Sereina Riniker: Catalogue data in Autumn Semester 2021

Name Prof. Dr. Sereina Riniker
FieldComputational 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
E-mailsriniker@ethz.ch
URLhttp://www.riniker.ethz.ch
DepartmentChemistry and Applied Biosciences
RelationshipAssociate Professor

NumberTitleECTSHoursLecturers
529-0002-00LAlgorithms and Programming in C++ Information 6 credits3GS. Riniker, G. Landrum
AbstractIntroduction 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++
ObjectiveDevelopment of programming skills and craftsmanship in order to be able to deal with the complexity of computer applications in chemistry.
ContentIntroduction 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 notesScript (in English) will be available
LiteratureT.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 / NoticeSince 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.
529-0004-01LClassical Simulation of (Bio)Molecular Systems Information 6 credits4GP. H. Hünenberger, J. Dolenc, S. Riniker
AbstractMolecular 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).
ObjectiveIntroduction to classical (atomistic) computer simulation of (bio)molecular systems, development of skills to carry out and interpret these simulations.
ContentMolecular 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 notesThe powerpoint slides of the lectures will be made available weekly on the website in pdf format (on the day preceding each lecture).
LiteratureSee: www.csms.ethz.ch/education/CSBMS
Prerequisites / NoticeSince 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
529-0460-00LComputer Simulation0 credits1SP. H. Hünenberger, S. Riniker
Abstract
Objective
Prerequisites / NoticeGroup meeting
529-0499-00LPhysical Chemistry1 credit1KM. Reiher, A. Barnes, G. Jeschke, B. H. Meier, F. Merkt, J. Richardson, R. Riek, S. Riniker, T. Schmidt, R. Signorell, H. J. Wörner
AbstractInstitute-Seminar covering current research Topics in Physical Chemistry
Objective
535-0022-00LComputer-Assisted Drug Design Information 1 credit1VS. Riniker, G. Landrum
AbstractThe 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
ObjectiveThe 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.
ContentThe topics include molecular representations and similarity, ligand-based virtual screening (similarity search, QSAR, etc.), and structure-based virtual screening (docking, physics-based models).
Lecture notesScript will be available.
LiteratureRecommended 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.