Sereina Riniker: Catalogue data in Autumn Semester 2023 |
| Name | Prof. Dr. Sereina Riniker |
| Field | Computational Chemistry |
| Address | Inst. Mol. Phys. Wiss. ETH Zürich, HCI G 225 Vladimir-Prelog-Weg 1-5/10 8093 Zürich SWITZERLAND |
| Telephone | +41 44 633 42 39 |
| sriniker@ethz.ch | |
| URL | http://www.riniker.ethz.ch |
| Department | Chemistry and Applied Biosciences |
| Relationship | Full Professor |
| Number | Title | ECTS | Hours | Lecturers | |||||||||||||||||||||||||||||
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| 529-0002-00L | Algorithms and Programming for Chemistry  | 6 credits | 3G | S. Riniker, G. Landrum | |||||||||||||||||||||||||||||
| Abstract | Introduction to algorithms (special focus on chemistry): Design of algorithms, data structures, search and sort algorithms, graphs, numerical algorithms, algorithms in cheminformatics, machine learning and bioinformatics Computer language: C++ | ||||||||||||||||||||||||||||||||
| Learning objective | Development of programming skills and craftsmanship in order to be able to deal with the complexity of computer applications in chemistry. | ||||||||||||||||||||||||||||||||
| Content | Introduction to algorithms (special focus on chemistry): Design of algorithms, data structures, search and sort algorithms, graphs, numerical algorithms, algorithms in cheminformatics, machine learning and cheminformatics Computer language: C++ | ||||||||||||||||||||||||||||||||
| Lecture notes | Script (in English) will be available | ||||||||||||||||||||||||||||||||
| Literature | T.H. Cormen, C. E. Leiserson, R. L. Rivest, C. Stein, "Introduction to Algorithms", MIT Press (2009) C++ programming: S. Oualline, "Practical C++ Programming", O'Reilly (2003) | ||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Since the exercises on the computer do convey and test essentially different skills as those being conveyed during the lectures and tested at the oral exam, the results of the exercises are taken into account when evaluating the results of the exam. | ||||||||||||||||||||||||||||||||
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| 529-0004-01L | Classical Simulation of (Bio)Molecular Systems | 6 credits | 4G | P. H. Hünenberger, J. Dolenc, S. Riniker | |||||||||||||||||||||||||||||
| Abstract | Molecular models, classical force fields, configuration sampling, molecular dynamics simulation, boundary conditions, electrostatic interactions, analysis of trajectories, free-energy calculations, structure refinement, applications in chemistry and biology. Exercises: hands-on computer exercises for learning progressively how to perform an analyze classical simulations (using the package GROMOS). | ||||||||||||||||||||||||||||||||
| Learning objective | Introduction to classical (atomistic) computer simulation of (bio)molecular systems, development of skills to carry out and interpret these simulations. | ||||||||||||||||||||||||||||||||
| Content | Molecular models, classical force fields, configuration sampling, molecular dynamics simulation, boundary conditions, electrostatic interactions, analysis of trajectories, free-energy calculations, structure refinement, applications in chemistry and biology. Exercises: hands-on computer exercises for learning progressively how to perform an analyze classical simulations (using the package GROMOS). | ||||||||||||||||||||||||||||||||
| Lecture notes | The powerpoint slides of the lectures will be made available weekly on the website in pdf format (on the day preceding each lecture). | ||||||||||||||||||||||||||||||||
| Literature | See: www.csms.ethz.ch/education/CSBMS | ||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Since the exercises on the computer do convey and test essentially different skills than those being conveyed during the lectures and tested at the oral exam, the results of the exercises are taken into account when evaluating the results of the exam (learning component, possible bonus of up to 0.25 points on the exam mark). For more information about the lecture: www.csms.ethz.ch/education/CSBMS | ||||||||||||||||||||||||||||||||
| Competencies |
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| 529-0460-00L | Computer Simulation | 0 credits | 1S | P. H. Hünenberger, S. Riniker | |||||||||||||||||||||||||||||
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| Prerequisites / Notice | Group meeting | ||||||||||||||||||||||||||||||||
| 529-0499-00L | Physical Chemistry | 0 credits | 1K | M. Reiher, A. Barnes, G. Jeschke, F. Merkt, J. Richardson, R. Riek, S. Riniker, T. Schmidt, R. Signorell, H. J. Wörner | |||||||||||||||||||||||||||||
| Abstract | Institute-Seminar covering current research Topics in Physical Chemistry | ||||||||||||||||||||||||||||||||
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| 535-0022-00L | Computer-Assisted Drug Design | 1 credit | 1V | S. Riniker, G. Landrum | |||||||||||||||||||||||||||||
| Abstract | The lecture series provides an introduction to computer applications in medicinal chemistry. The topics cover molecular representations and similarity, ligand-based virtual screening, and structure-based virtual screening. All theoretical concepts and algorithms presented are illustrated by practical applications and case studies | ||||||||||||||||||||||||||||||||
| Learning objective | The students will learn how molecules can be represented in computers and how molecular similarity is calculated. They will learn the concepts of ligand-based and structure-based virtual screening to identify potential drug candidates, and understand possibilities and limitations of computer-assisted drug design in pharmaceutical chemistry. As a result, they are prepared for professional assessment of computer-assisted drug design studies in medicinal chemistry projects. | ||||||||||||||||||||||||||||||||
| Content | The topics include molecular representations and similarity, ligand-based virtual screening (similarity search, QSAR, etc.) and structure-based virtual screening (docking, physics-based models). | ||||||||||||||||||||||||||||||||
| Lecture notes | Script will be available. | ||||||||||||||||||||||||||||||||
| Literature | Recommended textbooks: 1) G. Schneider, K.-H. Baringhaus (2008) "Molecular Design - Concepts and Applications", Wiley-VCH: Weinheim, New York. 2) H.-D. Höltje, W. Sippl, D. Rognan, G. Folkers (2008) "Molecular Modeling: Basic Principles and Applications", Wiley-VCH: Weinheim, New York. 3) G. Klebe (2009) "Wirkstoffdesign", Spektrum Akademischer Verlag: Heidelberg. | ||||||||||||||||||||||||||||||||
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