Pratical 1 - hands on UCSF Chimera

Molecular Manipulation and Visualization

Secondary structure - Binding site cavities - pka

Any computational modelling of biochemical processes starts with a good understanding of the structural properties of the biomolecules under study. Available pdb structures of the protein, their atomic resolution, their state of complexation are, in between others, of the key molecular variables to analyse prior to modelling. In this first tutorial, we will get familiar with a series of tools that can be used to visualize, explore and manipulate structural features of biological systems.

In a collaborative manner and helped by the teachers, you will initiate your practicals studying a series of human hormone receptors. In particular, we will begin with the structures of human androgen receptor binding protein (AR) (Pereira et al. Cantin L. et al. or Askew E. et al.). This part of the work will be performed using the program Chimera from the University of California San Franscisco.


  1. Look at the available structures of human androgen receptor binding protein at the Protein Data Bank (PDB - ) and download the structure of a HAR bound complexed with testosterone (2am9). Check the resolution of the structures and what is the experimental method used to characterize it.

  2. Once downloaded the structure, open the pdb file with a text editor and visualize it with the program chimera at the same time (You'll find the chimera icon in the shorcut widgets of your linux box). Discuss the different remarks mentioned in the pdb headers, how they could impact on the different kinds of modeling we talked about during the earlier weeks and eventually how you could solved some of these problems. For example, look for and at multiple rotamers of  residues, the position of the ligand in the binding site, the residues at close range with interaction with the ligand, the water molecules of interest, etc... Try to obtained a clear chemical map of the testosterone into the binding site of this receptor.

  3. Provide some clear pictural representations of 1) the protein on its whole 2) the binding site 3) the interactions of the binding site and any idea you have to get a 2dimensional impression of the 3dimensional reality.

  4. Once you have get used to with this initial structure, compare it with other crystalographic structures related to it. In this case aligning the proteins will be a particularly useful tools to do so. From the different interesting things we could do here, we can look at the structure obtained with different androgen like compounds (e.g. testosterone in pdb 2ama) compare the binding poses of the ligand for the different structure, also compared to some prostate treatment compound, with the structure some mutants of the protein that are resistant to prostate treatment, and finally with a progesterone binding protein. Discuss on the nature of the structures, the type of interactions between the ligand and the protein, etc.

  5. Assemble all the information gathered in this first practical like if you needed to present it to your classmates.

  6. Additional works:
Research of binding site cavity 

remove the ligand from the pdb file, go to the Q-sitefinder web site ([]) and enter your protein.  Discuss on the resulting pockets predicted

 Prediction of the pka of the residues


Go to the propka webpage and enter your protein pdb. Discuss on the outcome of the results propka provides in particular on the Histidine

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