Schrödinger Workshop: Latest developments and power use - Training
Schrödinger Workshop: Latest developments and power use
|Date:||14.05.2013 9:00 - 14.05.2013 17:00|
Schrödinger Senior Scientist and Annette Höglund
Introduction to selected advanced features of the Schrödinger Maestro Suite.
13th May 2013, at CSC
09.00 – 11.30 Protein Based Modelling(Glide, SiteMap, Induced Fit Docking, VSW, Consensus-IFD)
Latest advancements in Glide Docking will be covered, looking at individual options in the interface. SiteMap will be illustrated using the ATPase active site cavity – we will explore how to design optimal kinase compounds based on size and properties using the informative maps in the active site region. A TACE example showing how loops can be refined to accommodate the TACE selective ligand will be used to illustrate the use of the Prime Refinement protocol. Induced Fit Docking will then be discussed to show full protein modelling and flexibility in order to illustrate how this process is a natural progression in Docking Campaigns. A recent paper on consensus-induced fit docking will be discussed to show on-going research efforts in this important area.
11.30 – 12.00 Productivity(Knime Extensions Workflows)
Selected Knime workflows will be discussed with emphasis on Structure and Ligand Based Screening exploiting some of the GUI tasks tackled during the workshop session.
12.00 – 13.00 Lunch
13.00 – 15.00 Ligand Based Modelling
(E-Pharmacophores, Shape Screening, Canvas for Libraries)
We will discuss selected aspects of Ligand Based Design that illustrate the use of many features: energetic-based pharmacophores considering the Protein environment; Shape based screening; Library comparisons analysis and hole-filling. These methods will address the questions of Lead Finding and deciding which lead series to move on with during a screening campaign.
15.00 – 17.00 Protein-Protein Modelling(BioLuminate, Antigen/Antibody, Protein Preparation, Aggregation, Residue Scanning)
Using the BioLuminate interface we will illustrate protein-protein modelling through an antigen/antibody example and discuss the individual steps involved such as homologue-searches, CDR loop clustering and H3-loop predictions. Protein structure quality and analysis will be looked at including how to further relax the protein in the instance of steric clashes. We will examine aspects of aggregation prediction and finally residue scanning for predicting protein stability.