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Related Experiment Videos

Protein threading by PROSPECT: a prediction experiment in CASP3.

Y Xu1, D Xu, O H Crawford

  • 1Computational Protein Structure Group, Computational Biosciences Section, Life Sciences Division and Center for Engineering Science Advanced Research, Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830.

Protein Engineering
|December 10, 1999
PubMed
Summary

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PROSPECT, a novel protein fold recognition program, accurately identified correct or similar protein folds for 16 out of 23 targets in the CASP3 experiment. It also achieved good sequence-structure alignments for most identified folds.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Structure Prediction

Background:

  • Protein fold recognition is crucial for understanding protein function.
  • Accurate prediction of protein structures remains a significant challenge in bioinformatics.
  • The Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments benchmark prediction methods.

Purpose of the Study:

  • To evaluate the performance of the PROSPECT program in protein fold recognition.
  • To assess PROSPECT's ability to find optimal sequence-structure alignments.
  • To analyze PROSPECT's effectiveness in the CASP3 fold recognition and ab initio prediction categories.

Main Methods:

  • PROSPECT utilizes an alignment-scoring function with singleton fitness, pairwise contact preference, and gap penalties.

Related Experiment Videos

  • The program guarantees globally optimal sequence-structure alignments.
  • PROSPECT can incorporate user-defined constraints on protein structures.

    • Main Results:

    • PROSPECT correctly identified the most similar folds for 11 out of 23 CASP3 targets.
    • It predicted closely-similar folds for an additional five targets.
    • Good sequence-structure alignments were achieved for nine of the correctly identified folds.
    • PROSPECT located partial structures for three out of five ab initio prediction problems.

    Conclusions:

    • PROSPECT demonstrates significant success in protein fold recognition tasks.
    • The program's ability to find optimal alignments and handle constraints contributes to its effectiveness.
    • PROSPECT shows promise for both fold recognition and ab initio structure prediction.