Description of Individual Course Units
Course Unit CodeCourse Unit TitleType of Course UnitYear of StudySemesterNumber of ECTS Credits
9101036342008Computer Based Methods in Protein Structure and DynamicsElective128
Level of Course Unit
Third Cycle
Objectives of the Course
To give insight on the computational methods and softwares used in the determination of protein structures and dynamics.
Name of Lecturer(s)
Prof. Dr. Cenk Selçuki
Learning Outcomes
1To be able to interpret the computed data
2To understand the basic similarities/differences between the methods
3To gain ability to compare and interpret the advantages and disadvantages of the applied methods
4To be able to use the required softwares for efficient use of the methods
5To improve thinking and interpretation in three-dimension (3D)
6To learn the terminology used in computational science and technology
7To be skilled to choose the method that will be used in protein studies.
8To understand the fundamental principles of computational methods used in the determination of protein structures and dynamics
Mode of Delivery
Face to Face
Prerequisites and co-requisities
None
Recommended Optional Programme Components
None
Course Contents
General description of molecular modeling and its applications. Introduction to bioinformatics. Introduction to genomics. SCOP. CASP. Computational methods used in determination of protein structure and dynamics. Protein sequence analysis andrelated structure determination methods.
Weekly Detailed Course Contents
WeekTheoreticalPracticeLaboratory
1General Definition of Molecular Modeling and Its Applications
2Computational Methods in Protein Structure and Dynamics (Molecular Mechanics)
3Computational Methods in Protein Structure and Dynamics (Molecular Dynamics)
4Computational Methods in Protein Structure and Dynamics (Monte Carlo)
5Computational Methods in Protein Structure and Dynamics (Semiempirical Methods)
6Computational Methods in Protein Structure and Dynamics (Density Functional Theory (DFT) Methods)
7Computational Methods in Protein Structure and Dynamics (Ab initio Methods)
8Mid-term Exam
9Protein Sequence Analysis and Related Methods Used in Structure Prediction (Conformational Analysis)
10Protein Sequence Analysis and Related Methods Used in Structure Prediction (Homology Modeling)
11Protein Sequence Analysis and Related Methods Used in Structure Prediction (Threading, Lattice Model and Ramachandran Maps)
12Protein Sequence Analysis and Related Methods Used in Structure Prediction (CASP, SCOP and classification systems of other databases)
13Introduction to Genomics
14Introduction to Bioinformatics
15Project presentation
16Final Exam
Recommended or Required Reading
A. R. Leach, Molecular Modelling Principles and Applications, 2. Ed., Prentice Hall, (2001) T. Schlick, Molecular Modeling and Simulation, Springer, (2002) K. I. Ramachandran, G. Deepa, K. Namboori, Computational Chemistry and Molecular Modeling-Principles and Applications, Springer-Verlag, (2008) A. Warshel, Computer Modeling of Chemical Reactions in Enzymes and Solutions, John Wiley & Sons, Inc., (1991)
Planned Learning Activities and Teaching Methods
Activities are given in detail in the section of "Assessment Methods and Criteria" and "Workload Calculation"
Assessment Methods and Criteria
Term (or Year) Learning ActivitiesQuantityWeight
SUM0
End Of Term (or Year) Learning ActivitiesQuantityWeight
SUM0
SUM0
Language of Instruction
Turkish
Work Placement(s)
None
Workload Calculation
ActivitiesNumberTime (hours)Total Work Load (hours)
Midterm Examination122
Final Examination122
Attending Lectures14342
Practice7428
Report Preparation12020
Individual Study for Mid term Examination13030
Individual Study for Final Examination14545
Reading14570
TOTAL WORKLOAD (hours)239
Contribution of Learning Outcomes to Programme Outcomes
PO
1
PO
2
PO
3
PO
4
PO
5
PO
6
PO
7
PO
8
PO
9
PO
10
PO
11
PO
12
LO1 5 4544  5 4
LO244445544 435
LO3543 455 4  4
LO44 4 45   4 5
LO54345 443  54
LO6454 4 43 4 3
LO7      5 5  5
LO8            
* Contribution Level : 1 Very low 2 Low 3 Medium 4 High 5 Very High
 
Ege University, Bornova - İzmir / TURKEY • Phone: +90 232 311 10 10 • e-mail: intrec@mail.ege.edu.tr