MMBC may perform whatever types of molecular modeling, simulations, calculation, analysis, and design that are necessary for understanding detailed protein structures and mechanisms and/or to design promising biopharmaceutical candidates. The used computational techniques include but not limited to:
- Homology modeling
- Ab initio protein structure prediction
- Molecular docking
- Protein-protein docking and interaction free energy evaluation
- Molecular dynamics (MD) simulation
- Targeted MD simulation
- Monte Carlo simulation
- Brownian dynamics simulation
- Free energy perturbation (FEP)
- FEP simulations of transition states
- Multi-scaling computational simulations on complex biological systems
- First-principles quantum mechanical (QM) calculations
- QM calculations that accurately account for solvent environment effects
- Hybrid QM/MM calculations
- QM/MM-free energy (QM/MM-FE) calculations
- Potential-of-mean-force (PMF) calculations
- Molecular mechanics (MM)-based MD simulation on a transition state
- QM/MM based MD simulations and PMF calculations
- MM/Poisson-Boltzmann Surface Area (MM/PBSA) binding free energy calculations
- MM/Generalized Born Surface Area (MM/GBSA) binding free energy calculations
- QM/MM-PBSA and QM/MM-GBSA binding free energy calculations
- Ligand- and structure-based virtual screening of compound libraries
- Virtual screening of virtual biopharmaceutical candidates
- Transition-state based virtual screening
- De novo design of novel compounds
- Quantitative structure-activity relationship (QSAR) analysis
- Artificial neural network (ANN) analysis
- Druggability analysis
- ADME (absorption, distribution, metabolism, and excretion) profiling
- Toxicity prediction (to predict a variety of toxicities)
- Blood-brain barrier (BBB) permeability prediction