Abstract
Summary: Model Quality Assessment Programs (MQAPs) are used to predict the quality of modeled protein structures. These usually use two approaches: methods using consensus of many alternative models and methods requiring only a single model to do its prediction. The consensus methods are useful to improve overall accuracy; however, they frequently fail to pick out the best possible model and cannot be used to generate and score new structures. Single-model methods, on the other hand, do not have these inherent shortcomings and can be used to both sample new structures and improve existing consensus methods. Here, we present ProQM-resample, a membrane protein-specific single-model MQAP, that couples side-chain resampling with MQAP rescoring by ProQM to improve model selection. The side-chain resampling is able to improve side-chain packing for 96% of all models, and improve model selection by 24% as measured by the sum of the Z-score for the first-ranked model (from 25.0 to 31.1), even better than the state-of-the-art consensus method Pcons. The improved model selection can be attributed to the improved side-chain quality, which enables the MQAP to rescue good backbone models with poor side-chain packing.Availability and implementation: http://proqm.wallnerlab.org/download/.Contact: bjornw@ifm.liu.seSupplementary information: Supplementary data are available at Bioinformatics online.
Highlights
Protein structure modeling represents a fundamental challenge in structural bioinformatics and is crucial for a detailed understanding of the structure and biological function of molecules
The consensus methods are useful to improve overall accuracy; they frequently fail to pick out the best possible model and cannot be used to generate and score new structures
We present ProQM-resample, a membrane protein-specific single-model Model Quality Assessment Programs (MQAPs), that couples side-chain resampling with MQAP rescoring by ProQM to improve model selection
Summary
Protein structure modeling represents a fundamental challenge in structural bioinformatics and is crucial for a detailed understanding of the structure and biological function of molecules. External programs were used to calculate features, e.g. PSI-BLAST (Altschul et al, 1997), PSIPRED (McGuffin et al, 2000), Naccess (Hubbard and Thornton, 1993), Stride (Frishman and Argos, 1995), ProQres (Wallner and Elofsson, 2006), Zpred (Granseth et al, 2006), Topcons (Bernsel et al, 2009), MPRAP (Illergard et al, 2010) and SVM-light (Joachims, 2002). These dependencies made it difficult to distribute the program, run large batches and use it in conformational sampling. ProQM-resample uses the repack protocol to sample side-chain conformations followed by rescoring using ProQM to improve model selection
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