Course Information

Bi9410c Structural Biology - practice

Faculty of Science
Autumn 2023

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

doc. Mgr. David Bednář, Ph.D. (seminar tutor)
Mgr. Ondřej Vávra, Ph.D. (assistant)
Mgr. Martina Damborská (assistant)
prof. Mgr. Jiří Damborský, Dr. (seminar tutor)
Mgr. Jana Horáčková (seminar tutor)
MUDr. Jan Mičan (seminar tutor)

Guaranteed by

prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Mgr. David Bednář, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Mon 16:00–17:50 B11/333

Prerequisites

NOW( Bi9410 Structural Biology )
Knowledge on the level of basic lectures of biochemistry or molecular biology.

Course Enrolment Limitations

The course is offered to students of any study field.
The capacity limit for the course is 24 student(s).
Current registration and enrolment status: enrolled: 5/24, only registered: 0/24, only registered with preference (fields directly associated with the programme): 0/24

Course objectives

The aim of the course is learning students how to operate selected freely available web servers, programs and databases applicable to the study of structure, dynamics and function of proteins.

Learning outcomes

On successful completion of the course, students will be able to:
operate selected freely available web servers, programs and databases applicable to the study of structure, dynamics and function of biomacromolecules, interaction of proteins with proteins, nucleic acids and small organic molecules.
visualize structure of biomolecules
identify functionally relevant regions of proteins
predict a structure of proteins and theirs complexes
evaluate an effect of mutation on a protein functi

Syllabus

1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
4. Prediction of structure of macromolecular complexes.
5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
6. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
7. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
8. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
11. Application of structural biology – biological research, drug design and development, design of biocatalyst.

Literature

Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008

Teaching methods

individual practice in computer lab

Assessment methods

written practical test, 11 exercises awarded 100 points in total, 70 pints are needed to pass.

Language of instruction

Czech

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
General note: Předmět se doporučuje zapsat v 1. nebo 3. semestru.

Teacher's information

http://loschmidt.chemi.muni.cz/sbiol

The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022.

Bi9410c Structural Biology - practice

Faculty of Science
Autumn 2022

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

doc. Mgr. David Bednář, Ph.D. (seminar tutor)
Mgr. Jan Dvorský, Ph.D. (seminar tutor)
Mgr. Ondřej Vávra, Ph.D. (assistant)
Mgr. Martina Damborská (assistant)
prof. Mgr. Jiří Damborský, Dr. (seminar tutor)
Mgr. Jana Horáčková (seminar tutor)
MUDr. Jan Mičan (seminar tutor)

Guaranteed by

Timetable

Thu 12:00–13:50 B09/316

Prerequisites

NOW( Bi9410 Structural Biology )
Knowledge on the level of basic lectures of biochemistry or molecular biology.

Course Enrolment Limitations

The course is offered to students of any study field.
The capacity limit for the course is 24 student(s).
Current registration and enrolment status: enrolled: 3/24, only registered: 0/24, only registered with preference (fields directly associated with the programme): 0/24

Course objectives

The aim of the course is learning students how to operate selected freely available web servers, programs and databases applicable to the study of structure, dynamics and function of proteins.

Learning outcomes

Syllabus

1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
4. Prediction of structure of macromolecular complexes.
5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
6. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
7. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
8. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
11. Application of structural biology – biological research, drug design and development, design of biocatalyst.

Literature

Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008

Teaching methods

individual practice in computer lab

Assessment methods

written practical test, 11 exercises awarded 100 points in total, 70 pints are needed to pass.

Language of instruction

Czech

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
General note: Předmět se doporučuje zapsat v 1. nebo 3. semestru.

Teacher's information

http://loschmidt.chemi.muni.cz/sbiol

Bi9410c Structural Biology - practice

Faculty of Science
autumn 2021

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

Guaranteed by

Timetable

Thu 12:00–13:50 B09/316

Prerequisites

NOW( Bi9410 Structural Biology )
Knowledge on the level of basic lectures of biochemistry or molecular biology.

Course Enrolment Limitations

The course is offered to students of any study field.
The capacity limit for the course is 24 student(s).
Current registration and enrolment status: enrolled: 1/24, only registered: 0/24, only registered with preference (fields directly associated with the programme): 0/24

Course objectives

The aim of the course is learning students how to operate selected freely available web servers, programs and databases applicable to the study of structure, dynamics and function of proteins.

Learning outcomes

Syllabus

1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
4. Prediction of structure of macromolecular complexes.
5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
6. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
7. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
8. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
11. Application of structural biology – biological research, drug design and development, design of biocatalyst.

Literature

Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008

Teaching methods

individual practice in computer lab

Assessment methods

written practical test, 11 exercises awarded 100 points in total, 70 pints are needed to pass.

Language of instruction

Czech

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
General note: Předmět se doporučuje zapsat v 1. nebo 3. semestru.

Teacher's information

http://loschmidt.chemi.muni.cz/sbiol

Bi9410c Structural Biology - practice

Faculty of Science
Autumn 2020

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

Guaranteed by

Timetable

Thu 12:00–13:50 prace doma

Prerequisites

NOW( Bi9410 Structural Biology )
Knowledge on the level of basic lectures of biochemistry or molecular biology.

Course Enrolment Limitations

The course is offered to students of any study field.
The capacity limit for the course is 24 student(s).
Current registration and enrolment status: enrolled: 0/24, only registered: 0/24, only registered with preference (fields directly associated with the programme): 0/24

Course objectives

The aim of the course is learning students how to operate selected freely available web servers, programs and databases applicable to the study of structure, dynamics and function of proteins.

Learning outcomes

Syllabus

1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
4. Prediction of structure of macromolecular complexes.
5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
6. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
7. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
8. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
11. Application of structural biology – biological research, drug design and development, design of biocatalyst.

Literature

Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008

Teaching methods

individual practice in computer lab

Assessment methods

written practical test, 11 exercises awarded 100 points in total, 70 pints are needed to pass.

Language of instruction

Czech

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
General note: Předmět se doporučuje zapsat v 1. nebo 3. semestru.

Teacher's information

http://loschmidt.chemi.muni.cz/sbiol

Bi9410c Structural Biology - practice

Faculty of Science
Autumn 2019

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

Guaranteed by

Timetable

Thu 12:00–13:50 B09/316

Prerequisites

NOW( Bi9410 Structural Biology )
Knowledge on the level of basic lectures of biochemistry or molecular biology.

Course Enrolment Limitations

Course objectives

The aim of the course is learning students how to operate selected freely available web servers, programs and databases applicable to the study of structure, dynamics and function of proteins.

Learning outcomes

Syllabus

1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
4. Prediction of structure of macromolecular complexes.
5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
6. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
7. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
8. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
11. Application of structural biology – biological research, drug design and development, design of biocatalyst.

Literature

Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008

Teaching methods

individual practice in computer lab

Assessment methods

written practical test, 11 exercises awarded 100 points in total, 70 pints are needed to pass.

Language of instruction

Czech

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
General note: Předmět se doporučuje zapsat v 1. nebo 3. semestru.

Teacher's information

http://loschmidt.chemi.muni.cz/sbiol

Bi9410c Structural Biology - practice

Faculty of Science
Autumn 2018

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

doc. Mgr. David Bednář, Ph.D. (seminar tutor)
Mgr. Ondřej Vávra, Ph.D. (seminar tutor)

Guaranteed by

Timetable

Mon 17. 9. to Fri 14. 12. Thu 12:00–13:50 D29/347-RCX2

Prerequisites

NOW( Bi9410 Structural Biology )
Knowledge on the level of basic lectures of biochemistry or molecular biology.

Course Enrolment Limitations

Course objectives

Learning outcomes

Syllabus

1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
4. Prediction of structure of macromolecular complexes.
5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
6. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
7. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
8. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
11. Application of structural biology – biological research, drug design and development, design of biocatalyst.

Literature

Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009

Teaching methods

individual practice in computer lab

Assessment methods

written practical test, 11 exercises awarded 100 points in total, 70 pints are needed to pass.

Language of instruction

Czech

Further Comments

Study Materials
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/sbiol

The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.

Bi9410c Structural Biology - practice

Faculty of Science
autumn 2017

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

doc. Mgr. David Bednář, Ph.D. (seminar tutor)
Mgr. Eva Šebestová, Ph.D. (seminar tutor)
Mgr. Lukáš Daniel, Ph.D. (assistant)

Guaranteed by

Timetable

Mon 18. 9. to Fri 15. 12. Thu 13:00–14:50 B09/316

Prerequisites

NOW( Bi9410 Structural Biology )
Knowledge on the level of basic lectures of biochemistry or molecular biology.

Course Enrolment Limitations

Course objectives

Learning outcomes

Syllabus

1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
4. Prediction of structure of macromolecular complexes.
5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
6. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
7. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
8. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
11. Application of structural biology – biological research, drug design and development, design of biocatalyst.

Literature

Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008

Teaching methods

individual practice in computer lab

Assessment methods

written practical test, 11 exercises awarded 100 points in total, 70 pints are needed to pass.

Language of instruction

Czech

Further Comments

Study Materials
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/sbiol

The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.

Bi9410c Structural Biology - practice

Faculty of Science
Autumn 2016

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

Mgr. Jan Brezovský, Ph.D. (seminar tutor)
Mgr. Eva Šebestová, Ph.D. (seminar tutor)
doc. Mgr. David Bednář, Ph.D. (assistant)
Mgr. Lukáš Daniel, Ph.D. (assistant)

Guaranteed by

prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: Mgr. Jan Brezovský, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Mon 19. 9. to Sun 18. 12. Thu 13:00–14:50 B09/316

Prerequisites

NOW( Bi9410 Structural Biology )
Knowledge on the level of basic lectures of biochemistry or molecular biology.

Course Enrolment Limitations

Course objectives

Syllabus

1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
4. Prediction of structure of macromolecular complexes.
5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
6. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
7. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
8. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
11. Application of structural biology – biological research, drug design and development, design of biocatalyst.

Literature

Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009

Teaching methods

individual practice in computer lab

Assessment methods

written practical test, 11 exercises awarded 100 points in total, 70 pints are needed to pass.

Language of instruction

Czech

Further Comments

Study Materials
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/sbiol

The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.

Bi9410c Structural Biology - practice

Faculty of Science
Autumn 2015

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

Mgr. Jan Brezovský, Ph.D. (seminar tutor)
Mgr. Eva Šebestová, Ph.D. (seminar tutor)
doc. Mgr. David Bednář, Ph.D. (assistant)
Mgr. Lukáš Daniel, Ph.D. (assistant)

Guaranteed by

Timetable

Thu 10:00–11:50 B09/316

Prerequisites

NOW( Bi9410 Structural Biology )
Knowledge on the level of basic lectures of biochemistry or molecular biology.

Course Enrolment Limitations

Course objectives

Syllabus

1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
4. Prediction of structure of macromolecular complexes.
5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
6. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
7. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
8. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
11. Application of structural biology – biological research, drug design and development, design of biocatalyst.

Literature

Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009

Teaching methods

individual practice in computer lab

Assessment methods

written practical test, 11 exercises awarded 100 points in total, 70 pints are needed to pass.

Language of instruction

Czech

Further Comments

Study Materials
The course is taught annually.

Teacher's information

http://loschmidt.chemi.muni.cz/sbiol

The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.

Bi9410c Structural Biology - practice

Faculty of Science
Autumn 2014

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

Mgr. Jan Brezovský, Ph.D. (seminar tutor)
Mgr. Eva Šebestová, Ph.D. (seminar tutor)
doc. Mgr. David Bednář, Ph.D. (assistant)
Mgr. Lukáš Daniel, Ph.D. (assistant)

Guaranteed by

Timetable

Wed 18:00–19:50 B09/316

Prerequisites

NOW( Bi9410 Structural Biology )
Knowledge on the level of basic lectures of biochemistry or molecular biology.

Course Enrolment Limitations

Course objectives

Syllabus

1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
4. Prediction of structure of macromolecular complexes.
5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
6. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
7. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
8. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
11. Application of structural biology – biological research, drug design and development, design of biocatalyst.

Literature

Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009

Teaching methods

individual practice in computer lab

Assessment methods

written practical test, 11 exercises awarded 100 points in total, 70 pints are needed to pass.

Language of instruction

Czech

Further Comments

Study Materials
The course is taught annually.

The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.

Bi9410c Structural Biology - practice

Faculty of Science
Autumn 2013

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

Mgr. Jan Brezovský, Ph.D. (seminar tutor)
Mgr. Eva Šebestová, Ph.D. (seminar tutor)

Guaranteed by

Timetable

Mon 16. 9. to Fri 6. 12. Wed 15:00–16:50 B09/316

Prerequisites

NOW( Bi9410 Structural Biology )
Knowledge on the level of basic lectures of biochemistry or molecular biology.

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Syllabus

1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
4. Prediction of structure of macromolecular complexes.
5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
6. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
7. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
8. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
11. Application of structural biology – biological research, drug design and development, design of biocatalyst.

Literature

Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009

Teaching methods

individual practice in computer lab

Assessment methods

written practical test, 11 exercises awarded 100 points in total, 70 pints are needed to pass.

Language of instruction

Czech

Further Comments

Study Materials
Course is no more offered.

The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.

Bi9410c Structural Biology - practice

Faculty of Science
Autumn 2012

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

Mgr. Jan Brezovský, Ph.D. (seminar tutor)
Mgr. Eva Šebestová, Ph.D. (seminar tutor)

Guaranteed by

Timetable

Wed 14:00–15:50 B09/316

Prerequisites

NOW( Bi9410 Structural Biology )
Knowledge on the level of basic lectures of biochemistry or molecular biology.

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Students will acquire practical understanding of freely available web servers, programs and databases applicable to the study of structure, dynamics and function of biomacromolecules, interaction of proteins with proteins, nucleic acids and small organic molecules.

Syllabus

1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
4. Prediction of structure of macromolecular complexes.
5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
6. Protein-protein complexes – evaluation of complex, analysis of interacions; databases.
7. Protein-DNA complexes – evaluation of complex, analysis of interacions; databases.
8. Protein-ligand complexes – evaluation of complex, analysis of interacions; databases.
9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
11. Application of structural biology – biological research, drug design and development, design of biocatalyst.

Literature

Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009

Teaching methods

individual practice in computer lab

Assessment methods

written test

Language of instruction

Czech

Further Comments

Study Materials
Course is no more offered.

The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.

Bi9410c Structural Biology - practice

Faculty of Science
Autumn 2011

The course is not taught in Autumn 2011

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

Mgr. Jan Brezovský, Ph.D. (lecturer)
prof. Mgr. Jiří Damborský, Dr. (lecturer)

Guaranteed by

prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: Mgr. Jan Brezovský, Ph.D.

Prerequisites (in Czech)

! Bi6901 Structural Biology - practice

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives

Syllabus

1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
4. Prediction of structure of macromolecular complexes.
5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
6. Protein-protein complexes – evaluation of complex, analysis of interacions; databases.
7. Protein-DNA complexes – evaluation of complex, analysis of interacions; databases.
8. Protein-ligand complexes – evaluation of complex, analysis of interacions; databases.
9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
11. Application of structural biology – biological research, drug design and development, design of biocatalyst.

Literature

Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009

Teaching methods

individual practice in computer lab

Assessment methods

written test

Language of instruction

Czech

Further Comments

Course is no more offered.
The course is taught every week.

Bi9410c Structural Biology - practice

Faculty of Science
Autumn 2011 - acreditation

The information about the term Autumn 2011 - acreditation is not made public

Extent and Intensity

0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).

Teacher(s)

Mgr. Jan Brezovský, Ph.D. (lecturer)
prof. Mgr. Jiří Damborský, Dr. (lecturer)

Guaranteed by

prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: Mgr. Jan Brezovský, Ph.D.

Prerequisites (in Czech)

! Bi6901 Structural Biology - practice

Course Enrolment Limitations

The course is offered to students of any study field.

Course objectives (in Czech)

Cílem cvičení je osvojit si praktické využití volně dostupných webových serverů, programů a databází ke studiu struktury, dynamiky a funkce proteinů, interakcí proteinů s proteiny, nukleovými kyselinami a malými organickými molekulami.

Syllabus (in Czech)

1. Struktura biologických makromolekul – složení, metody stanovení, využití v biologii.
2. Databáze experimentálních struktur – depozice, získání a hodnocení struktur makromolekul, strukturní databáze PDB, PDBsum, EDS, NDB.
3. Vizualizace struktur – možnosti zobrazení, dostupné programy.
4. Modely struktur – databáze modelů, metody hodnoceni kvality modelů, příprava modelů.
5. Predikce struktury makromolekulárních komplexů.
6. Analýza struktury proteinu – identifikace důležitých regionů: vazebná/aktivní místa, transportní cesty, flexibilní regiony, katalytické aminokyseliny.
7. Dynamika makromolekul – analýza dynamiky a její databáze.
8. Komplexy protein-protein – hodnocení komplexu, analýza interakcí a jejich databáze.
9. Komplexy protein-DNA – hodnocení komplexu, analýza interakcí a jejich databáze.
10. Komplexy protein-ligand – hodnocení komplexu, analýza interakcí a jejich databáze.
11. Modifikace struktury proteinu – stanovení vlivu mutace na strukturu a funkci proteinu.
12. Aplikace strukturní biologie – biologický výzkum, hledání nových léčiv, design biokatalyzátorů.

Literature

Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008

Teaching methods (in Czech)

samostatné cvičení v počítačové učebně

Assessment methods (in Czech)

písemný test

Language of instruction

Czech

Further Comments

Course is no more offered.
The course is taught every week.

The course is also listed under the following terms Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.

Enrolment Statistics (recent)

Course Information

Bi9410c Structural Biology - practice

Bi9410c Structural Biology - practice

Bi9410c Structural Biology - practice

Bi9410c Structural Biology - practice

Bi9410c Structural Biology - practice

Bi9410c Structural Biology - practice

Bi9410c Structural Biology - practice

Bi9410c Structural Biology - practice

Bi9410c Structural Biology - practice

Bi9410c Structural Biology - practice

Bi9410c Structural Biology - practice

Bi9410c Structural Biology - practice

Bi9410c Structural Biology - practice

Bi9410c Structural Biology - practice

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