NBIC PhD course Protein Structures: production, prowess, power, promises, and problems Date: 4 – 8 Nov 2013 Course coordinator: Gert Vriend Location: Center for Molecular and Biomolecular Informatics (CMBI), UMC Radboud, Nijmegen, the Netherlands Website: http://www.nbic.nl/education/nbic-phd-school/course-schedule/protein-structu... Registration: http://www.nbic.nl/education/nbic-phd-school/enrolment/ Target audience The course is suitable for both PhD students working in structural bioinformatics as well as for PhD students in the life sciences who want to learn more about using structural informatioin in their research. The course schedule accommodates both groups, parallel sessions for both groups will be scheduled when necessary. Course Description In the right hands, protein structures are a 'power'ful tool to answer bio-molecular questions. Knowledge of the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the 'production' of protein structures by NMR, X-ray, and homology modelling. These methods all have their pro's and cons so a certain 'prowess' is needed to follow all 'promises' and start attacking bio-medical 'problems' using protein structures. The course will be split in three parts. Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms. Part 2) Protein structure determination (prediction) with NMR, X-ray, and homology modelling, and the possibilities and problems that come with each of these three techniques. Part 3) Applying all that was learned in real-life example studies. Course topics Day 1: Homology modelling Day 2: Protein structure determination and validation Day 3: Electrostatics and molecular dynamics Day 4: Protein structure comparison Day 5: Own project executed with help from CMBI staff. Examples of questions you will be able to answer after following the course: · Why is a person with this mutation sick? Or in other words, how does the molecular phenotype cause a disease state? · This enzyme converts mannose. Can I make is specificity broader? · This enzyme doesn't function in my in vitro assay. Should I add some ions? · I want to add a tag to my enzyme, should I put it on the N-terminus, the C-terminus, or is something different needed? · This receptor binds a ligand, but if I look at the structure, that ligand doesn't fit at all. Can I predict motions that take place upon ligand binding? NBIC PhD School This course is part of the Education Programme of the NBIC PhD School. The NBIC PhD School offers training and education for PhD students in bioinformatics. More information about the NBIC PhD School can also be found on http://www.nbic.nl => Education => NBIC PhD School. More information For more information about the course you can contact Celia van Gelder (NBIC Education) at celia.van.gelder@nbic.nl<mailto:celia.van.gelder@nbic.nl>. -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder@umcn.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl>, www.nbic.nl<http://www.nbic.nl> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.