Teaching material

First Floor Projects / Research Areas

Description of the group, for help picking projects and seminars

• Introduction
• Similarity
• Cluster Analysis
• Secondary structure prediction

• Protein Struktur (optional, flexible)
• Cluster Analysis Übung

• Introduction
• Protein Struktur (optional, flexible)
• NMR (Nuclear Magnetic Resonance Spectroscopy)

• Chimera - A Molecular Graphics Program
• Distance Geometry Methods

Old summer semester 2009

• Atomistic Energy Models
• Simulations / statistical mechanics / ...
• Monte Carlo and MD simulations
• Applications - MD / MC
• Exotic Monte Carlo
• Water models / solvation
• Coarse grain models (continuous)
• Lattice Models
• Molecular Evolution
• Protein Folding

• Forces, triangles and angles, vectors till you bleed
• Monte Carlo Methods
• Monte Carlo, Molecular Dynamics
• Molecular Dynamics Simulation of a Protein
• Stochastic simulations - simple version
• revision - Free energy calculations, unusual Monte Carlo and Molecular Dynamics
• revision - lattices and coarse grain proteins

• Introduction
• RNA Chemistry & Structure
• The RNA world
• RNA Structure Prediction
• RNA Folding / Kinetics

• Sequence Alignments
• Protein Modelling
• Multiple Alignments

• Linux
• Alignments
• Homology Modelling

Old winter semester 2008/09

• Introduction / Protein Structure
• Sequence Similarity
• Cluster Analysis
• Secondary Structure Prediction
• Protein Domains
• Protein Function Prediction
• Protein Design
• Protein Fold Recognition

• Proteingrundlagen
• Deriving the Jukes-Cantor relations
• Cluster Analysis Übung
• Secondary Structure Prediction
• Protein Function Prediction
• Breakdown of sequence homology
• Revision

• Grundlagen, Protein Struktur
• Protein Struktur (optional, flexible)
• NMR (Nuclear Magnetic Resonance Spectroscopy)
• Protein Stability
• Crystal Structure Determination of Biological Macromolecules - An Overview by Manfred Weiss
• Analysis, Comparison of Proteins
• First floor topics
• Comparative /Homology Modelling

• Chimera, A Molecular Graphics Program
• Distance Geometry Methods
• Protein Classification
• Revision
• Electron density maps
• Protein Structure Comparison
• Homology Modeling
• Revision

Old summer semester 2008

• Atomistic Energy Models
• Simulations / statistical mechanics / ...
• Monte Carlo and MD simulations
• Applications - MD / MC
• Exotic Monte Carlo
• Water models / solvation
• Coarse grain models (continuous)
• Lattice Models
• Molecular evolution
• Protein Folding

• Übung I: Forces, triangles and angles, vectors till you bleed
• Übung II: Molecular Dynamics Simulation of a Protein
• keine Übung: Eine Erklaerung der Temperatur-Bade-Formel
• Übung III: Monte Carlo, Molecular Dynamics
• Übung IV: Monte Carlo Methods
• Übung V: Revision 2
• Übung VI: Stochastic simulations
• Übung VII: Revision - lattices and coarse grain proteins

• Sequence Alignments
• Multiple Alignments
• Protein structures and comparisons
• Protein classification

• Vorbesprechung
• RNA Chemistry & Structure
• The RNA world
• RNA Structure Prediction
• RNA Folding / Kinetics

Old winter semester 2007/2008

• Introduction
• Sequence Similarity
• Cluster Analysis
• Secondary Structure Prediction
• Protein Domains
• Protein Function Prediction
• Protein Design
• Protein Fold Recognition

• Übung I: Deriving the Jukes-Cantor relations
• Übung II: Cluster Analysis
• Übung III: Secondary Structure Prediction
• Übung IV: Protein Function Prediction
• Übung V: Breakdown of sequence homology
• Übung VI: Revision - Übung

• Introduction
• Protein Structure
• NMR (Nuclear Magnetic Resonance Spectroscopy)
• Motions, frequencies and proteins
• Crystal Structure Determination of Biological Macromolecules - An Overview
• Analysis, Comparison of Proteins
• Comparative / Homology Modelling
• Revision - Übung

Übungen zu 00.908

• Übung I: Chimera, A Molecular Graphics Program
• Übung II: Distance Geometry Methods
• Übung III: Electron Density Maps
• Übung IV: Protein Classifications
• Übung V: Protein Structure Comparison
• Übung VI: Homology Modeling

• Markov chains
• Protein Sequence Design

Old 2006

• Atomistic Energy Models
• Simulations / statistical mechanics / ...
• Monte Carlo and MD simulations
• MD applications, free energy calculations, simulated annealing, structure refinement
• Advanced Monte Carlo, replica exchange, configurational biased MC
• Water models / solvation
• Coarse grain models (continuous)
• Lattice Models
• Molecular evolution
• Protein Folding

Notes für Molecular Dynamics Simulation of a Protein

• Übung I: Molecular Dynamics Simulation of a Protein
• Übung: revision 1 - atomistic force fields, MD and MC
• Übung: Monte Carlo Methods
• Übung: revision 2 - free energies, interesting Monte Carlo and MD
• Übung: Numerical Optimisation Methods
• Übung: Lattices and coarse grain proteins

The best single book for this course (00.912) is Leach, A, "Molecular Modelling: Principles and Applications (2nd Edition)" Prentice Hall.

For Monte Carlo methods, Frenkel, D and Smit, B. "Understanding Molecular Simulation" Academic Press.

• RNA Chemistry & Structure
• The RNA world
• RNA structure prediction 1

• Übung I: RNA Structure Prediction Tools
• Übung II: RNA Structure Prediction Quality Assessment & Improvement
• Übung II: Riboswitchin

Old 2006

• Modelling and basic protein structure
• Similarity
• Cluster analysis
• Secondary structure prediction
• Protein domains
• Protein function prediction
• Protein Design

• Übung I: Jukes-Cantor model
• Übung II: Clustering
• Übung III: Secondary Structure Prediction
• Übung IV: Protein function prediction
• Übung V: Protein homology breakdown
• Übung VI: Übung - revision

Old 2006 / 2007

• Introduction
• Protein structure
• X-ray crystallography
• NMR
• Structure comparison
• Comparative / Homology Modelling
• Revision Day - please read the questions before the lecture time

• Übung I: Chimera, A Molecular Graphics Program
• Übung II: Electron density maps
• Übung III: Distance Geometry Algorithm
• Übung VI: Protein Classifications
• Übung V: Protein Structure Comparison
• Übung VI: Homology Modeling

This course (00.908) takes material from many places, but here is an attempt to list the most important ones.

• For X-ray crystallography: Rhodes, G. "Crystallography made crystal clear", Academic Press, San Diego, 2000.
• For NMR, there are good introductions written by
  • Thomas James and
  • Joseph Hornak

00.938 Statistik fuer Bioinformatik-Studierende

Markov Chains, substitution matrices,...

Last Updated November 11, 2009