301186 VU Structural Bioinformatics (2025S)
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Registration/Deregistration
Note: The time of your registration within the registration period has no effect on the allocation of places (no first come, first served).
Details
max. 36 participants
Language: English
Lecturers
Classes (iCal) - next class is marked with N
Important note!
All registered students, including those on the waiting list, MUST attend the first course!
According to the University rules, for all courses with continuous assessment attendance during the first course unit is mandatory. Students who do not show at the first course must be de-registered and their place will be filled with students from the waiting list.
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Wednesday
02.04.
10:00 - 15:00
BZB EDV-Raum CCR01, 6.Ebene 6.505, Dr.-Bohr-Gasse 9, 1030 Wien
BZB EDV-Raum CCR02, 6.Ebene 6.506, Dr.-Bohr-Gasse 9, 1030 Wien -
Thursday
03.04.
10:00 - 15:00
BZB EDV-Raum CCR01, 6.Ebene 6.505, Dr.-Bohr-Gasse 9, 1030 Wien
BZB EDV-Raum CCR02, 6.Ebene 6.506, Dr.-Bohr-Gasse 9, 1030 Wien -
Friday
04.04.
10:00 - 15:00
BZB EDV-Raum CCR01, 6.Ebene 6.505, Dr.-Bohr-Gasse 9, 1030 Wien
BZB EDV-Raum CCR02, 6.Ebene 6.506, Dr.-Bohr-Gasse 9, 1030 Wien -
Monday
07.04.
10:00 - 15:00
BZB EDV-Raum CCR01, 6.Ebene 6.505, Dr.-Bohr-Gasse 9, 1030 Wien
BZB EDV-Raum CCR02, 6.Ebene 6.506, Dr.-Bohr-Gasse 9, 1030 Wien -
Tuesday
08.04.
10:00 - 15:00
BZB EDV-Raum CCR01, 6.Ebene 6.505, Dr.-Bohr-Gasse 9, 1030 Wien
BZB EDV-Raum CCR02, 6.Ebene 6.506, Dr.-Bohr-Gasse 9, 1030 Wien -
Wednesday
09.04.
10:00 - 15:00
BZB EDV-Raum CCR01, 6.Ebene 6.505, Dr.-Bohr-Gasse 9, 1030 Wien
BZB EDV-Raum CCR02, 6.Ebene 6.506, Dr.-Bohr-Gasse 9, 1030 Wien -
Thursday
10.04.
10:00 - 15:00
BZB EDV-Raum CCR01, 6.Ebene 6.505, Dr.-Bohr-Gasse 9, 1030 Wien
BZB EDV-Raum CCR02, 6.Ebene 6.506, Dr.-Bohr-Gasse 9, 1030 Wien -
Friday
11.04.
10:00 - 15:00
BZB EDV-Raum CCR01, 6.Ebene 6.505, Dr.-Bohr-Gasse 9, 1030 Wien
BZB EDV-Raum CCR02, 6.Ebene 6.506, Dr.-Bohr-Gasse 9, 1030 Wien
Information
Aims, contents and method of the course
Assessment and permitted materials
The assessment strategy for the course is designed to evaluate both active participation during the course and the ability to apply the learned tools and techniques to real-world problems. Below is a detailed breakdown of the assessment components:1. Active Participation and In-class Performance (40%)
o Engagement in Discussions:
Active participation in class discussions, asking questions, and contributing ideas.
Demonstrating understanding of the concepts taught in lectures.
o Performance in Exercises:
Completing hands-on exercises during the course.
Demonstrating proficiency in using bioinformatics tools and techniques.
Collaborating with peers during group activities.
Grading Criteria:
o Quality and depth of contributions during discussions.
o Accuracy and completeness of exercise results.
o Willingness to engage with peers and instructors.2. Final Written Report (60%)
The final report is a comprehensive assignment that allows students to apply the tools and techniques learned in the course to analyze protein targets and drug-bound proteins. It consists of two parts:Part 1: Analysis of Given Targets (30%)
Students will analyze provided protein targets using the tools and techniques covered in the course.
Tasks may include:
Retrieving and annotating protein sequences.
Predicting protein structures using tools like AlphaFold and SWISS-MODEL.
Analyzing structural features (e.g., binding sites, domains, disorder) using tools like PyMol, PDBsum, or IUPred3.
Assessing druggability using tools like FTMap or DoGSiteScorer.
Grading Criteria:
o Accuracy and completeness of the analysis.
o Appropriate use of tools and techniques.
o Clear and logical presentation of results.Part 2: In-depth Examination of a Drug-bound Protein (30%)
Students will select a protein of their choice that is bound to a drug and conduct an in-depth analysis.
Tasks may include:
Retrieving the protein structure from the PDB and analyzing the drug-binding site.
Visualizing the protein-drug interaction using PyMol or Chimera.
Evaluating the drug-likeness of the bound ligand using tools like SwissADME.
Discussing the molecular mechanism of the drug and its implications for drug design.
Grading Criteria:
o Depth and originality of the analysis.
o Integration of multiple tools and techniques.
o Critical evaluation of the protein-drug interaction.
o Clarity and organization of the report.3. Submission Deadlines
The final report should be submitted within four weeks after the course, i.e. the latest by Friday, the 9th of May, 2025.
o Engagement in Discussions:
Active participation in class discussions, asking questions, and contributing ideas.
Demonstrating understanding of the concepts taught in lectures.
o Performance in Exercises:
Completing hands-on exercises during the course.
Demonstrating proficiency in using bioinformatics tools and techniques.
Collaborating with peers during group activities.
Grading Criteria:
o Quality and depth of contributions during discussions.
o Accuracy and completeness of exercise results.
o Willingness to engage with peers and instructors.2. Final Written Report (60%)
The final report is a comprehensive assignment that allows students to apply the tools and techniques learned in the course to analyze protein targets and drug-bound proteins. It consists of two parts:Part 1: Analysis of Given Targets (30%)
Students will analyze provided protein targets using the tools and techniques covered in the course.
Tasks may include:
Retrieving and annotating protein sequences.
Predicting protein structures using tools like AlphaFold and SWISS-MODEL.
Analyzing structural features (e.g., binding sites, domains, disorder) using tools like PyMol, PDBsum, or IUPred3.
Assessing druggability using tools like FTMap or DoGSiteScorer.
Grading Criteria:
o Accuracy and completeness of the analysis.
o Appropriate use of tools and techniques.
o Clear and logical presentation of results.Part 2: In-depth Examination of a Drug-bound Protein (30%)
Students will select a protein of their choice that is bound to a drug and conduct an in-depth analysis.
Tasks may include:
Retrieving the protein structure from the PDB and analyzing the drug-binding site.
Visualizing the protein-drug interaction using PyMol or Chimera.
Evaluating the drug-likeness of the bound ligand using tools like SwissADME.
Discussing the molecular mechanism of the drug and its implications for drug design.
Grading Criteria:
o Depth and originality of the analysis.
o Integration of multiple tools and techniques.
o Critical evaluation of the protein-drug interaction.
o Clarity and organization of the report.3. Submission Deadlines
The final report should be submitted within four weeks after the course, i.e. the latest by Friday, the 9th of May, 2025.
Minimum requirements and assessment criteria
1. Compulsory Attendance
1a. Requirement:
o Students are required to attend all sessions of the course.
o A maximum of 1 day may be missed only for important reasons (e.g., illness, emergencies).
1b. Documentation:
o If a day is missed, students must provide valid documentation (e.g., medical certificate) to the course instructor.
1c. Consequences of Non-Compliance:
o Missing more than 1 day without a valid reason may result in disqualification from the course or a reduction in the final grade.2. Active Participation
2a. Requirement:
o Students should actively engage in discussions, ask questions, and contribute to class activities.
o Participation in hands-on exercises is mandatory, and students should demonstrate effort and understanding.
2b. Assessment Criteria:
o Quality of contributions: Depth and relevance of questions and comments during discussions.
o Engagement in exercises: Effort and accuracy in completing practical tasks.
o Collaboration: Willingness to work with peers and share insights.
2c. Consequences of Non-Compliance:
o Lack of active participation may result in a lower grade for the Active Participation and In-class Performance component (40% of the final
grade).3. Final Written Report
3a. Requirement:
o Students need to complete both parts of the final written report:
Analysis of Given Targets (30%).
In-depth Examination of a Drug-bound Protein (30%).
o The report should be completed using the software and tools learned during the course.
3b. Assessment Criteria:
o Analysis of Given Targets:
x Accuracy and completeness of the analysis.
x Appropriate use of tools and techniques.
x Clear and logical presentation of results.
o In-depth Examination of a Drug-bound Protein:
Depth and originality of the analysis.
x Integration of multiple tools and techniques.
x Critical evaluation of the protein-drug interaction.
x Clarity and organization of the report.
3c. Consequences of Non-Compliance:
o Failure to complete either part of the report will result in a significant reduction in the final grade.
o Reports that do not use the required tools or fail to meet the formatting guidelines may be penalized.4. Additional Guidelines
4a. Plagiarism:
o All work submitted must be original. Plagiarism or unauthorized collaboration will result in disciplinary action, including potential disqualification from the course.
4b. Timely Submission:
o The final report must be submitted by the specified deadline. Late submissions will incur penalties unless prior approval is granted.
4c. Feedback:
o Students are encouraged to seek clarification and feedback throughout the course to ensure they meet the requirements.By adhering to these requirements and assessment criteria, students will be well-prepared to succeed in the course and apply their knowledge and skills in structural bioinformatics and drug discovery.
1a. Requirement:
o Students are required to attend all sessions of the course.
o A maximum of 1 day may be missed only for important reasons (e.g., illness, emergencies).
1b. Documentation:
o If a day is missed, students must provide valid documentation (e.g., medical certificate) to the course instructor.
1c. Consequences of Non-Compliance:
o Missing more than 1 day without a valid reason may result in disqualification from the course or a reduction in the final grade.2. Active Participation
2a. Requirement:
o Students should actively engage in discussions, ask questions, and contribute to class activities.
o Participation in hands-on exercises is mandatory, and students should demonstrate effort and understanding.
2b. Assessment Criteria:
o Quality of contributions: Depth and relevance of questions and comments during discussions.
o Engagement in exercises: Effort and accuracy in completing practical tasks.
o Collaboration: Willingness to work with peers and share insights.
2c. Consequences of Non-Compliance:
o Lack of active participation may result in a lower grade for the Active Participation and In-class Performance component (40% of the final
grade).3. Final Written Report
3a. Requirement:
o Students need to complete both parts of the final written report:
Analysis of Given Targets (30%).
In-depth Examination of a Drug-bound Protein (30%).
o The report should be completed using the software and tools learned during the course.
3b. Assessment Criteria:
o Analysis of Given Targets:
x Accuracy and completeness of the analysis.
x Appropriate use of tools and techniques.
x Clear and logical presentation of results.
o In-depth Examination of a Drug-bound Protein:
Depth and originality of the analysis.
x Integration of multiple tools and techniques.
x Critical evaluation of the protein-drug interaction.
x Clarity and organization of the report.
3c. Consequences of Non-Compliance:
o Failure to complete either part of the report will result in a significant reduction in the final grade.
o Reports that do not use the required tools or fail to meet the formatting guidelines may be penalized.4. Additional Guidelines
4a. Plagiarism:
o All work submitted must be original. Plagiarism or unauthorized collaboration will result in disciplinary action, including potential disqualification from the course.
4b. Timely Submission:
o The final report must be submitted by the specified deadline. Late submissions will incur penalties unless prior approval is granted.
4c. Feedback:
o Students are encouraged to seek clarification and feedback throughout the course to ensure they meet the requirements.By adhering to these requirements and assessment criteria, students will be well-prepared to succeed in the course and apply their knowledge and skills in structural bioinformatics and drug discovery.
Examination topics
The examination will cover all materials taught during the course, including:
o Protein structure and functional analysis tools.
o Structure prediction and validation techniques.
o Structure-based drug discovery methods.
o Druggability prediction tools.
o Drug design and assessment.
o Real-world applications of bioinformatics in drug development.
o Protein structure and functional analysis tools.
o Structure prediction and validation techniques.
o Structure-based drug discovery methods.
o Druggability prediction tools.
o Drug design and assessment.
o Real-world applications of bioinformatics in drug development.
Reading list
Relative publications and reading materials will be suggested throughout the course.
Association in the course directory
MMB III-1a:, PhD MB
Last modified: Tu 25.02.2025 16:26
This 8-day course on structural bioinformatics is designed to provide a robust foundation in both theoretical concepts and practical applications, equipping students with the skills necessary to analyze biological macromolecules and apply bioinformatics tools in structural analysis and drug discovery.Contents:
1. Understand the Basics of 3D Structures of Biological Macromolecules
o Gain foundational knowledge of the three-dimensional structures of proteins, RNA, and DNA.
o Learn about the relationship between structure and function in biological macromolecules.
2. Learn Key Structural Bioinformatics Tools
o Know how to use online platforms such as UniProt (protein databases), BLAST (sequence alignment), PSIPRED (secondary structure prediction), IUPred3 (disorder prediction), ODiNPred (order/disorder prediction), PDB (Protein Data Bank), PDBsum (structure summaries), SMART (domain analysis), etc. to search and analyze protein sequences and structures.
3. Understand Principles of Structure Determination
o Learn the principles and procedures of experimental methods for structure determination, including X-ray crystallography, nuclear magnetic resonance (NMR) and cryo-electron microscopy (Cryo-EM).
o Understand the strengths and limitations of each method.
4. Critical Assessment of 3D Structures
o Learn how to download and analyze three-dimensional structures using tools like PyMol and other software.
o Evaluate the quality and reliability of structural data.
5. Protein Structure Prediction and Analysis
o Become familiar with advanced methods for protein structure prediction, including SWISS-MODEL (homology modeling), ESMFold (deep learning-based prediction), RoseTTAFold (deep learning-based prediction), AlphaFold (state-of-the-art AI-based prediction), etc.
o Understand their applications in scientific research.
6. Predict Druggability of Biological Macromolecules
o Learn how to use online servers such as FTMap and DoGSiteScorer to predict the druggability of proteins and other macromolecules.
o Explore structure-based drug discovery approaches.
7. Assess Drug-Likeness of Chemical Compounds
o Learn how to evaluate pharmacokinetics and medicinal chemistry friendliness of small molecules by SwissADME, SwissBioisostere, etc.
o Understand key parameters such as bioavailability, solubility, and toxicity.
8. Drug Design and Docking
o Perform swift virtual screening using Pharmit to identify potential drug candidates.
o Learn how to quickly perform protein-ligand docking using the SwissDock web server.
o Understand the principles of molecular docking and its role in drug design.
9. Case Study of Real Drugs
o Study of molecular mechanisms behind several common drugs, including:
Aspirin: Mechanism of action as a cyclooxygenase (COX) inhibitor.
Quinine: Antimalarial drug targeting the Plasmodium parasite.
Dorzolamide: Carbonic anhydrase inhibitor used in glaucoma treatment.
o Lessons learned from real-world examples of drug development.Methods:
o Interactive Lectures: Provide the theoretical foundation and context for the tools and techniques covered in the course.
o Hands-On Sessions: Reinforce the concepts taught in the lectures & provide students with real-world experience in using bioinformatics tools.
o Group Discussions: Collaborative problem-solving and discussion of key concepts.