Coarse-grained protein models and their applications

S Kmiecik, D Gront, M Kolinski, L Wieteska… - Chemical …, 2016 - ACS Publications
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 …

Discovery and design of soft polymeric bio-inspired materials with multiscale simulations and artificial intelligence

C Zhai, T Li, H Shi, J Yeo - Journal of Materials Chemistry B, 2020 - pubs.rsc.org
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** …

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 …

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 …

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 …

PEPCONF, a diverse data set of peptide conformational energies

VK Prasad, A Otero-de-La-Roza, GA DiLabio - Scientific data, 2019 - nature.com
We present an extensive and diverse database of peptide conformational energies. Our
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 …

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 …

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 …

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 …