dr hab. inż. Emilia Lubecka | Gdańsk University of Technology

Time-averaged restraints from nuclear magnetic resonance (NMR) measurements have been implemented in the UNRES coarse-grained model of polypeptide chains in order to develop a tool for data-assisted modeling of the conformational ensembles of multistate proteins, intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs), many of which are essential in cell biology. A numerically stable variant...

Secondary structure is a solid scaffold on which the three-dimensional structure of a protein is built. Therefore, care must be taken to reproduce the secondary structure as accurately as possible in the simulations of protein systems. In this chapter, we summarize the physics-based energy terms that govern secondary-structure formation, the auxiliary restraints on secondary structure derived from bioinformatics and from the experimental...

The third version of the UNRES web server is described, in which the range of biological macromolecules treated and calculation types has been extended significantly. DNA and RNA molecules have been added to enable the user to run simulations of their folding/hybridization and dynamics. To increase the accuracy of the simulated proteins models, the restraints on secondary structure have been enhanced to include the probabilities...

Coarse-grained models are nowadays extensively used in biomolecular simulations owing to the tremendous extension of size- and time-scale of simulations. The physics-based UNRES (UNited RESidue) model of proteins developed in our laboratory has only two interaction sites per amino-acid residue (united peptide groups and united side chains) and implicit solvent. However, owing to rigorous physics-based derivation, which enabled...

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups...