Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions



Short description: 
SURPASS coarse-grained protein model of low-resolution


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).


Below, schematic illustration presents the projection from all-atom to coarse-grained SURPASS representation for two protein fragments: helical (left panel) and β-strand (right panel). 




The movie below shows example protein folding simulation using SURPASS model for 2gb1 protein system.