AI Article Synopsis
- The Feig group presented their protein structure refinement process during CASP11, using molecular dynamics simulations with enhanced selection and averaging techniques.
- On average, they achieved modest improvement in protein structures, with some showing significant enhancements based on the initial models provided.
- They developed a new protocol that successfully refined local stereochemical features, resulting in high-quality structures with low MolProbity scores while requiring minimal computational resources.
Article Abstract
Protein structure refinement during CASP11 by the Feig group was described. Molecular dynamics simulations were used in combination with an improved selection and averaging protocol. On average, modest refinement was achieved with some targets improved significantly. Analysis of the CASP submission from our group focused on refinement success versus amount of sampling, refinement of different secondary structure elements and whether refinement varied as a function of which group provided initial models. The refinement of local stereochemical features was examined via the MolProbity score and an updated protocol was developed that can generate high-quality structures with very low MolProbity scores for most starting structures with modest computational effort. Proteins 2016; 84(Suppl 1):282-292. © 2015 Wiley Periodicals, Inc.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493977 | PMC |
| http://dx.doi.org/10.1002/prot.24871 | DOI Listing |
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