Predicting protein folds with fold-specific pssm libraries

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

Research output: Contribution to journalArticle

4 Citations (Scopus)

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
StatePublished - Jun 22 2011

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Libraries
Proteins
amino acid sequences
proteins
Position-Specific Scoring Matrices
Protein Databases
Sequence Alignment
sequence alignment
Proteomics
proteomics
Amino Acid Sequence
prediction
Amino Acids
methodology
Experiments

All Science Journal Classification (ASJC) codes

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

Cite this

Hong, Y., Chintapalli, S. V., Ko, K. D., Bhardwaj, G., Zhang, Z., Van Rossum, D. B., & 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
Hong, Yoojin ; Chintapalli, Sree Vamsee ; Ko, Kyung Dae ; Bhardwaj, Gaurav ; Zhang, Zhenhai ; Van Rossum, Damian B. ; Patterson, Randen L. / Predicting protein folds with fold-specific pssm libraries. In: PLoS One. 2011 ; Vol. 6, No. 6.
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Hong, Y, Chintapalli, SV, Ko, KD, Bhardwaj, G, Zhang, Z, Van Rossum, DB & Patterson, RL 2011, 'Predicting protein folds with fold-specific pssm libraries', PLoS One, vol. 6, no. 6, e20557. https://doi.org/10.1371/journal.pone.0020557

Predicting protein folds with fold-specific pssm libraries. / Hong, Yoojin; Chintapalli, Sree Vamsee; Ko, Kyung Dae; Bhardwaj, Gaurav; Zhang, Zhenhai; Van Rossum, Damian B.; Patterson, Randen L.

In: PLoS One, Vol. 6, No. 6, e20557, 22.06.2011.

Research output: Contribution to journalArticle

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Hong Y, Chintapalli SV, Ko KD, Bhardwaj G, Zhang Z, Van Rossum DB et al. Predicting protein folds with fold-specific pssm libraries. PLoS One. 2011 Jun 22;6(6). e20557. https://doi.org/10.1371/journal.pone.0020557