Schrödinger Senior Applications Scientist Jas Bhachoo will be conducting workshops in Computational Chemistry and Protein Modeling on June 4th - 5th, 2013 at The Centre de Serveis Científics i Acadèmics de Catalunya (CESCA) in Barcelona, Spain, http://www.cesca.cat/
Schedule
Tuesday, June 4th, 2013 – All day session 9.30 – 17.00
09.30 Welcome and Introduction
09.45 Session I: Lead finding – Exploring Various Approaches with Ligand-based Methods (Hands-on Session)
- Tools to be used: e-Pharmacophores, Phase, Canvas
- 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 comparison 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.
12.15 Local Schrödinger User Presentation
- Maria José Ojeda - Nutrigenomics Research Group (Dr Gerard Pujadas), Biochemistry and Biotechnology Department, Universitat Rovira i Virgili "Identification of Novel Human Dipeptidyl Peptidase-IV Inhibitors of Natural Origin (Part I): Virtual Screening and Activity Assays."
12.45 Lunch Break
14.00 Session II: Discussion of Latest Scientific Papers / Projects from Schrödinger
- Approaches to Improve Virtual Screening Enrichments: Protein Preparation, Consensus IFD, Ensemble Docking and Data Fusion
- Tools/Methods to be discussed: Protein Prep Wizard Settings, Shape and IFD, MD, SiteMap, Clustering, Glide, Shape, FingerPrints in Canvas
- Type II Kinase Inhibitors in Parkinson's Disease LRRK2
- Tools/Methods to be discussed: Desmond-Meta Dynamics
17.00 Close
Wednesday, June 5th, 2013 – Morning session 9.30 – 13.00
9.30 Welcome and Introduction
9.45 Facilitating Structure-based Biologics Design: An Introduction to BioLuminate (Hands-on Session)
- Tools to be used: BioLuminate
- Using the BioLuminate interface we will illustrate protein-protein modeling 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. Finally, will examine aspects of aggregation-prediction and residue scanning for predicting protein stability.
- Discussion of Recent Schrödinger Project: Modeling Protein-Peptide Affinities with Various QSAR Approaches and Sequence Based QSAR Approaches.
- Tools to be discussed: SiteMap, FBQSAR, QSAR, Prime, BioLuminate
13.00 Close
Registration
This workshop is being offered free of charge, but your registration is needed as space is limited. Please fill in the following registration form before May 28th to complete your registration: Registration form for the "Computational Chemistry and Protein Modeling" Workshop.