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Protein Analysis and Design Group @ UCD

Principal Investigator: Jens Erik Nielsen

What We Do

Proteins and enzymes in particular are highly sophisticated molecules that play important roles in all aspects of life. We work on developing accurate theoretical models for predicting biophysical characteristics of proteins and enzymes. We do this to understand how enzymes and proteins work, and to figure out how we can manipulate them to help us cure diseases or improve their use industrial processes.

We are particularly interested in re-engineering enzymatic pH-activity profiles and in understanding the determinants of enzyme catalytic activity, but we invest significant efforts in developing tools for many other areas of protein function.


We develop a a large number of software packages, that are in various stages of usefulness. Below is a short overview of current and past software development projects for biomolecular simulation and structural bioinformatics.

  • PEAT Protein Engineering Analysis Tool
    • PEAT_DB - Database
    • PEAT_SA - Structure Analysis (protein stability, protein-ligand binding, protein delta pKa values)
  • MDAT - Molecular Dynamics Analysis Tool
  • pKaTool - Analysis and execution of protein pKa calculations
  • GoodVibes - Prediction of residues of importance for protein dynamics

To find out more look in the Software section.


If you are interested in finding out more about us and what we do, then visit the sections below

  • Group members - List of current and former group members
  • Science - Descriptions of our current research projects
  • Teaching - Informations on the courses Jens teaches
  • Software - Links to all our software packges
  • Links - Links to outside resources and collaborators

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