Protein structure from contact maps: A case-based reasoning Approach

Information Systems Frontiers

Volumn 8, Issue 1, 2006, Pages 29-36

  Glasgow, Janice ^a,b   Kuo, Tony ^a   Davies, Jim ^a  

^a QUEEN S UNIVERSITY   (Canada)

^b Department of Biomedical Computing ^*  (Canada)

Author keywords

Analogy; Case based reasoning; Contact maps; Protein structure; Secondary structure

Indexed keywords

CASE-BASED REASONING; CONTACT MAPS; PROTEIN STRUCTURE; SECONDARY STRUCTURE;

AMINO ACIDS; PHYSICAL PROPERTIES; PROTEINS;

FUZZY SETS;

EID: 33144473275     PISSN: 13873326     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10796-005-6101-9     Document Type: Article

References (25)

1. Aaronson JS, Juergen H, Overton GC. Knowledge discovery in genbank. In: Hunter L, Searls D, and Shavlik J, eds. In: Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, AAAI Press, 1993;3-11.
2. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, SHindyalov IN, Bourne PE. Protein data bank. Nucleic Acids Research 2000;28:235-242.
3. Epstein S. For the right reasons: The FORR architecture for learning in a skill domain. Cognitive Science 1994;18(3):479-511.
4. Epstein S. Pragmatic navigation: Reactivity, heuristics and search. Artificial Intelligence 1998;100:275-322.
5. Epstein S, Gelfand J, Lock E. Learning game-specific spatially oriented heuristics. Constraints: An International Journal 1998;2:239-251.
6. Fariselli P, Olmea O, Valencia A, Casadio R. Prediction of contact maps with neural networks and correlated mutations. Protein Engineering 2001;14(11):835-843.
7. Haralick RM, Shanmugam K, Dinstein I. Textural features for image classification. IEEE Transactions on Systems, Man and Cybernetics SMC-1973;3(6):610-621.
8. Hennessy D, Buchanan B, Subramanian D, Wilkosz PA, Rosenberg JM. Statistical methods for the objective design of screening procedures for macromolecular crystallization. Acta Crystallogr D Biol Crystallogr 2000;56(Pt 7):817-827.
9. Jaccard P. Nouvelles recherches sur la distribution florale. Bulletin de la Société Vaudoise des Sciences Naturelles 1908;44:223-270.
10. Jurisica 1, Glasgow J. Applications of case-based reasoning in molecular biology. AI Magazine Winter, 2004.
11. Jurisica 1, Rogers P, Glasgow J, Fortier S, Luft J, Wolfley J, Bianca M, Weeks D, DeTitta GT. Intelligent decision support for protein crystal growth. IBM Systems Journal, Special Issue on Deep Computing for Life Sciences 2001;40(2):394-409.
12. Kettler B, Darden L. Protein sequencing experiment planning using analogy. In: Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, 1993;216-224.
13. Kleywegt GJ, Jones TA. Model-building and refinement practice. In: Methods in Enzymology 1997;(277):208-230.
14. Kolodner J. Case-Based Reasoning. Morgan Kaufmann, 1993.
15. Leng B, Buchanan BG, Nicholas HB. Protein secondary structure prediction using two-level case-based reasoning. In: Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, 1993;251-259.
16. Luthy R, Bowie JU, Eisenber D. Assessment of protein models with three-dimensional profiles. Nature 1992;356:83-85.
17. Nilges M, Clore GM, Gronenborn AM. Determination of the three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms. FEBS Lett. 1988;229:129-136.
18. Pollastri G, Baldi P. Prediction of contact maps by recurrent neural network architectures and hidden context propagation from all four cardinal corners. Bioinformatics 2002;1(1):1-9.
19. Punta M, Rost B. Profcon: Novel prediction of long-range contacts. Bioinformatics 2005;21(13):2960-2968.
20. Riesbeck C, Schank R. Inside Case-Based Reasoning. Lawrence Erlbaum: Hillsdale, NJ, 1989.
21. Shavlik J. Finding genes by case-based reasoning in the presence of noisy case boundaries. In: Proceedings of the 1991 DARPA Workshop on Case-Based Reasoning Morgan-Kauffman, 1991.
22. Smith JR, Chang SF. Quad-tree segmentation for texture-based image query. Proceedings of the second ACM international conference on = Multimedia 1994:279-286.
23. Sullivan GJ, Baker RL. Efficient quadtree coding of images and video. IEEE Transactions on Image Processing 1994;3(3):327-331.
24. Vendruscolo M, Kussell E, Domany E. Recovery of protein structure from contact maps. Folding and Design 1997;2:295-306.
25. Won CS, Park DK, Park SJ. Efficient use of mpeg-7 edge histogram descriptor. Electronics and Telecommunications Research Institute Journal 2002;24:23.