Molecular Modeling Connect is an international, peer-reviewed, open-access journal dedicated to advancing the theory, methods, and applications of molecular modeling and simulation. The journal provides a forum for high-quality research that deepens our understanding of molecular systems and supports the rational design of molecules, materials, and biological therapeutics. Submissions should demonstrate scientific rigor, methodological transparency, and clear relevance to molecular modeling or simulation.
Core Areas of Interest
The journal focuses on computational molecular modeling and simulation, with particular emphasis on the following areas:
- Molecular dynamics and enhanced sampling methods
- Free-energy calculations and alchemical transformations
- Quantum chemistry, QM/MM, and multiscale modeling approaches
- Molecular docking, virtual screening, and structure-based design (see quality expectations below)
- Protein structure prediction, protein–ligand and protein–protein interactions
- Machine learning and artificial intelligence methods applied to molecular modeling, property prediction, and generative molecular design
- Computational materials modeling and soft-matter simulation
- Development, validation, and benchmarking of computational methods, force fields, and software tools
- Analysis, visualization, and interpretation of molecular simulation data
Quality Expectations for Docking and Related Studies
In line with established practices in the field, Molecular Modeling Connect generally does not consider straightforward applications of molecular docking to a single target system that lack adequate complementary evidence. The availability of an experimental structure does not, by itself, constitute sufficient validation of a predicted interaction.
Docking-based studies are expected to include meaningful additional support, such as molecular dynamics simulations, free-energy estimates, rigorous protocol validation, consensus approaches, or relevant experimental data. Purely speculative or minimally validated docking investigations fall outside the journal's scope.
Article Types
The journal welcomes:
- Original research articles
- Reviews and mini-reviews
- Perspectives and opinion pieces
- Methodological and technical notes