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New UNRES force field package with Fortan 90

Lubecka E. A., Liwo A.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2016

Vol. 20, No 4

399--408

UNRES is a coarse-grained model of polypeptide chains. Until now, each version of UNRES (UNRESPACK v.3.2 and earlier ones) has been written in Fortran 77. Due to the fact that Fortran 77 enables us to use only static arrays, the Fortran 77 version has significant memory problems, and consequently, UNRESPACK has had to be split into many programs. Our recent work was focused on creating a new UNRES package with Fortran 90 (UNRESPACK v.4.0), based on the previous Fortran 77 versions. Fortran 90 provides dynamic memory allocation, user defined data types, and structuring the code into modules which encompass subroutines, functions, and variables. Moreover, Fortran 90 adds internal functions and subroutines, providing greater flexibility. The whole code of UNRES with Fortran 90 has been restructured, so that it now consists of modules that can be assembled to create the main simulation program and companion programs. This approach enabled us to eliminate the redundancy of the code, while keeping all functions of the package.

Mechanical unfolding of Ddfln4 studied by coarse-grained knowledge-based cabs model

Kouza M., Jamroz M., Gront D., Kmiecik S., Koliński A.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2014

Vol. 18, No 4

373--378

Mechanical unfolding of the fourth domain of Distyostelium discoideum fi lamin ( DDFLN 4) was studied using a CABS – coarse-grained knowledge-based protein model. Our study demonstrates that CABS is capable of reproducing the unfolding free energy landscape of protein unfolding and highlights an important role of non-native interacti ons in the protein unfolding process. The obtained three peaks in the force-extension profile suggest a four-state picture of DDFLN 4 protein unfolding and correspond reasonably to the results of the all-at om simulation in explicit solvent.

Coarse-grained modeling of protein structure, dynamics and protein-protein interactions

Koliński A., Kmiecik S., Jamróz M., Błaszczyk M., Kouza M., Kurciński M.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2014

Vol. 18, No 3

219--229

Theoretical prediction of protein structures and dynamics is essent ial for understanding the molecular basis of drug action, metabolic and signaling pathway s in living cells, designing new technologies in the life science and material sciences . We developed and validated a novel multiscale methodology for the study of protein folding proces ses including flexible docking of proteins and peptides. The new modeling technique starts fr om coarse-grained large-scale simulations, followed by selection of the most plausible final structu res and intermediates and, finally, by an all-atom rectification of the obtained structures. Except f or the most basic bioinformatics tools, the entire computational methodology is based on the models an d algorithms developed in our lab. The coarse-grained simulations are based on a high-resol ution lattice representation of protein structures, a knowledge based statistical for ce field and efficient Monte Carlo dynamics schemes, including Replica Exchange algorithms. This p aper focuses on the description of the coarse-grained CABS model and its selected applications.