Venue:	Institute of Neurosciences and Biophysics 1, Cellular Biophysics Seminar-Room 249, 1st Floor, Building: 15.1, E-2
Start:	Wednesday, April, 16th, 2008
Time:	13.30 - 15.00 (1st lecture) 15.30 - 17.00 (2nd lecture)

April, 16^th, 2008 (Roomchange: IFF-Lecture Hall)

• Baumgärtner: Protein Simulations

After a short introduction to the phenomenology of membrane proteins, the various types of modeling of membrane proteins will be reviewed, including coarse-grained models and atomistic models. Simulations of the activities of membrane proteins will be dicussed in details. This includes the translocation and the insertion of proteins into lipid bilayer membranes, the aggregation of proteins in membranes, and the transport of ions and macromolecules across membranes mediated by membrane proteins. The physical concepts underlying these processes, as far as known, will be presented.

June, 11^th, 2008

• Zacharias (Bioinformatics and Comp. Biology, IU Bremen):
  Modelling protein-ligand binding using computational docking methods

The lecture will give an overview on current computational approaches to predict the structure of protein-protein complexes and the binding of organic ligands to proteins. Such methods can be useful in cases where experimental determination is difficult or too expensive. Ligand-receptor docking approaches are also frequently used to identify lead compounds for drug design. The lecture will include the concepts and algorithms of common docking approaches and will also cover methods to evaluate (score) docking solutions. Ligand binding to a receptor can involve conformational changes. However, due to the large computational demand required to include conformational flexibility many of the existing docking methodologies still employ rigid receptor structures. Approaches to efficiently include flexibility during docking searches will be introduced and possible future improvements and research directions will be discussed.

• Granzin: Protein Structure Prediction (homology modeling/comparative modeling) (Geb. 05.2, Eingang E4 im Raum 1020a, Kellergeschoss)

Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by a three-dimensional X-ray structure of the studied protein. Three-dimensional structure determinations of natural proteins are guided by 3 principles: "get enough protein", "get crystals of sufficient quality" and "get the phases". Comparative modelling relies on detectable similarity spanning most of the modelled sequence and at least one known X-ray structure. When the structure of one protein in the family has been determined by experiment, the other members of the family can be modelled based on their alignment to the known structure.

Keywords: Multiple Sequence Alignment, Database Searching, Secondary Structure Prediction, Protein Fold Recognition, Template Structure, Comparative Modelling, Model Assessment

July, 9^th, 2008

• Fischer (Institute of Biophotonics, School of Biomedical Science and Engeneering, National Yang-Ming University, Taiwan):
  Membranes and Their Proteins - in silico Investigations

Membrane proteins are difficult to crystallize and compared to soluble proteins, only for some of them the structures are resolved. Computer simulations may step in and bridge the time gap until more structures are available. But even if the structure of the protein is known it represents a snapshot of the conformational space the protein is covering throughout its mode of action. Again computational methods allow 'connecting' the snapshots and to derive a 'realistic' dynamics. The dynamics of drugs and their interaction with the target is an additional field for in silico developments.

A brief introduction to the world of membrane proteins will be given followed by the use of MD simulations in respect to membrane proteins. Docking tools for small molecule binding will be outlined. Computational work on viral membrane proteins forms the background of the lectures.