Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
Discovery and design of soft polymeric bio-inspired materials with multiscale simulations and artificial intelligence
Materials chemistry is at the forefront of the global “Fourth Industrial Revolution”, in part by
establishing a “Materials 4.0” paradigm. A key aspect of this paradigm is develo** …
establishing a “Materials 4.0” paradigm. A key aspect of this paradigm is develo** …
Spin-state energetics of heme-related models from DFT and coupled cluster calculations
M Radon - Journal of Chemical Theory and Computation, 2014 - ACS Publications
Spin-state energetics of metalloporphyrins and heme groups is elucidated by performing
high-level coupled cluster calculations for their simplified mimics. An efficient computational …
high-level coupled cluster calculations for their simplified mimics. An efficient computational …
Approaching the Complete Basis Set Limit for Spin-State Energetics of Mononuclear First-Row Transition Metal Complexes
G Drabik, M Radoń - Journal of Chemical Theory and …, 2024 - ACS Publications
Convergence to the complete basis set (CBS) limit is analyzed for the problem of spin-state
energetics in mononuclear first-row transition metal (TM) complexes by taking under scrutiny …
energetics in mononuclear first-row transition metal (TM) complexes by taking under scrutiny …
Spin-state energetics of Fe (III) and Ru (III) aqua complexes: Accurate ab initio calculations and evidence for huge solvation effects
M Radon, K Gąssowska, J Szklarzewicz… - Journal of Chemical …, 2016 - ACS Publications
Aqua complexes of transition metals are useful models for understanding the electronic
structure of metal-oxide species relevant in photocatalytic water splitting. Moreover, spin …
structure of metal-oxide species relevant in photocatalytic water splitting. Moreover, spin …
PEPCONF, a diverse data set of peptide conformational energies
We present an extensive and diverse database of peptide conformational energies. Our
database contains five different classes of model geometries: dipeptides, tripeptides, and …
database contains five different classes of model geometries: dipeptides, tripeptides, and …
Disordered peptide chains in an α-C-based coarse-grained model
Ł Mioduszewski, M Cieplak - Physical Chemistry Chemical Physics, 2018 - pubs.rsc.org
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 …
intrinsically disordered proteins at significantly longer timescales than in the all-atom …
Experimental and Computational Insight into the Mechanism of NO Binding to Ferric Microperoxidase. The Likely Role of Tautomerization to Account for the pH …
M Oszajca, G Drabik, M Radon, A Franke… - Inorganic …, 2021 - ACS Publications
According to the current paradigm, the metal–hydroxo bond in a six-coordinate porphyrin
complex is believed to be significantly less reactive in ligand substitution than the analogous …
complex is believed to be significantly less reactive in ligand substitution than the analogous …
Intrinsically Disordered Malaria Antigens: An Overview of Structures, Dynamics and Molecular Simulation Opportunities
PCC Silva, L Martínez - Journal of the Brazilian Chemical Society, 2024 - SciELO Brasil
The proteome of Plasmodium falciparum (Pf) is abundant in intrinsically disordered proteins
(IDPs). Their important roles in the malaria life cycle and the limitations of experimental and …
(IDPs). Their important roles in the malaria life cycle and the limitations of experimental and …
Predicting Spin States of Iron Porphyrins with DFT Methods Including Crystal Packing Effects and Thermodynamic Corrections
M Radoń - Physical Chemistry Chemical Physics, 2024 - pubs.rsc.org
Accurate computational treatment of spin states for transition metal complexes, exemplified
by iron porphyrins, lies at the heart of quantum bioinorganic chemistry, but at the same time …
by iron porphyrins, lies at the heart of quantum bioinorganic chemistry, but at the same time …