Publications by authors named "Sebastian Kalinowski"
MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, RNA-modifying enzymes and location of modified residues in RNA sequences. In the current database version, accessible at http://modomics.genesilico.
View Article and Find Full Text PDFThe replica exchange (RE) method is increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. Recently, we implemented the united-residue UNRES force field for mesoscopic MD. Initial results from UNRES MD simulations show that we are able to simulate folding events that take place in a microsecond or even a millisecond time scale.
View Article and Find Full Text PDFArticle Synopsis
- The study focuses on improving the united-residue (UNRES) force field for predicting protein structures and folding processes.
- Researchers tested this improved force field on three specific protein models, addressing previous biases towards alpha-helical structures due to the neglect of conformational entropy in earlier versions.
- They introduced a hierarchical optimization method that organizes a protein's conformational space by degrees of native-like structure, enabling a more accurate representation of free energies and enhancing overall protein folding simulations.