MMBC Molecular Modeling and Design

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