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


The Molecular Modeling and Biopharmaceutical Center seeks new opportunities to develop innovative research partnerships with UK investigators. For more information and to request services, please contact us.