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

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 A ̊ when superimposed to the 3D structure. The remaining 26 % low reliably models (30 out of 117) could super-impose 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 per-forming 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 a