Services & Resources

We offer a number of specific (cheminformatics-related) projects with focus in these areas: ontology development, structure-based drug design, biological categorization and analysis of screening data, systematic data modeling and analysis of very large chemical structure-activity data sets, library diversity analysis and design, structure-activity data visualization, modeling of adverse drug reactions and toxicity, in-silico synthetic chemistry, machine learning, algorithm development, chemoinformatics software development and integration. Projects are suitable for graduate- and undergraduate level research of students with interest in pharmacology, biology, biochemistry, computer science and engineering, computational chemistry, or synthetic chemistry.

Our capabilities include:

Screening data

  • Analysis and interpretation of small molecule high‐throughput screening data
  • Analysis / visualization of structure activity relationships (SAR)
  • Guidance to follow‐up on experimental screening results

Ligand‐based methods

  • Development and interpretation of small molecule activity and small molecule property data(model‐based, model free, statistical and non‐statistical); QSAR QSPR
  • Computation / prediction of physicochemical properties and numerous chemical andphysicochemical descriptors (e.g. Lipinski, ADME, lead‐likeness, pKa, membrane permeability,toxicity flags; topological, geometric, electronic, pharmacophoric properties)
  • Virtual screening / prioritization of commercially available compounds
  • Development pharmacophore models, pharmacophore elucidation, and pharmacophorebasedvirtual screening

Diversity / virtual libraries

  • Generation and screening of (chemically feasible) virtual libraries
  • Design of focused screening libraries
  • Diversity analysis and visualization of compound libraries

Structure‐based methods

  • Prediction, analysis and characterization of small‐molecule protein interactions (docking,binding energies, interaction features)
  • Development and optimization of protein structure models (homology modeling, molecularmechanics)
  • Molecular modeling (force fields, small molecule and protein structure minimization,conformer analysis, dynamics)

Please contact Stephan Schürer (sschurer@med.miami.edu) for details.