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Computational Biochemistry
 
February 27 - March 3
Doctoral Program in Experimental Biology and Biomedicine (PDBEB) 
2016/2017 Edition

Computational Biochemistry


Contact: Irina Moreira:
irm2223@gmail.com

Alexandra Carvalho:
apirescarvalho@gmail.com


Date:

February 27-03 March, 2017


Place:
CNC (FMUC, POLO I building) and Chemistry Department (FCUC)


Monday, February 27th

Structure Prediction  
Irina Moreira

Schedule

10:30-12h30
•    Homology Modeling
•    G-protein Coupled receptors (GPCRs)

14:00-18:00
Tutorial: Homology Modeling of the Dopamine receptor

Module description
To be able construct a tridimensional representation of a protein.

Learning outcomes
•    Understand basis of homology modelling
•    Understand structural motifs of GPCRs


Tuesday, February 28th

Irina Moreira

Schedule

10:30-12h30
•    Molecular docking
•    Hot-Spot Detection

14:00-18:00
•    Tutorial: Protein-protein docking of Dopamine receptor and G-Protein

Module description
To be able construct a trdimentional representation of a protein-protein complex.

Learning outcomes
•    Understand the concept of protein-protein docking
•    Understand the concept of HS
•    Characterize a binding interface


Wednesday, March 1st
Biomolecular simulations
Alexandra Carvalho

Schedule

10:30-12h30
•    Equations of motion
•    Force fields
•    Energy minimization
•    Molecular dynamics (MD) simulations

14:00-18:00
Tutorial: Molecular dynamics simulations of the Amyloid beta peptide (part I)

Module description
The objective of this module is to give an introduction to the basic concepts in biomolecular simulations.
Practical implementation will be conducted in the tutorial.  

Learning outcomes
•    Understand basic concepts of molecular mechanics and classical molecular dynamics simulations
•    Develop practical skills necessary to perform a molecular dynamics simulation


Thursday, March 2nd
Computational Enzyme catalysis and applications  
Alexandra Carvalho

Schedule

10:30-12h30
•    Enzyme catalysis basic concepts revision
•    Computational enzymology
•    Case studies

14:00-18:00
Tutorial: Molecular dynamics simulations of the Amyloid beta peptide (part II)

Module description
The objective of this module is to discuss an important field of application of biomolecular simulations that is the study of enzymes function and evolution.  Case studies will be presented.

Learning outcomes
•    Understand basic concepts of enzyme catalysis
•    Assess applications of computational enzymology that helped address important biological questions
•    Develop practical skills necessary to analyse the results of a MD simulation
•    Interpret the results of a MD simulation study


Friday, March 3rd

Course Evaluation



Schedule



Morning – free time to prepare project and presentations

14:00 –Presentations and evaluation


Recommended reading

•    Melo R, Fieldhouse R, Melo A, Correia JD, Cordeiro MN, Gümüş ZH, Costa J, Bonvin AM, Moreira IS, A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces, Int J Mol Sci. 2016 Jul 27;17(8). pii: E1215. doi: 10.3390/ijms17081215.

•    Moreira IS., Structural features of the G-protein/GPCR interactions, Biochim Biophys Acta. 2014 Jan;1840(1):16-33. doi: 10.1016/j.bbagen.2013.08.027

•    van Zundert GC, Rodrigues JP, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond AS, van Dijk M, de Vries SJ, Bonvin AM, ,The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes, J Mol Biol. 2016 Feb 22;428(4):720-5. doi: 10.1016/j.jmb.2015.09.014.

•    Durrant and McCammon BMC Biology 2011, 9:71
http://www.biomedcentral.com/1741-7007/9/71

•    Challenges in computational studies of enzyme structure, function and dynamics. Alexandra T.P. Carvalho, Alexandre Barrozo, Dvir Doron, Alexandra Vardi Kilshtain, Dan Thomas Major, Shina Caroline Lynn Kamerlin, Journal of Molecular Graphics and Modelling, Volume 54, November 2014, Pages 62-79, ISSN 1093-3263, http://dx.doi.org/10.1016/j.jmgm.2014.09.003. (http://www.sciencedirect.com/science/article/pii/S1093326314001570)

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