Design of the SURPASS (Single United Residue per Pre-Averaged Secondary Structure fragment) protein model is unique and strongly supported by the statistical analysis of structural regularities characteristic for protein systems. Coarse-graining of protein chain structures assumes a single center of interactions per residue and accounts for pre-averaged effects of four adjacent residue fragments. Knowledge-based statistical potentials encode complex interaction patterns of these fragments (knowledge-based statistics of the SURPASS force field can be downloaded from here). In order to increase the usability of the model, a non-trivial algorithm for the reconstruction of Cα-trace from SURPASS pseudo atoms was developed. The reconstructed alpha carbon positions reproduce the local geometry of the polypeptide chain and correct spatial orientation of secondary structure elements (knowledge-based SURPASS Rebuild Library, SUReLib, can be downloaded from here).
More details on the SURPASS model and its applications can be found in the following publications:
- SURPASS Low-Resolution Coarse-Grained Protein Modeling [DOI]
- The Interplay between Secondary Structure Propensities and Protein Fold Assembly [DOI]
- Reconstruction of higher resolution protein structures from deeply coarse-grained SURPASS models
The movie shows example protein folding simulation using SURPASS model for 2gb1 protein system.