This study reviews and analyzes the different AI-based strategies used to model protein structure and dynamics and simulate macromolecular assemblies, comparing them with traditional methods, and shows that hybrid solutions and combinations of methods can be devised to maximize their strengths.
Margherita Bini, Valentina Tozzini· Frontiers in Molecular Biosc...· 0 citations
The cluster expansion is a widely used approach for predicting the finite-temperature thermodynamics of alloys from zero-kelvin first-principles calculations, but its conventional formulation becomes intractable for materials with more than three or four chemical species. High-entropy alloys have therefore remained lar...
Yann L. Müller, Claire A. Paetsch, A. Natarajan· 1 citation
We present a method for efficiently predicting approximate binary convex hulls through the automatic generation of a minimal basis set of representative structural templates. The approach is based on the assumption that chemical space can be partitioned into a limited number of regions with similar bonding characterist...
Caja Annweiler, Alessandro Serafini, Simone di Cataldo et al.· npj Computational Materials· 0 citations
First-principles calculations play a pivotal role in contemporary chemical studies. The most commonly employed algorithms are based on density functional theory (DFT), and in certain instances, the Hartree-Fock method is also utilized. Although these two methods can efficiently yield accurate results for small-to-mediu...
Developing accurate coarse-grained (CG) molecular models is crucial for constructing databases of complex chemical molecules and enabling data-driven research. Here we present the OLJCG model for small organic molecules, with Lennard-Jones (LJ) parameters optimized via the Lennard-Jones Static Potential Matching method...
Ren-Jie Zhu, Tong Zhu, Rui-Bo Wu et al.· Journal of Physical Chemistr...· 0 citations
We present SMartini, an automated pipeline for deriving Martini 3 coarse-grained force-field parameters for arbitrary small molecules. Starting from a molecular structure or a SMILES string, the pipeline maps the all-atom molecule onto a coarse-grained bead representation and automatically fits both bonded and non-bond...
Danis Yangaliev, S. B. Ozkan· bioRxiv· 0 citations
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