alexa Structure-dependent sequence alignment for remotely related proteins.
Pharmaceutical Sciences

Pharmaceutical Sciences

Journal of Bioequivalence & Bioavailability

Author(s): Yang AS

Abstract Share this page

Abstract MOTIVATION: The quality of a model structure derived from a comparative modeling procedure is dictated by the accuracy of the predicted sequence-template alignment. As the sequence-template pairs are increasingly remote in sequence relationship, the prediction of the sequence-template alignments becomes increasingly problematic with sequence alignment methods. Structural information of the template, used in connection with the sequence relationship of the sequence-template pair, could significantly improve the accuracy of the sequence-template alignment. In this paper, we describe a sequence-template alignment method that integrates sequence and structural information to enhance the accuracy of sequence-template alignments for distantly related protein pairs. RESULTS: The structure-dependent sequence alignment (SDSA) procedure was optimized for coverage and accuracy on a training set of 412 protein pairs; the structures for each of the training pairs are similar (RMSD< approximately 4A) but the sequence relationship is undetectable (average pair-wise sequence identity = 8\%). The optimized SDSA procedure was then applied to extend PSI-BLAST local alignments by calculating the global alignments under the constraint of the residue pairs in the local alignments. This composite alignment procedure was assessed with a testing set of 1421 protein pairs, of which the pair-wise structures are similar (RMSD< approximately 4A) but the sequences are marginally related at best in each pair (average pair-wise sequence identity = 13\%). The assessment showed that the composite alignment procedure predicted more aligned residues pairs with an average of 27\% increase in correctly aligned residues over the standard PSI-BLAST alignments for the protein pairs in the testing set.
This article was published in Bioinformatics and referenced in Journal of Bioequivalence & Bioavailability

Relevant Expert PPTs

Relevant Speaker PPTs

Recommended Conferences

Relevant Topics

Peer Reviewed Journals
 
Make the best use of Scientific Research and information from our 700 + peer reviewed, Open Access Journals
International Conferences 2017-18
 
Meet Inspiring Speakers and Experts at our 3000+ Global Annual Meetings

Contact Us

Agri, Food, Aqua and Veterinary Science Journals

Dr. Krish

[email protected]

1-702-714-7001 Extn: 9040

Clinical and Biochemistry Journals

Datta A

[email protected]

1-702-714-7001Extn: 9037

Business & Management Journals

Ronald

[email protected]

1-702-714-7001Extn: 9042

Chemical Engineering and Chemistry Journals

Gabriel Shaw

[email protected]

1-702-714-7001 Extn: 9040

Earth & Environmental Sciences

Katie Wilson

[email protected]

1-702-714-7001Extn: 9042

Engineering Journals

James Franklin

[email protected]

1-702-714-7001Extn: 9042

General Science and Health care Journals

Andrea Jason

[email protected]

1-702-714-7001Extn: 9043

Genetics and Molecular Biology Journals

Anna Melissa

[email protected]

1-702-714-7001 Extn: 9006

Immunology & Microbiology Journals

David Gorantl

[email protected]

1-702-714-7001Extn: 9014

Informatics Journals

Stephanie Skinner

[email protected]

1-702-714-7001Extn: 9039

Material Sciences Journals

Rachle Green

[email protected]

1-702-714-7001Extn: 9039

Mathematics and Physics Journals

Jim Willison

[email protected]

1-702-714-7001 Extn: 9042

Medical Journals

Nimmi Anna

[email protected]

1-702-714-7001 Extn: 9038

Neuroscience & Psychology Journals

Nathan T

[email protected]

1-702-714-7001Extn: 9041

Pharmaceutical Sciences Journals

John Behannon

[email protected]

1-702-714-7001Extn: 9007

Social & Political Science Journals

Steve Harry

[email protected]

1-702-714-7001 Extn: 9042

 
© 2008-2017 OMICS International - Open Access Publisher. Best viewed in Mozilla Firefox | Google Chrome | Above IE 7.0 version
adwords