301 citations · 2.5k across the 73 of their papers we have counts for
73 papers
Contact-based molecular dynamics of structured and disordered proteins in a coarse-grained model: fixed contacts, switchable contacts and those described by pseudo-improper-dihedral angles
Łukasz Mioduszewski, Jakub Bednarz, Mateusz Chwastyk +1
We present a coarse-grained C-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential…
Conformational Biases of α-Synuclein and Formation of Transient Knots
Mateusz Chwastyk, Marek Cieplak
We study local conformational biases in the dynamics of α-synuclein by using all-atom simulations with explicit and implicit solvents. The biases are related to the frequency of th…
Self-assembly of model proteins into virus capsids
Karol Wolek, Marek Cieplak
We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RN…
Disordered peptide chains in an α-C-based coarse-grained model
Łukasz Mioduszewski, Marek Cieplak
We construct a one-bead-per-residue coarse-grained dynamical model to describe intrinsically disordered proteins at significantly longer timescales than in the all-atom models. In…
Proteins at air-water and oil-water interfaces in an all-atom model
Yani Zhao, Marek Cieplak
We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interfac…
Structural entanglements in protein complexes
Yani Zhao, Mateusz Chwastyk, Marek Cieplak
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behav…