Computer-aided drugs design
0800-16KML-DW
During exercises will be discuses the following topics:
- introduction to drug chemistry
- structure and function of proteins and their interaction with other molecules
- stages of drug design
- the use of online databases useful in drug design
- searching for pharmacophores
- pharmacophore optimization
To accomplish the above goals, we will use software for docking (AutoDock, Glide), comparison of possible pharmacists to existing ones, searching for pharmacists based on the known structure of the protein - drugs interactions (OpenEye package). Modifications of pharmacophores and checking their activity will be carried out using the programs from the OpenEye Glide and AutoDock packages.
Total student workload
Hours carried out with the participation of teachers (31 hours):
- participation in exercises - 30 hours
- consultation with an academic teacher - 1 hour
Time devoted to individual work of a student (44 hours):
for example.
- preparation for exercises - 15 hours
- writing works, projects - 19 hours
- reading literature - 10 hours
Total: 75 hours (3 ECTS)
Learning outcomes - knowledge
W1 - has knowledge in the field of physics, chemistry, computer science biology and mathematics necessary to describe and model simple phenomena related to the design and operation of drugs (informatics K_W01, physics K_W01, technical physics K_W01)
W2 - Knows advanced numerical techniques allowing to plan and perform a complex drug design procedure, knows methods, techniques and tools, libraries used in drug design (physics K_W02, technical physics K_W05, informatics K_W05, K_W03).
W3 - knows the advanced methods of theoretical physics used in the study of drug-protein interactions and how to use them in practice using ready-made software (physics K_W03, technical physics K_W05, informatics K_W05).
W4 - has ethical knowledge about modern genetic therapies, understands the threat arising from the design of modern drugs (physics K_W07, technical physics K_W07).
W5 - has in-depth knowledge of mathematics useful for advanced aspects of bioinformatics and chemoinformatics (informatics K_W01)
Learning outcomes - skills
U1 - effectively knows how to search for the necessary information to solve IT problems, has the ability to independently search and use information in the field of computer science physics and technical physics, necessary for the design of medicines (e.g. bioinformatics chemoinformatics) (informatics K_U01, physics K_U01, technical physics K_U01)
U2 - has extended independent and group work skills, is able to determine the necessary scope of knowledge to be acquired to implement a specific IT project, has the ability to acquire knowledge / learn, develop his knowledge, uses various techniques to access information on drug design . (informatics K_U07, technical physics K_U10, physics K_U12)
U3 - is able to evaluate and apply new technologies, new diagnostic tools, is able to make their selection for the implementation of given problems in drug design (informatics K_U08)
U4 - can design extensions or improvements to IT projects, increase efficiency by using more advanced algorithms, or change the technologies of IT infrastructure devices, can achieve several goals and use several tools by combining information with them. (informatics K_U09)
U5 - Can find and adapt knowledge of physics, computer science and biology in effective drug design (technical physics K_U03 K_U05, physics K_U04 K_U05, informatics K_U11)
U6 - has the ability to use programming resources and databases related to the study of specialties in drug design (informatics K_U11)
U7 - Can determine the directions of further supplementing knowledge in the field of physics, chemistry, biology and computer science in order to design and model drugs more effectively (technical physics K_U10, physics K_U11, KU_05)
Learning outcomes - social competencies
K1 - understands the need for continuous training caused by the emergence of new achievements, new technologies, etc. understands the need to exchange information in groups of people involved in computer science, understands the possibilities offered by academic education, can critically assess his knowledge and received content related to drug design (informatics K_K01, physics K_K01, technical physics K_K01)
K2 - is able to demonstrate effectiveness in the implementation of scientific research projects entering the study program or implemented outside the studies (informatics K_K04)
K3 - is able to convey information about the achievements of computer science, physics and various aspects of the profession of computer science or physics in a commonly understood way (informatics K_K05)
K4 - understands the need for professional and ethical behavior, understands the importance of intellectual honesty (physics K_K02, technical physics K_K02, informatics K_K03)
Expository teaching methods
- description
- informative (conventional) lecture
Exploratory teaching methods
- practical
- brainstorming
- project work
- case study
Prerequisites
Elementary knowledge (high school level) in physics, chemistry and biology. Basics of Linux system usage
Course coordinators
Assessment criteria
Passing classes (on grade) will be based on class attendance and written colloquia
(verification of effects W1, W2, W3, W4, W5) and final projects developed in groups or individually (verification of effects U1, U2, U3, U4, U5, U6, U7).
Criteria for assessing colloquia:
ndst - 0-49% points
dst- 50-59% points
dst plus- 60-69% points
db- 70-79% points
db plus - 80-89% points
very good - 90-100% of points
projects will be assessed on the basis of:
1) Description of the problem to be solved
2) Methods used
3) Conclusions drawn from conducted simulations
4) The indicated literature describing the problem
The final grade will be the average brewed grade for the test (weight 1) and the project (weight 2).
Bibliography
An Introduction to Medicinal Chemistry, G. Patrick, Oxford University Press 2017
Essential bioinformatics, Jin Xiong, Cambridge University Press 2006 or newer
"Bioinformatics and molecular evolution" P. Higgs; T. Attwood, Wiley-Blackwell, 2006 or newer.
AutoDock, OpenEye, Schrodinger Software manuals
Additional information
Additional information (registration calendar, class conductors,
localization and schedules of classes), might be available in the USOSweb system: