POSA: A user-driven, interactive multiple protein structure alignment server

Nucleic Acids Research

Volumn 42, Issue W1, 2014, Pages

  Li, Zhanwen ^a   Natarajan, Padmaja ^a   Ye, Yuzhen ^b   Hrabe, Thomas ^a   Godzik, Adam ^a  

^a BURNHAM INSTITUTE   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ZINC FINGER PROTEIN;

ALGORITHM; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SYSTEM; INFORMATION PROCESSING; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; WORKFLOW;

ALGORITHMS; INTERNET; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN; USER-COMPUTER INTERFACE;

EID: 84904796362     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku394     Document Type: Article

References (21)

1. Ye,Y. and Godzik,A. (2005) Multiple flexible structure alignment using partial order graphs. Bioinformatics, 21, 2362-2369.
2. Ye,Y. and Godzik,A. (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics, 19(Suppl. 2), ii246-ii255.
3. Leibowitz,N., Nussinov,R. and Wolfson,H.J. (2001) MUSTA - a general, efficient, automated method for multiple structure alignment and detection of common motifs: application to proteins. J. Comput. Biol., 8, 93-121.
4. Guda,C., Lu,S., Scheeff,E.D., Bourne,P.E. and Shindyalov,I.N. (2004) CE-MC: a multiple protein structure alignment server. Nucleic Acids Res., 32, W100-W103.
5. Shatsky,M., Nussinov,R. and Wolfson,H.J. (2002) MultiProt - a multiple protein structural alignment algorithm. Algorith. Bioinformatics, 2452, 235-250.
6. Menke,M., Berger,B. and Cowen,L. (2008) Matt: local flexibility aids protein multiple structure alignment. PLoS Comput. Biol., 4, e10.
7. Micheletti,C. and Orland,H. (2009) MISTRAL: a tool for energy-based multiple structural alignment of proteins. Bioinformatics, 25, 2663-2669.
8. Sun,H., Sacan,A., Ferhatosmanoglu,H. andWang,Y. (2012) Smolign: a spatial motifs-based protein multiple structural alignment method. IEEE/ACM Trans. Comput. Biol. Bioinformatics/IEEE, ACM, 9, 249-261.
9. Wang,S., Peng,J. and Xu,J. (2011) Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling. Bioinformatics, 27, 2537-2545.
10. Braberg,H., Webb,B.M., Tjioe,E., Pieper,U., Sali,A. and Madhusudhan,M.S. (2012) SALIGN: a web server for alignment of multiple protein sequences and structures. Bioinformatics, 28, 2072-2073.
11. Shealy,P. and Valafar,H. (2012) Multiple structure alignment with msTALI. BMC Bioinformatics, 13, 105-120.
12. Leonard,S., Joseph,A.P., Srinivasan,N., Gelly,J.C. and de Brevern,A.G. (2014) mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet. J. Biomol. Struct. Dyn., 32, 661-668.
13. Wang,S., Ma,J., Peng,J. and Xu,J. (2013) Protein structure alignment beyond spatial proximity. Sci. Rep., 3, 1448.
14. Konagurthu,A.S.,Whisstock,J.C., Stuckey,P.J. and Lesk,A.M. (2006) MUSTANG: a multiple structural alignment algorithm. Proteins, 64, 559-574.
15. Krissinel,E. and Henrick,K. (2005) Multiple alignment of protein structures in three dimensionsLecture Notes in Computer Science 3695 67-78
16. Leibowitz,N., Fligelman,Z.Y., Nussinov,R. and Wolfson,H.J. (1999) Multiple structural alignment and core detection by geometric hashing. In: Proceedings of International Conference on Intelligent Systems for Molecular Biology, Vol. 1999, pp. 169-177. http://www.aaai.org/Papers/ISMB/1999/ISMB99- 020. pdf (13 May 2014, date last accessed).
17. Theobald,D.L. and Steindel,P.A. (2012) Optimal simultaneous superpositioning of multiple structures with missing data. Bioinformatics, 28, 1972-1979.
18. Lancia,G. (2008) Mathematical programming in computational biology: an annotated bibliography. Algorithms, 1, 100-129.
19. Feng,D.F. and Doolittle,R.F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25, 351-360.
20. Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/. (13 May 2014, date last accessed).
21. Pettersen,E.F., Goddard,T.D., Huang,C.C., Couch,G.S., Greenblatt,D.M.,Meng,E.C. and Ferrin,T.E. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem., 25, 1605-1612.