Aims and scope

The Journal of Molecular Modeling publishes high quality specialized 3D molecular modeling studies that pass peer review and fall 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:

Computer-Aided Drug Design
 

• Computer-aided molecular design, rational drug design, de novo ligand design, receptor modeling and docking, molecular-dynamics simulations used for drug design.
  • Manuscripts that report new methodology are welcome, as are those that report new techniques and their validation. Extensive validation on a number of diverse datasets is necessary.
  • Studies that use commercially available techniques or web services for docking, ADMET evaluation or MD simulations are discouraged.
  • Protein structures used for docking studies must be equilibrated adequately using MD simulations of at least 500 ns.
  • At least 3 different conformations of the target (from multiple crystal structures or generated using an MD simulation of at least 500ns) must be used to generate consensus poses for docking studies.
  • Docked poses must again be proved stable using at least three MD simulations, each  of at least 200, or a single simulation of at least 500ns.
  • MD simulations should be analyzed to identify key interactions and provide a binding model for predictive drug design. Simply testing the short-term stability of the docked pose using RSMD or radius of gyration is discouraged.

• Homology modeling
  • Homology models are welcome if they are validated by adequate MD simulations (at least 500 ns).
• Simulation of proteins, DNA, carbohydrates and other biopolymers
  • Manuscripts that provide mechanistic insights or offer novel interpretation of the experimental data are welcome. Molecular-dynamics simulations must be run for at least 500ns and in triplicate (or correspondingly longer single simulations) and sampling convergence demonstrated.

• Modeling biological reaction mechanisms
  • Modeling studies of biological reaction mechanisms are welcome. Protein flexibility must be taken into account.

• Combined experimental/computational studies in which calculations play a dominant role
  • Manuscripts that place the main emphasis on the calculations and use them to provide information not available from experiment are welcome.
  • Manuscripts in which standard calculations are used as an adjunct to an otherwise experimental study are discouraged.

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.