Code: | Q4034 | Acronym: | Q4034 |
Keywords | |
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Classification | Keyword |
OFICIAL | Chemistry |
Active? | Yes |
Responsible unit: | Department of Chemistry and Biochemistry |
Course/CS Responsible: | Master in Bioinformatics and Computational Biology |
Acronym | No. of Students | Study Plan | Curricular Years | Credits UCN | Credits ECTS | Contact hours | Total Time |
---|---|---|---|---|---|---|---|
E:BBC | 1 | PE_Bioinformatics and Computational Biology | 1 | - | 6 | 42 | 162 |
M:BBC | 18 | The study plan since 2018 | 1 | - | 6 | 42 | 162 |
The aim of this course is to give to the student a broad view of the Computational Biochemistry field. The course will focus on molecular dynamics of biological macromolecules. The students will learn to prepare, execute and analyse molecular dynamics simulations of biomolecules
Capacity to perform and analyse molecular dynamics simulations . Capacity to predict the properties of biological systemas that do not involve electronic rearrangements.
1. Introduction 1.1. Introduction to Computational Biochemistry 1.2. Most common methods used in the study of biochemical systems. 1.3. Relation between the system size and the method of simulation. 2. Molecular Mechanics 2. 1. Introduction 2. 2. Force Fields 2.3. Bond Enegy 2.4. Angle Energy 2.5. Torsion Energy 2.6. Van der Waals Energy 2.7. Coulombic Energy 2.8. Crossed terms 2.9. Parameterization 2.10. Most used force fields 3. Molecular Dynamics 3.1. Introduction 3.2. Integration of the Equations of Motion 3.3. Periodic Boundary Conditions 3.4. Long Range Interactions 3.4.1 Smoothing functions 3.4.2 Particle Mesh-Ewald 3.5. Examples of Properties Calculated from Molecular Dynamics Trajectories 3.5.1 Density 3.5.2 Diffusion Coefficients 3.5.3 Orientational Dynamics 3.5.4 Root Mean Square Deviations in atomic positions 3.5.5 Root Mean Square Fluctuations in atomic positions 3.5.6 Radial Distribution Functions 3.5.7 Molecular Orientation.
Problem-Based Learning
designation | Weight (%) |
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Exame | 50,00 |
Participação presencial | 25,00 |
Trabalho prático ou de projeto | 25,00 |
Total: | 100,00 |
designation | Time (hours) |
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Elaboração de relatório/dissertação/tese | 24,00 |
Estudo autónomo | 70,00 |
Frequência das aulas | 56,00 |
Total: | 150,00 |
The students must attend at least 75% of the practical classes
The final classification will be the weighted average of the theory classification (50%) and the practical classification (50%).
The theory classification is essentially the result of the theoretical exam, with a small influence from the continuous evaluation made by the teacher during the classes. It can not be less than 7/20 for the student to obtain approval at the course.
The practical classification will be averaged out with the continuous evaluation during the practical classes (25%) and the classification of a report concerning the work developed in classroom during the semester (25%).
The student can repeat the theoretical examination within the calendar and rules defined by the Conselho Pedagógico. The practical classification cannot be improved as it reflects the progress of the student along the year.