20042019

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2019

Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors

Sumanaweera, D., Allison, L. & Konagurthu, A., 5 Jul 2019, In : Bioinformatics. 35, 14, p. i360-i369 10 p., btz368.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2017

Statistical inference of protein structural alignments using information and compression

Collier, J. H., Allison, L., Lesk, A. M., Stuckey, P. J., Garcia De La Banda, M. & Konagurthu, A. S., 1 Apr 2017, In : Bioinformatics. 33, 7, p. 1005-1013 9 p.

Research output: Contribution to journalArticleResearchpeer-review

3 Citations (Scopus)
2015

On sufficient statistics of least-squares superposition of vector sets

Konagurthu, A. S., Kasarapu, P., Allison, L., Collier, J. H. & Lesk, A. M., 2015, In : Journal of Computational Biology. 22, 6, p. 487-497 11 p.

Research output: Contribution to journalArticleResearchpeer-review

1 Citation (Scopus)
2014

A new statistical framework to assess structural alignment quality using information compression

Collier, J., Allison, L., Lesk, A. M., Garcia De La Banda, M. J. & Konagurthu, A. S., 2014, In : Bioinformatics. 30, 17, p. 512 - 518 7 p.

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)

How precise are reported protein coordinate data?

Konagurthu, A. S., Allison, L., Abramson, D. A., Stuckey, P. J. & Lesk, A. M., 2014, In : Acta Crystallographica Section D: Biological Crystallography. 70, 3, p. 904 - 906 3 p.

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)

On representing protein folding patterns using non-linear parametric curves

Kasarapu, P., Garcia De La Banda, M. J. & Konagurthu, A. S., 2014, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 11, 6, p. 1218 - 1228 11 p.

Research output: Contribution to journalArticleResearchpeer-review

2012

Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs

Mahmood, K., Webb, G. I., Song, J., Whisstock, J. C. & Konagurthu, A. S., 2012, In : Nucleic Acids Research. 40, 6 (Art. ID: e44), p. 1 - 11 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
16 Citations (Scopus)

Minimum message length inference of secondary structure from protein coordinate data

Konagurthu, A. S., Lesk, A. M. & Allison, L., 2012, In : Bioinformatics. 28, 12, p. i97 - i105 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
18 Citations (Scopus)

Super: A web server to rapidly screen superposable oligopeptide fragments from the protein data bank

Collier, J., Lesk, A. M., Garcia De La Banda, M. J. & Konagurthu, A. S., 2012, In : Nucleic Acids Research. 40, p. 1 - 6 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
4 Citations (Scopus)
2011

Piecewise linear approximation of protein structures using the principle of minimum message length

Konagurthu, A., Allison, L., Stuckey, P. & Lesk, A., 2011, In : Bioinformatics. 27, 13, p. i43 - i51 9 p.

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)
2010

A fast indexing approach for protein structure comparison

Zhang, L., Bailey, J., Konagurthu, A. S. & Ramamohanarao, K., 2010, In : BMC Bioinformatics. 11, S1, p. 1 - 9 9 p.

Research output: Contribution to journalArticleResearchpeer-review

8 Citations (Scopus)

Cataloging topologies of protein folding patterns

Konagurthu, A. S. & Lesk, A. M., 2010, In : Journal of Molecular Recognition. 23, 2, p. 253 - 257 5 p.

Research output: Contribution to journalArticleResearchpeer-review

7 Citations (Scopus)

EGM: Encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes

Mahmood, K., Konagurthu, A. S., Song, J., Buckle, A. M., Webb, G. I. & Whisstock, J. C., 2010, In : Bioinformatics. 26, 17, p. 2076 - 2084 9 p.

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)

MUSTANG-MR structural sieving server: Applications in protein structural analysis and crystallography

Konagurthu, A. S., Reboul, C. F., Schmidberger, J. W., Irving, J. A., Lesk, A. M., Stuckey, P. J., Whisstock, J. C. & Buckle, A. M., 2010, In : PLoS ONE. 5, 4 (e10048), p. 1 - 7 7 p.

Research output: Contribution to journalArticleResearchpeer-review

36 Citations (Scopus)
2008

On the origin of distribution patterns of motifs in biological networks

Konagurthu, A. S. & Lesk, A. M., 2008, In : BMC Systems Biology. 2, p. 1 - 8 8 p.

Research output: Contribution to journalArticleResearchpeer-review

23 Citations (Scopus)

Single and multiple input modules in regulatory networks

Konagurthu, A. S. & Lesk, A. M., 2008, In : Proteins: Structure, Function, and Bioinformatics. 73, 2, p. 320 - 324 5 p.

Research output: Contribution to journalArticleResearchpeer-review

8 Citations (Scopus)

Structural search and retrieval using a tableau representation of protein folding patterns

Konagurthu, A. S., Stuckey, P. J. & Lesk, A., 2008, In : Bioinformatics. 24, 5, p. 645 - 651 7 p.

Research output: Contribution to journalArticleResearchpeer-review

25 Citations (Scopus)
2006

MUSTANG: a multiple structural alignment algorithm

Konagurthu, A. S., Whisstock, J. C., Stuckey, P. J. & Lesk, A. M., 2006, In : Proteins: Structure, Function, and Bioinformatics. 64, 3, p. 559 - 574 16 p.

Research output: Contribution to journalArticleResearchpeer-review

472 Citations (Scopus)

Optimal sum-of-pairs multiple sequence alignment using incremental Carrillo and Lipman bounds

Konagurthu, A. S. & Stuckey, P. J., 2006, In : Journal of Computational Biology. 13, 3, p. 668 - 685 18 p.

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)
2004

Progressive multiple alignment using sequence triplet optimizations and three-residue exchange costs

Konagurthu, A., Whisstock, J. & Stuckey, P., 2004, In : Journal of Bioinformatics and Computational Biology. 2, 4, p. 719 - 745 27 p.

Research output: Contribution to journalArticleResearchpeer-review

9 Citations (Scopus)