Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions


Optimization of protein models


Wiley Interdisciplinary Reviews: Computational Molecular Science, 2:479–493, 2012


Protein structure predictions, and experimentally derived protein structures, very often require certain structure improvement (refinement), which means bringing it closer to real, usually in vivo working conformations. In respect to the variety of protein models to be refined, computational optimization procedures could be divided into localized (applied to a small part of a structure) and global (whole structure). Generally speaking, the first problem is usually tractable, and the latter remains to be extremely challenging for systems larger then peptides or small proteins: optimization complexity and difficulty dramatically increase with the size of structures to be optimized.