Connectivity inference in mass spectrometry based structure determination

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 8125 LNCS, Issue , 2013, Pages 289-300

  Agarwal, Deepesh ^a   Araujo, Julio Cesar Silva ^a,b   Caillouet, Christelle ^a,b   Cazals, Frederic ^a   Coudert, David ^a,b   Pérennes, Stephane ^a,b  

^a INRIA   (France)

^b UNIVERSITÉ CÔTE D'AZUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CONSENSUS SOLUTIONS; GREEDY ALGORITHMS; INFERENCE PROBLEM; MIXED INTEGER LINEAR PROGRAMMING; OPTIMAL SOLUTIONS; STRUCTURAL BIOLOGY; STRUCTURE DETERMINATION; UNION-FIND DATA STRUCTURES;

APPROXIMATION ALGORITHMS; BIOLOGY; GRAPH THEORY; LINEAR PROGRAMMING; MASS SPECTROMETRY; OPTIMIZATION; PROTEINS;

PROBLEM SOLVING;

EID: 84884316951     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-40450-4_25     Document Type: Conference Paper

References (26)

1. Agarwal, D., Araujo, J., Caillouet, C., Cazals, F., Coudert, D., Pérennes, S.: Connectivity inference in mass spectrometry based structure determination. Technical Report 8320, Inria (2013), http://hal.inria.fr/hal- 00837496
2. Agarwal, D., Cazals, F., Malod-Dognin, N.: Stoichiometry determination for mass-spectrometry data: the interval case (2013), http://hal.inria.fr/hal- 00741491
3. Alber, F., Dokudovskaya, S., Veenhoff, L.M., Zhang, W., Kipper, J., Devos, D., Suprapto, A., Karni-Schmidt, O., Williams, R., Chait, B.T., Rout, M.P., Sali, A.: Determining the Architectures of Macromolecular Assemblies. Nature 450(7170), 683-694 (2007)
4. Alber, F., Förster, F., Korkin, D., Topf, M., Sali, A.: Integrating Diverse Data for Structure Determination of Macromolecular Assemblies. Ann. Rev. Biochem. 77, 11.1-11.35 (2008)
5. Alon, N., Moshkovitz, D., Safra, S.: Algorithmic construction of sets for k-restrictions.ACM Trans. Algorithms 2, 153-177 (2006)
6. Bocker, S., Liptak, Z.: A fast and simple algorithm for the money changing problem. Algorithmica 48(4), 413-432 (2007)
7. Cai, Q., Todorovic, A., Andaya, A., Gao, J., Leary, J.A., Cate, J.H.D.: Distinct regions of human eIF3 are sufficient for binding to the hcv ires and the 40s ribosomal subunit. Journal of Molecular Biology 403(2), 185-196 (2010)
8. Cazals, F., Proust, F., Bahadur, R., Janin, J.: Revisiting the Voronoi description of protein-protein interfaces. Protein Science 15(9), 2082-2092 (2006)
9. ElAntak, L., Tzakos, A.G., Locker, N., Lukavsky, P.J.: Structure of eIF3b rna recognition motif and its interaction with eIF3j. Journal of Biological Chemistry 282(11), 8165-8174 (2007)
10. Hernández, H., Dziembowski, A., Taverner, T., Séraphin, B., Robinson, C.V.: Subunit architecture of multimeric complexes isolated directly from cells. EMBO Reports 7(6), 605-610 (2006)
11. Janin, J., Bahadur, R.P., Chakrabarti, P.: Protein-protein interaction and quaternary structure. Quarterly Reviews of Biophysics 41(2), 133-180 (2008)
12. Kao, A., Randall, A., Yang, Y., Patel, V.R., Kandur, W., Guan, S., Rychnovsky, S.D., Baldi, P., Huang, L.: Mapping the structural topology of the yeast 19s proteasomal regulatory particle using chemical cross-linking and probabilistic modeling. Molecular & Cellular Proteomics (2012)
13. Karp, R.M.: Reducibility among combinatorial problems. In: Complexity of Computer Computations. The IBM Research Symposia Series, pp. 85-103. Plenum Press, New York (1972)
14. Lasker, K., Förster, F., Bohn, S., Walzthoeni, T., Villa, E., Unverdorben, P., Beck, F., Aebersold, R., Sali, A., Baumeister, W.: Molecular architecture of the 26s proteasome holocomplex determined by an integrative approach. Proceedings of the National Academy of Sciences 109(5), 1380-1387 (2012)
15. Levy, E., Erba, E.-B., Robinson, C., Teichmann, S.: Assembly reflects evolution of protein complexes. Nature 453(7199), 1262-1265 (2008)
16. Loriot, S., Cazals, F.: Modeling macro-molecular interfaces with intervor. Bioinformatics 26(7), 964-965 (2010)
17. Lund, C., Yannakakis, M.: On the hardness of approximating minimization problems. J. ACM 41, 960-981 (1994)
18. Makino, D.L., Baumgärtner, M., Conti, E.: Crystal structure of an rna-bound 11-subunit eukaryotic exosome complex. Nature 495(7439), 70-75 (2013)
19. Raghavan, S.: Formulations and algorithms for network design problems with connectivity requirements. PhD thesis, MIT, Cambridge, MA, USA (1995)
20. Sharon, M., Robinson, C.V.: The role of mass spectrometry in structure elucidation of dynamic protein complexes. Annu. Rev. Biochem. 76, 167-193 (2007)
21. Sharon, M., Taverner, T., Ambroggio, X.I., Deshaies, R.J., Robinson, C.V.: Structural organization of the 19s proteasome lid: insights from ms of intact complexes. PLoS Biology 4(8), e267 (2006)
22. Stengel, F., Aebersold, R., Robinson, C.V.: Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Molecular & Cellular Proteomics 11(3) (2012)
23. Sun, C., Todorovic, A., Querol-Audí, J., Bai, Y., Villa, N., Snyder, M., Ashchyan,J., Lewis, C.S., Hartland, A., Gradia, S.: et al. Functional reconstitution of human eukaryotic translation initiation factor 3 (eIF3). Proceedings of the National Academy of Sciences 108(51), 20473-20478 (2011)
24. Tarjan, R.E.: Data Structures and Network Algorithms. CBMS-NSF Regional Conference Series in Applied Mathematics, vol. 44. Society for Industrial and Applied Mathematics, Philadelphia (1983)
25. Taverner, T., Hernández, H., Sharon, M., Ruotolo, B.T., Matak-Vinkovic, D., Devos, D., Russell, R.B., Robinson, C.V.: Subunit architecture of intact protein complexes from mass spectrometry and homology modeling. Accounts of Chemical Research 41(5), 617-627 (2008)
26. Zhou, M., Sandercock, A.M., Fraser, C.S., Ridlova, G., Stephens, E., Schenauer, M.R., Yokoi-Fong, T., Barsky, D., Leary, J.A., Hershey, J.W., Doudna, J.A., Robinson, C.V.: Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3. Proceedings of the National Academy of Sciences 105(47), 18139-18144 (2008)