The Journal of Molecular Modeling publishes all quality science that passes peer review and falls within the scope of the journal. Because of the number of manuscripts submitted to the journal and the high rejection rate, the following guidelines are provided to help assess your own work:
Life Science Modeling
- Computer-aided molecular design, rational drug design, de novo ligand design, receptor modeling and docking, QSAR, QSPR and ADME modeling.
o Manuscripts that report fundamentally new methodology or provide experimental confirmation of the results are welcome, as are those that report new techniques and their validation. Those that use only commercially available techniques are discouraged.
o For docking studies, at least 3 different conformations of the target (from multiple crystal structures or generated using an MD simulation of at least 10ns) must be used to generate consensus poses. Docked poses must again be confirmed using MD simulations of at least 5-10 ns if there is no experimental validation.
o Homology models are welcome if they are validated by adequate MD simulations.
- Simulation of proteins, DNA, carbohydrates and other biopolymers
o Manuscripts that provide mechanistic insights or offer novel interpretation of the experimental data are welcome. Molecular-dynamics simulations must be run for at least 20ns and in triplicate (or correspondingly longer single simulations) and sampling convergence demonstrated.
- Modeling biological reaction mechanisms
o Models of biological reaction mechanisms that treat both the Hamiltonian and the conformational sampling adequately are welcome.
- Combined experimental/computational studies in which calculations play a major role
o Manuscripts that place the main emphasis on the calculations and use them to provide information not available from experiment are welcome.
- Classical or quantum mechanical modeling of materials, their mechanical and physical properties.
o Studies of proposed new compounds that clearly demonstrate and document that there is a rational basis for investigating them are welcome. Standard applications on hypothetical systems of no practical relevance will not be considered.
- Modeling zeolites, layered minerals etc.
- Modeling catalytic reaction mechanisms and computational catalysis optimization
- 3D polymer modeling
- Nanomaterials, fullerenes and nanotubes
o State of the art work on nanomaterials that goes beyond applications of standard methodology is welcome.
- New classical or quantum mechanical techniques and parameter sets, including ab initio DFT and semiempirical MO-methods, basis sets etc.
- New hybrid QM/MM techniques
- New visualization techniques for 3D molecular modeling
- New methods for modeling biopolymers
- New software and new versions of existing software
- New techniques for simulating environments or solvent
- Classical and quantum mechanical modeling of chemical structures and reactions
o Studies of interest to the modeling community that report significant new results of high chemical interest are welcome. Standard studies that reproduce experimental data will not be considered.
- Molecular recognition and sensors (taking conformational sampling into account)
- Conceptual and Computational Developments on Chemical Structure and Reactions
Please do not hesitate to contact the editorial office if you are in doubt as to whether your work falls within the scope of the Journal.