Abstract

The project is divided into 4 subprojects:? ? 1.Iterative automatic methods for refining multiple sequence alignment. Currently starting point of constructing CDD database is a multiple alignment imported form protein family models as SMART and PFAM. Since all known multiple sequence alignment algorithms are less than perfect the imported alignment have errors that are now removed by hand. The goal of the project is to provide reduce and simplify this manual work (ref. 1). ? 2.New approaches for detecting structural similarities. The goal of this subproject is to develop new approaches for fast detection of structural similarities that would complement currently used method (VAST). Thus particular attention is given to loop structure and developing of indexing methods (ref 7). ? 3.Applications of methods based on sequence and structure similarities to study protein evolution (and co-evolution). Particular interests include prediction of protein interaction from sequence co-evolution (ref 3,4,6). ? 4. Classifaction and prediction of protein structure (ref 2).? 5. Sequence based methods to detect protein orthology and homology (ref 5).

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Library of Medicine (NLM)
Type
Intramural Research (Z01)
Project #
1Z01LM779892-05
Application #
7594480
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
5
Fiscal Year
2007
Total Cost
$158,885
Indirect Cost

  Institution

Name
National Library of Medicine
Department
Type
DUNS #
City
State
Country
United States
Zip Code

  Publications

Jeong, Jieun; Berman, Piotr; Przytycka, Teresa M (2008) Improving strand pairing prediction through exploring folding cooperativity. IEEE/ACM Trans Comput Biol Bioinform 5:484-91
Zheng, Jie; Rogozin, Igor B; Koonin, Eugene V et al. (2007) Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation. Mol Biol Evol 24:2583-92
Zotenko, Elena; Dogan, Rezarta Islamaj; Wilbur, W John et al. (2007) Structural footprinting in protein structure comparison: the impact of structural fragments. BMC Struct Biol 7:53
Jothi, Raja; Przytycka, Teresa M; Aravind, L (2007) Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics 8:173
Kann, Maricel G; Jothi, Raja; Cherukuri, Praveen F et al. (2007) Predicting protein domain interactions from coevolution of conserved regions. Proteins 67:811-20
Jothi, Raja; Zotenko, Elena; Tasneem, Asba et al. (2006) COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. Bioinformatics 22:779-88
Jeong, Jieun; Berman, Piotr; Przytycka, Teresa (2006) Fold classification based on secondary structure--how much is gained by including loop topology? BMC Struct Biol 6:3
Chakrabarti, Saikat; Lanczycki, Christopher J; Panchenko, Anna R et al. (2006) State of the art: refinement of multiple sequence alignments. BMC Bioinformatics 7:499
Jothi, Raja; Cherukuri, Praveen F; Tasneem, Asba et al. (2006) Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol 362:861-75
Chakrabarti, Saikat; Lanczycki, Christopher J; Panchenko, Anna R et al. (2006) Refining multiple sequence alignments with conserved core regions. Nucleic Acids Res 34:2598-606

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