Predicting protein folds with fold-specific pssm libraries

Yoojin Hong, Sree Vamsee Chintapalli, Kyung Dae Ko, Gaurav Bhardwaj, Zhenhai Zhang, Damian van Rossum, Randen L. Patterson

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5 Scopus citations

Abstract

Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies. Herein, we outline an effective method for fold recognition using sets of PSSMs, each of which is constructed for different protein folds. Our analyses demonstrate that FSL (Fold-specific Position Specific Scoring Matrix Libraries) can predict/relate structures given only their amino acid sequences of highly divergent proteins. This ability to detect distant relationships is dependent on low-identity sequence alignments obtained from FSL. Results from our experiments demonstrate that FSL perform well in recognizing folds from the "twilight-zone" SABmark dataset. Further, this method is capable of accurate fold prediction in newly determined structures. We suggest that by building complete PSSM libraries for all unique folds within the Protein Database (PDB), FSL can be used to rapidly and reliably annotate a large subset of protein folds at proteomic level. The related programs and fold-specific PSSMs for our FSL are publicly available at: http://ccp.psu.edu/download/FSLv1.0/.

Original languageEnglish (US)
Article numbere20557
JournalPloS one
Volume6
Issue number6
DOIs
Publication statusPublished - Jun 22 2011

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All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Hong, Y., Chintapalli, S. V., Ko, K. D., Bhardwaj, G., Zhang, Z., van Rossum, D., & Patterson, R. L. (2011). Predicting protein folds with fold-specific pssm libraries. PloS one, 6(6), [e20557]. https://doi.org/10.1371/journal.pone.0020557