NCBI Structure - THREADING
Author: Structure_threading
Description: Protein threading predicts the three-dimensional structure of a protein sequence by threading it through known structures and calculating its energy (NCBI Structure Group Threading Page).
Keywords: national center for biotechnology information, ncbi, national library of medicine, nlm, national institutes of health, nih, database, archive, bioinformatics, biomedicine, pubmed, pubmed central, bookshelf, structure, cn3d, vast, threading, mmdb, pkb

CASP3 1998 prediction experiment CASP2 1996 prediction experiment Leptin predictions Evaluation of 1995 predictions NCBI Threading package Installation and help document |  |
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
See evaluation results for models submitted to CASP3 by the Bryant team. See evaluation results for models submitted to CASP2 by the Bryant team.
Selected Online Publications: 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 |  |
Software:
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.
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