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CPHmodels-3.0—remote homology modeling using structure-guided sequence profiles

By Morten Nielsen, Claus Lundegaard, Ole Lund and Thomas Nordahl Petersen

Abstract

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile–profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models for 94% of the targets (117 out of 128), 74% were predicted as high reliability models (87 out of 117). These achieved an average RMSD of 4.6 Å when superimposed to the 3D structure. The remaining 26% low reliably models (30 out of 117) could superimpose to the true 3D structure with an average RMSD of 9.3 Å. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is <20 min. The web server is available at http://www.cbs.dtu.dk/services/CPHmodels/

Topics: Articles
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:2896139
Provided by: PubMed Central

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Citations

  1. (2003). 3D-Jury: a simple approach to improve protein structure predictions.
  2. (2009). A generic method for assignment of reliability scores applied to solvent accessibility predictions.
  3. (2008). A multi-template combination algorithm for protein comparative modeling.
  4. (1995). Evaluation of comparative protein modelling by MODELLER.
  5. (2008). Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre.
  6. (1993). Improved prediction of protein secondary structure by use of sequence profiles and neural networks.
  7. (2000). Improving the quality of twilight-zone alignments.
  8. (1998). Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases.
  9. (1995). Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution.
  10. (2000). Prediction of protein secondary structure at 80% accuracy.
  11. (1998). Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
  12. (2007). Real-SPINE: an integrated system of neural networks for real-value prediction of protein structural properties.
  13. (1992). Selection of representative protein data sets.
  14. (2005). The HHpred interactive server for protein homology detection and structure prediction.
  15. (2008). Using multiple templates to improve quality of homology models in automated homology modeling.