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CASP11 – An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline
| Content Provider | PubMed Central |
|---|---|
| Author | Fischer, Axel W. Heinze, Sten Putnam, Daniel K. Bian, Li Pino, James C. Xia, Yan Lopez, Carlos F. Meiler, Jens |
| Editor | Zhang, Yang |
| Copyright Year | 2016 |
| Abstract | In silico prediction of a protein’s tertiary structure remains an unsolved problem. The community-wide Critical Assessment of Protein Structure Prediction (CASP) experiment provides a double-blind study to evaluate improvements in protein structure prediction algorithms. We developed a protein structure prediction pipeline employing a three-stage approach, consisting of low-resolution topology search, high-resolution refinement, and molecular dynamics simulation to predict the tertiary structure of proteins from the primary structure alone or including distance restraints either from predicted residue-residue contacts, nuclear magnetic resonance (NMR) nuclear overhauser effect (NOE) experiments, or mass spectroscopy (MS) cross-linking (XL) data. The protein structure prediction pipeline was evaluated in the CASP11 experiment on twenty regular protein targets as well as thirty-three ‘assisted’ protein targets, which also had distance restraints available. Although the low-resolution topology search module was able to sample models with a global distance test total score (GDT_TS) value greater than 30% for twelve out of twenty proteins, frequently it was not possible to select the most accurate models for refinement, resulting in a general decay of model quality over the course of the prediction pipeline. In this study, we provide a detailed overall analysis, study one target protein in more detail as it travels through the protein structure prediction pipeline, and evaluate the impact of limited experimental data. |
| Related Links | http://dx.doi.org/10.1371/journal.pone.0152517 |
| Starting Page | 152517 |
| File Format | |
| ISSN | 19326203 |
| e-ISSN | 19326203 |
| Journal | PLoS ONE |
| Issue Number | 4 |
| Volume Number | 11 |
| Language | English |
| Publisher | Public Library of Science |
| Access Restriction | Open |
| Rights Holder | Public Library of Science |
| Subject Keyword | Research in Higher Education |
| Content Type | Text |
| Resource Type | Article |
| Subject | Multidisciplinary |
