Jens Erik Nielsen

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I am a senior lecturer in the School of Biomolecular and Biomedical Science at University College Dublin. My office and lab are located in the UCD Conway Institute.

Currently I am on a 5 year career break at Novozymes A/S in Copenhagen. To contact me please use my gmail address.


Research interests

My research interests are proteins and enzymes in particular. I like using both computational and experimental methods to solve a problem. Below you will find a list of my past and present projects. Most of the projects included experimental work at some point to verify our predictions, but occasionally you will find a purely theoretical project, or possibly a project where we haven't gotten around to validate the predictions yet.

Predicting and analysing the effects of point mutations on enzymatic activity

The ability of understand and predict the effects that point mutations have on the catalytic activity of an enzyme is of high importance for the understanding of the evolution of enzymes and for re-designing enzymes for industrial processes.

To construct an algorithm that can predict how point mutations affect enzymatic activity, it is necessary to collect large amounts of experimental data. Current online databases typically contain very limited amounts of experimental data that, in detail, describes the effect that a point mutation has on the catalytic activity of an enzyme. This is bad news for theoreticians since we therefore lack data that we can benchmark our calculations on.
We have sought to remedy this situation by constructing a software application (PEAT) that help experimental and theoretical researchers working with protein engineering/protein optimisation.

Protein Engineering Analysis Tool (PEAT)

PEAT consists of

Protein pKa calculations

One of my major interests is to understand the determinants of protein pKa values. For this purpose we have developed a quite substantial amount of software to study protein energetics.

  • Recently we have released the pKD webserver for predicting sets of mutations that change protein pKa values in a desired direction.
  • pKaTool is another little nifty piece of software. pKaTool lets you study artificial systems of titratable groups, and will also help you understand the results of the pKD server and WIpKa.
  • I am also the author of the WHAT IF pKa calculation package (WIpKa), which is a part of the WHAT IF package. WIpKa allows you to calculate the pKa values of protein residues. WIpKa works particularly well for buried residues and enzyme active site residues.

Protein Electrostatics

Connected with the effort to understand the factors governing protein pKa values is the PDB2PQR project. This project is a collaboration with Nathan Baker in St. Louis and Jan Jensen in Copenhagen. The PDB2PQR Server converts (almost) any PDB file to a PQR file suitable for protein electrostatics calculations.

Enzyme Dynamics

Proteins are dynamic entities, and it has been hypothesized that the dynamic properties of enzymes are of special importance for their catalytic efficiency. In the present project we are using MD simulations, normal-mode analysis and home-wound tools to analyze the dynamic properties of enzymes.

Protein kinase activation

Protein kinase activation is an area of immense importance for signal transduction and cell regulation. We are investigating protein kinases using computer simulation methods, in order to elucidate the structural features that allow protein kinases to undergo activation. In the future it is likely that we will embark on an experimental project to test the hypotheses that we have developed during our computer studies.

Past projects

  • Protein folding and stability: The " FOLD-X server.
  • Chitinase A pKa Calculations


If you are really bored you could look at my Hotlist, check my publication list, my CV, or you could look at where I've worked before.

Contact details

My Email address is "Jens.Nielsen" at "" and you can find by PGP public key here.

My mail address is:
Jens Erik Nielsen
School of Biomolecular and Biomedical Science

Centre for Synthesis and Chemical Biology
UCD Conway Institute
University College Dublin
Dublin 4

Tel: +353 1 716 6724

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