Protein sequence-structure threading

We are working on methods for the assertion of homology by comparing sequences to structural templates. If structural similarity between target and template is sufficiently large, their relationship may be detected even in the absence of statistically significant sequence similarity. Research topics include:

• Combination of contact-based scoring schemes and position-specific scoring matrices (PSSMs).
• Significance of Threading database search results
• Development of user-friendly tools for browsing Threading results
• Structural templates (cores) based on models of structural evolution
• Range of structural similarities detected by threading

Selected Publications:

Panchenko A.R., Marchler-Bauer A., and Bryant S.H. (2000) J. Mol. Biol. 296:1319-1331 Combination of threading potentials and sequence profiles improves fold recognition.

Wheelan S.J., Marchler-Bauer A., and Bryant S.H. (2000) Bioinformatics 16:613-619 Domain Size Distributions Can Predict Domain Boundaries

Panchenko A., Marchler-Bauer A., and Bryant S.H. (1999) Proteins Suppl. 3:133-140 Threading with Explicit Models for Evolutionary Conservation of Structure and Sequence

Marchler-Bauer A., and Bryant S.H. (1999) Proteins Suppl. 3:218-225 A measure of progress in fold recognition?

Marchler-Bauer A., and Bryant S.H. (1997) Trends Biochem Sci., 22:236-240 A measure of success in fold recognition

Download PKB and Threading from the NCBI FTP-site (requires Splus).

Download format-validation and evaluation software used in the fold recognition category of the CASP2 community experiment.