 Jan 2008

  9. Lancia G, Carr R, Walenz B, Istrail S (2001) 101 optimal PDB structure alignments: A branch-and-cut algorithm for the maximum contact map overlap problem. In: Proceedings of Annual International Conference on Computational Biology (RECOMB), Montreal, April 2001. pp 193–202

    Google Scholar 

  10. Melvin J, Sokol J, Tovey C (2006) Finding optimal solutions to large CMO instances. (preprint)

    Google Scholar 

  11. Strickland DM, Barnes E, Sokol JS (2005) Optimal protein structure alignment using maximum cliques. Oper Res 53(3):389–402

    Article  MathSciNet  MATH  Google Scholar 

  12. Xie W, Sahinidis NV (2006) A branch-and-reduce algorithm for the contact map overlap problem. In: Apostolico A, Guerra C, Istrail S, Pevzner P, Waterman M (eds) RECOMB 2006. Lect Note Comput Sci 3909:516–529

    Article  Google Scholar 

  13. Xie W, Sahinidis NV (2006) A reduction-based exact algorithm for the contact map overlap problem. J Comput Biol 14(5):637–654

    Article  MathSciNet  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag

About this entry

Cite this entry

Xie, W., Sahinidis, N.V. (2008). Contact Map Overlap Maximization Problem, CMO . In: Floudas, C., Pardalos, P. (eds) Encyclopedia of Optimization. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-74759-0_86

Download citation

Publish with us

Policies and ethics