Abstract

The processing of biomolecular sequence and structure data is central to bioinformatics. No attention, however, has been paid to the problem of the optimization of data processing, in order to minimize the loss of information in transformation of biomolecular data. The work embodied in this proposal is directed toward this question. We intend to study protein sequence and structure data processing with reference to the following goals. The optimization of sequence representation for a specified structure representation, in order to guarantee that the maximum possible amount of structural information is carried by the sequence representation. The optimization of structure representation for a specified sequence representation, in order to guarantee that the maximum amount of information is carried by the structure representation.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Library of Medicine (NLM)
Type
Research Project (R01)
Project #
5R01LM006789-03
Application #
6605017
Study Section
Special Emphasis Panel (ZLM1-SJP-S (M3))
Program Officer
Ye, Jane
Project Start
2001-02-15
Project End
2005-02-14
Budget Start
2003-02-15
Budget End
2005-02-14
Support Year
3
Fiscal Year
2003
Total Cost
$339,000
Indirect Cost

  Institution

Name
Mount Sinai School of Medicine
Department
Biostatistics & Other Math Sci
Type
Schools of Medicine
DUNS #
078861598
City
New York
State
NY
Country
United States
Zip Code
10029

  Publications

Solis, Armando D; Rackovsky, Shalom R (2010) Information-theoretic analysis of the reference state in contact potentials used for protein structure prediction. Proteins 78:1382-97
Rackovsky, S (2010) Global characteristics of protein sequences and their implications. Proc Natl Acad Sci U S A 107:8623-6
Solis, Armando D; Rackovsky, Shalom R (2010) Fold homology detection using sequence fragment composition profiles of proteins. Proteins 78:2745-56
Rackovsky, S (2009) Sequence physical properties encode the global organization of protein structure space. Proc Natl Acad Sci U S A 106:14345-8
Solis, Armando D; Rackovsky, S (2008) Information and discrimination in pairwise contact potentials. Proteins 71:1071-87
Solis, A D; Rackovsky, S (2007) Property-based sequence representations do not adequately encode local protein folding information. Proteins 67:785-8
Kuznetsov, Igor B; Rackovsky, Shalom (2004) Comparative computational analysis of prion proteins reveals two fragments with unusual structural properties and a pattern of increase in hydrophobicity associated with disease-promoting mutations. Protein Sci 13:3230-44
Kuznetsov, Igor B; Rackovsky, Shalom (2004) Class-specific correlations between protein folding rate, structure-derived, and sequence-derived descriptors. Proteins 54:333-41
Kuznetsov, Igor B; Rackovsky, S (2003) Similarity between the C-terminal domain of the prion protein and chimpanzee cytomegalovirus glycoprotein UL9. Protein Eng 16:861-3
Kuznetsov, Igor B; Rackovsky, S (2003) On the properties and sequence context of structurally ambivalent fragments in proteins. Protein Sci 12:2420-33

Showing the most recent 10 out of 12 publications