Bogdan Barz
University of Düsseldorf
40 Papers
176 Citations
Bogdan Barz is an academic researcher from University of Düsseldorf. The author has contributed to research in topics: Protein aggregation & Chemistry. The author has an hindex of 17, co-authored 37 publications. Previous affiliations of Bogdan Barz include Drexel University & University of Missouri.
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Papers
Dimer formation enhances structural differences between amyloid β-protein (1-40) and (1-42): an explicit-solvent molecular dynamics study.
Bogdan Barz,Brigita Urbanc +1 more
TL;DR: Here, a large ensemble of DMD–derived A and A monomers and dimers was subjected to fully atomistic molecular dynamics simulations using the OPLS-AA force field combined with two water models, SPCE and TIP3P, and the resulting all-atom conformations were slightly larger, less compact, had similar turn and lower -strand propensities than those predicted by DMD.
MUFOLD: A new solution for protein 3D structure prediction
TL;DR: A systematic protocol was developed to identify useful templates and fragments from Protein Data Bank for a given target protein, and an efficient process was applied for iterative coarse‐grain model generation and evaluation at the Cα or backbone level, which shows significant and systematic improvement over previous methods.
85
Kinetic Monte Carlo and cellular particle dynamics simulations of multicellular systems
TL;DR: Two computer simulation methods are formulated: a kinetic Monte Carlo (KMC) and a cellular particle dynamics (CPD) method, which are capable of describing and predicting the shape evolution in time of three-dimensional multicellular systems during their biomechanical relaxation.
73
A kinetic approach to the sequence-aggregation relationship in disease-related protein assembly.
TL;DR: Molecular dynamics simulations are performed to follow peptide aggregation on the microsecond time scale and identify transition networks, disconnectivity graphs, and first passage time distributions to describe the kinetics of the assembly process.
72
Calculating potentials of mean force and diffusion coefficients from nonequilibirum processes without Jarzynski's equality
TL;DR: In this paper, a simple and efficient method, referred to as the FR method, was proposed for calculating simultaneously both the PMF U(z) and the corresponding diffusion coefficient D(z), along a reaction coordinate z for a classical many particle system by employing a small number of fast SMD pullings in both forward (F) and time reverse (R) directions, without invoking JE.