Degree | Type | Year | Semester |
---|---|---|---|
2502444 Chemistry | OT | 4 | 0 |
Chemical Thermodynamics
Quantum Chemistry
Physical Chemistry
Previous background in Biochemistry is not essential.
This course has as main objective to introduce students to the basic principles of biomolecular simulations that allow the interpretation at the atomic level of how biological processes take place and of the biomedical and biotechnological applications of biomolecules (drugs, nanoparticles, vaccines...).
Biomolecular simulations are based on the molecular modeling of the biological system or biomolecule of interest.
This modeling involves a series of steps that will be explained in this course both theoretically and in practices, in a balanced equilibrium between concepts, physical equations and on-hands lab:
1) Calculation of the energy of the system as a function of the coordinates (3D structure) of its atoms and molecules by means of Molecular Mechanics and Quantum Mechanics methods;
2) Study of the computational techniques that allow to determine how the energy of the system varies according to its coordinates:
a) Docking techniques;
b) Techniques to minimize the energy;
c) Molecular Dynamics simulations;
d) Methods to calculate free energies.
These different methodologies will be used to study basic biological aspects of biomolecules, as well as in applications for drug design and the study of enzymatic catalysis.
BIOMOLECULAR SIMULATIONS
1. Introduction to molecular modeling of biomolecules.
2. Biomolecules: structure and function. An overview.
3. Molecular mechanics methods for the calculation of the energy.
4. Conformational exploration in biomolecules.
5. Protein-ligand interaction: Docking techniques and drug design.
6. Simulation methods: Molecular Dynamics.
7. Hybrid QM/MM methods for the calculation of the potential energy.
8. Calculations of free energy differences.
9. Enzymatic catalysis: mechanisms and reaction rate.
The subject BIOMOLECULAR SIMULATIONS is an optional subject of 6 ECTS belonging to the specialization in BIOLOGICAL CHEMISTRY but it can also be coursed outside this particular specialization.
The teaching methodology of the subject consists on theoretical lecturers in the classroom and practical sessions in the computer room supervised by the professor in charge. Theoretical and practical classes are completed with tutoring hours supervised by teachers in order to resolve doubts. The student must work autonomously on the theoretical contents and the questions posed by the professors in the face-to-face sessions, in the realization of the practices, and in the elaboration of the works of the asignatura that will entail a part of bibliographical research.
Annotation: Within the schedule set by the centre or degree programme, 15 minutes of one class will be reserved for students to evaluate their lecturers and their courses or modules through questionnaires.
Title | Hours | ECTS | Learning Outcomes |
---|---|---|---|
Type: Directed | |||
Practical sessions | 18 | 0.72 | 2, 5, 7, 8, 19, 20, 11, 10, 13, 14, 15, 18, 21 |
Theoretical lectures | 34 | 1.36 | 2, 4, 5, 19, 20, 11, 10, 14, 21 |
Type: Supervised | |||
Tutoring | 2 | 0.08 | 7, 8 |
Type: Autonomous | |||
Bibliographic serach | 2 | 0.08 | 8, 9 |
Quizz/Practical reports/Assigned deliverable tasks | 14 | 0.56 | 1, 2, 6, 3, 16, 4, 5, 7, 8, 19, 20, 17, 9, 11, 10, 12, 13, 14, 15, 22, 18, 21 |
Study | 70 | 2.8 | 1, 2, 6, 4, 5, 7, 8, 19, 20, 9, 11, 10, 13, 14, 15 |
EVALUATION
This subject uses the continuous evaluation to support and assess the learning achievements of the contents and competences by the students.
This continuous assessment will consist of two types of activities: exams and follow-up activities.
Exams (70%)
There will be two partial exams on the content of the subject: Partial 1 (P1) (35%) and Partial 2 (P2) (35%).
Assessment activities (30%)
Throughout the course, there will be two series (S1 and S2) of follow-up activities (quizzes, practical reports, deliverable tasks) that will serve as evidences of the individual work and learning by the student. These activities do not have a minimum grade required.
QUALIFICATIONS
To pass the course, the following three conditions must be met:
1) Score of each partial exam (NP1 and NP2) equal to or greater than 3,5 and the minimum average mark of the two exams is 4,0.
2) Final grade: Final grade = 0.70 * (0.50 * (NP1 + NP2)) + 0.30 * (0.50 * (NS1 + NS2)) equal to or greater than 5.0.
3) Have attended all the practical sessions and delvered the practical report when applicable.
When requirements 1) and 2) are not fulfilled, students can take a second exam for each partial. This second exam can correspond to only one partial exam or to the total contents of the course. The score obtained in these exams will replace that obtained in the corresponding first attempt.
Assisting to the practical sessions is mandatory.
To have the right of being evaluated in these second exams, it is compulsory to have been previously evaluated in a set of evaluation activities whose weight equalsat least two thirds (66.6%) of the total grade ofthe course. Thus, the second exams cannot be taken if any of the partial exams has not been taken first.
If the student has only been evaluated for up to 25% of the evaluation activities and abandons the course, the final grade will be NON-EVALUABLE.
Title | Weighting | Hours | ECTS | Learning Outcomes |
---|---|---|---|---|
Assessment activities | 30% | 4 | 0.16 | 1, 2, 6, 3, 16, 4, 5, 7, 8, 19, 20, 17, 9, 11, 10, 12, 13, 14, 15, 22, 18, 21 |
Exams | 70% | 6 | 0.24 | 1, 6, 3, 16, 5, 7, 8, 20, 12, 13, 15, 18 |
1) Introduction to Computational Chemistry. Frank Jensen. ISBN: 0470011874JohnWiley § Sons Ltd. (2007). (Electronic document availabale at the UAB Library Services)
2) Essentials of Computational Chemistry: Theories and Models. Cristopher J. Cramer. ISBN: 0470091827. JohnWiley § Sons Ltd. (2004). (Electronic and printed documend availabble at the UAB Library Services)
3) Molecular Modelling. Principles and Applications. Andrew R Leach. ISBN: 978-0-582-38210-7. Pearson (2001). (Printed documend availabble from the UAB Library Services)
USCF Chimera
Autodock Vina
CHARMM-GUI (web interface)