Thursday, October 31, 2013

PhD position in molecular modeling at University of Copenhagen

Do you want to help prevent drug resistance in viral diseases?

PhD Scholarship available at the University of Copenhagen, Denmark

A PhD position in in Molecular Simulations and Computational Biology is available from January 1, 2014 at the Department of Biology, University of Copenhagen, Denmark. The aim of the project is to study how drug resistance mutations in pathogenic viruses arise and how resistance can be circumvented. The students will work under the primary supervision of Kresten Lindorff-Larsen in tight collaboration with experimental groups both here and abroad.

The PhD student will use a range of methods from computational structural biology to study the interactions of viral drug targets with drug molecules. The goal is to predict and understand how mutations can give rise to drug resistance, and to validate and integrate experimental data in such studies. The student will combine high-throughput calculations with more detailed molecular dynamics simulations to study the interactions between drug molecules and their targets.

It is essential that the candidate has a strong background in protein science and in using computational methods to study e.g. protein structure, function and dynamics. Applicants should hold an MSc degree, and research experience with molecular modelling of proteins or other biomacromolecules is a prerequisite. Hands-on research experience in e.g. molecular dynamics simulations and free energy calculations is a distinct advantage as is experience in computational studies of protein-ligand/drug interactions. Good interpersonal and communication skills. The working language in the group is English, and the candidate must master both written and spoken English.

For further information about the PhD position including salary, the complete set of requirements and how to apply see the full ad at:

The deadline for applications is Dec 1, 2013.

Further information can also be obtained via email to Associate Professor Kresten Lindorff- Larsen, e-mail: , website: 

Thursday, October 3, 2013

Computational Chemistry Course - Exploring a PES

I made this video to illustrate the basic ideas behind the generation of a reaction profile. I show how to "explore" the potential energy surface for a basic Diels-Alder reaction.

The small animations were produced visualizing with Molden actual calculation done with Gaussian at HF/sto-3g level and screencasted with ScrenFlow. The entire video is another ScreenFlow capture of a PowerPoint presentation with my voice over.