Lehre

67-102 Vorlesung Angewandte Bioinformatik: Sequenzen

1 Sequence Alignments
2 Multiple sequence alignments
3 Genomes and Assembly
4 Variation - the issues

67-103 Übung zu Angewandte Bioinformatik: Sequenzen

0 Introduction
1 a Informationstheorie / Codierung
1 b Informationstheorie / Folien
2a Datenbanken / Alignments
2b Datenbanken / Alignments Folien
3a Log Odds Matrix
3b Log Odds Matrix Folien
4a Python
4b Python Folien
5a Needleman / Wunsch Algorithmus
5b Needleman / Wunsch Algorithmus Folien
6a Konservierung
6b Konservierung Folien
7 BLAST
8a Sequenzassemblierung
8b Sequenzassemblierung Folien
9 Galaxy

67-122 Vorlesung Struktur und Simulation

1 Atomistic Energy Models
2 Monte Carlo and MD simulation
3 Modern Monte Carlo
4 Water models / solvation
5 Lattice Models
6 Kinetics

67-123 Übung zu Struktur und Simulation

1 Calculating gradients and forces
2 Statistical Mechanics forces and Simple Monte Carlo Integration
3 Metropolis Monte Carlo
4 A Molecular Dynamics Program
5 Force Fields
6 Molecular Simulation of a Protein
7 Revision

67-251 Proseminar CiS-Biochemie
Einführung

67-113 Übungen Grundlagen der Strukturanalyse
1 Chimera
2 Distance Geometry
3 Floyd
4 Coot
5 Strukturevaluation
6 Revision 1
7 PDB Structure Comparison

67-112 Vorlesung Grundlagen der Strukturanalyse
1 Einführung GST
2 Protein Struktur
3 NMR (Nuclear Magnetic Resonance Spectroscopy)
4 X-ray sociology
5 Classifying and comparing proteins
6 Protein spaces
7 Comparative / Homology Modelling
8 Motions, frequencies and proteins

67-105 Übungen Angewandte Bioinformatik: Strukturen
1 Chimera
2 Genauigkeit
2.1 Genauigkeit Zusatz
3 Qualität
4 Seitenketten Rotamere
5 Konservierung
6 Homology Modelling
7 Simulated Annealing
8 RNA

67-104 Vorlesung Angewandte Bioinformatik: Strukturen
0 Introduction
1 NMR vs X-ray, precision, certainty
2 Energies
3 Analysis and comparison
4 Comparative / Homology Modelling
5 Protein Design
6 Nucleotides

67-102 Vorlesung Angewandte Bioinformatik: Sequenzen

1 Sequence Alignments
2 Multiple sequence alignments similarity without sequence similarity
3 Sequence vs structure comparisons

67-103 Übung Angewandte Bioinformatik: Sequenzen

7 Phyton

67-122 Vorlesung Struktur und Simulation

1 Atomistic Energy Models
2 Monte Carlo and MD simulations
3 Modern Monte Carlo
4 Water models / solvation
5 Lattice Models
6 Evolution
7 Kinetics
8 Low Numbers

67-123 Übung zu Struktur und Simulation

67-410 Vorlesung Programmierung für Naturwissenschaften

67-411 Übung Programmierung für Naturwissenschaften

R Übung 1
R and a bit of statistics
Examples Programming in R

62-455.1 RNA Biochemistry

1 The RNA world

67-251 Proseminar CiS-Biochemie

Einführung (pdf, 657 KB)

67-113 Übungen Grundlagen der Strukturanalyse

1 Chimera (pdf, 1.1 MB)
2 Distance Geometry (pdf, 160 KB)
3 Floyd (pdf, 76 KB)
4 Structure Comparision (pdf, 111 KB)
5 Revision 1 (pdf, 380 KB)
6 Revision 2 (pdf, 137 KB)

67-112 Vorlesung Grundlagen der Strukturanalyse

1 Einführung GST (pdf, 343 KB)
2 Protein Struktur (pdf, 4.2 MB)
3 NMR (pdf, 2.2 MB)
4 Protein spaces (pdf, 832 KB)
5 X-ray sociology (pdf, 8.0 MB)
6 Classifying and comparing proteins (pdf, 2.3 MB)
7 Comparative / Homology Modelling (pdf, 1.7 MB)
8 Motions, frequencies and proteins (pdf, 2.2 MB)

67-105 Übungen Angewandte Bioinformatik: Strukturen

1 Chimera (pdf, 1.3 MB)
2 Mobility (pdf, 291 KB)
2.1 Mobility II (pdf, 176 KB)
3 Analysis Comparison (pdf, 353 KB)
4 Sidechain Rotamers (pdf, 336 KB)
5 Conservation (pdf, 215 KB)
6 Homology Modelling (pdf, 244 KB)
7 Homology Modelling 2 (pdf, 269 KB)
8 Simulated Annealing (pdf, 252 KB)
9 RNA Prediction / Design (pdf, 230 KB)

67-104 Vorlesung Angewandte Bioinformatik: Strukturen

0 Einführung (pdf, 494 KB)
1 Genauigkeit (pdf, 3.7 MB)
2 Energies (pdf, 1.2 MB)
3 Analysis and comparison (pdf, 4.0 MB)
4 Comparative / Homology Modelling (pdf, 1.8 MB)
5 Protein Design (pdf, 0.9 MB)
6 Nucleotides (pdf, 1.8 MB)
7 RNA structure, predictions (pdf, 2.6 MB)
8 Nucleotide Design (pdf, 2.4 MB)

67-202 Übungen Bioinformatik

1 Linux (pdf, 1.5 MB)
2 Chimera (pdf, 1.0 MB)
3 Homology modeling (pdf, 339 KB)
4 Revision (pdf, 266 KB)

67-201 Vorlesung Bioinformatik

1 Sequence Alignments (pdf, 3.7 MB)
2 Multiple sequence alignments similarity without sequence similarity (pdf, 2.3 MB)

67-123 Übungen zu Struktur und Simulation

1 Calculating gradients and forces (pdf, 191 KB)
2 Statistical Mechanics and Simple Monte Carlo Integration (pdf, 161 KB)
3 Metropolis MC (pdf, 204 KB)
4 A molecular dynamics program (pdf, 47 KB)
5 Revision (pdf, 508 KB)
6 Last revision (pdf, 581 KB)

67-122 Vorlesung Struktur und Simulation

1 Atomistic Energy Models (pdf, 1.0 MB)
2 Simulations / statistical mechanics / ... (pdf, 688 KB)
3 Monte Carlo and MD simulations (pdf, 1.7 MB)
4 Modern Monte Carlo (pdf, 843 KB)
5 Water models / solvation (pdf, 721 KB)
6 Coarse grain models (continuous) ... potentials of mean force (pdf, 2.0 MB)
7 Lattice Models (pdf, 1.5 MB)

62-455.2 Seminar zur Biochemie der RNA

62-455.1 Biochemie der RNA

0 Vorbesprechung (pdf, 688 KB)
1 RNA Structure (pdf, 5.3 MB)
2 The RNA world (pdf, 2.0 MB)

67-251 Proseminar CiS-Biochemie

1 Introduction (pdf, 660 KB)

67-113 Übungen Grundlagen der Strukturanalyse

1 Chimera (pdf, 0.9 MB)
2 Electron Density Maps (pdf, 135 KB)
3 Coot (pdf, 44 KB)
4 Distance Geometry (pdf, 110 KB)
5 Revision 1 (pdf, 304 KB)
6 Structure Comparison (pdf, 97 KB)
7 Homology Modeling (pdf, 216 KB)
8 Temperature Dependence of Motions (pdf, 165 KB)
9 Revision 2 (pdf, 110 KB)

67-112 Vorlesung Grundlagen der Strukturanalyse

1 Introduction (pdf, 384 KB)
2 Protein Struktur (pdf, 3.6 MB)
3 NMR (pdf, 2.1 MB)
4 Protein spaces (pdf, 813 KB)
5 Classifying and comparing proteins (pdf, 2.3 MB)
6 Comparative / Homology Modelling (pdf, 1.4 MB)
7 Protein Stability (pdf, 1.3 MB)

67-105 Übungen Angewandte Bioinformatik: Strukturen

0a Linux Introduction (pdf, 77 KB)
0b Linux Introduction (pdf, 86 KB)
1 Clustering (pdf, 144 KB)
2 Protein Domains (pdf, 70 KB)
3 Sequence Homology (pdf, 121 KB)
4 RNA Sequence Design (pdf, 142 KB)

67-104 Vorlesung Angewandte Bioinformatik: Strukturen

1 Introduction / Modelling (pdf, 1.5 MB)
2 Cluster analysis (pdf, 1.2 MB)
3 Protein Domains (pdf, 2.6 MB)
4 Protein Function Prediction (pdf, 2.5 MB)
5 Protein Design (pdf, 1.5 MB)
6 Nucleotide Design (pdf, 5.6 MB)
7 Correlated Mutations (pdf, 1.2 MB)
8 Intrinsically disordered proteins (pdf, 1.3 MB)
9 Self-consistent mean fields (pdf, 0.9 MB)

67-202 Übungen Bioinformatik

1 Linux (pdf, 1.2 MB)
2 Chimera (pdf, 0.9 MB)
3 Homology Modeling (pdf, 216 KB)
4 Revision (pdf, 254 KB)

67-201 Vorlesung Bioinformatik

1 Sequence Alignments (pdf, 2.7 MB)
2 Multiple sequence alignments similarity without sequence similarity (pdf, 3.0 MB)

67-123 Übungen zu Struktur und Simulation

1 Calculating gradients and forces (pdf, 163 KB)
2 Statistical Mechanics and Simple Monte Carlo Integration (pdf, 131 KB)
3 Metropolis Monte Carlo (pdf, 109 KB)
4 A Molecular Dynamics Program (pdf, 115 KB)
5 Monte Carlo and Revision (pdf, 105 KB)
6 Gromacs (pdf, 122 KB)
7 Revision#mce_temp_url# (pdf, 111 KB)

67-122 Vorlesung Struktur und Simulation

1 Atomistic Energy Models (pdf, 1.0 MB)
2 Simulations / statistical mechanics / ... (pdf, 561 KB)
3 Monte Carlo and MD simulations (pdf, 1.0 MB)
4 Modern Monte Carlo (pdf, 711 KB)
5 Water Models (pdf, 718 KB)
6 Coarse grain models (continuous)...potentials of mean force (pdf, 1.4 MB)
7 Lattice Models (pdf, 1.2 MB)
8 Molecular Evolution (pdf, 0.9 MB)
9 Protein Folding (pdf, 1.0 MB)

62-455.1 Biochemie der RNA

1 RNA Structure (pdf, 5.5 MB)

67-251 Proseminar CiS-Biochemie

1 Introduction (pdf, 495 KB)

67-113 Übung zu Grundlagen der Strukturanalyse

1 Chimera (pdf, 799 KB)
2 Distance Geometry (pdf, 103 KB)
3 Revision 1 (pdf, 287 KB)
4 Electron Density Maps (pdf, 127 KB)
5 Coot (pdf, 297 KB)
6 Structure Comparison (pdf, 88 KB)
7 Homology Modelling (pdf, 153 KB)
8 Temperature Dependence of Motions (pdf, 167 KB)
9 Revision 2 (pdf, 110 KB)

67-112 Vorlesung Grundlagen der Strukturanalyse

1 Introduction (pdf, 290 KB)
2 Protein structure (pdf, 3.4 MB)
3 NMR (Nuclear Magnetic Resonance Spectroscopy) (pdf, 1.7 MB)
4 Protein spaces (pdf, 732 KB)
6 Classifying and comparing proteins (pdf, 2.1 MB)
7 Comparative / Homology Modelling (pdf, 1.4 MB)
8 Protein stability (pdf, 1.3 MB)
9 Protein Folding (pdf, 1.2 MB)

67-105 Übung zu Angewandte Bioinformatik: Strukturen

0a Arbeiten mit Linux und an der Kommandozeile, Teil 1 (pdf, 84 KB)
0b Arbeiten mit Linux und an der Kommandozeile, Teil 2 (pdf, 80 KB)
1 Cluster Analysis (pdf, 98 KB)
2 Protein Domains (pdf, 63 KB)
3 Sequence Homology (pdf, 116 KB)
4 Protein Function Prediction (pdf, 117 KB)
5 RNA Sequence Design (pdf, 160 KB)
6 Revision 1 (pdf, 64 KB)
6 Revision 2 (pdf, 36 KB)

67-104 Vorlesung Angewandte Bioinformatik: Strukturen

1 Introduction / Modelling (pdf, 1.3 MB)
2 Cluster analysis (pdf, 1.0 MB)
3 Protein Domains (pdf, 2.4 MB)
4 Protein function prediction (pdf, 2.2 MB)
5 Protein Design (pdf, 1.4 MB)
6 Nucleotide Design (pdf, 5.4 MB)
7 Correlated Mutations - structure prediction (pdf, 835 KB)
8 Self-consistent mean field methods (pdf, 1.0 MB)

67-202 Übungen zu Bioinformatik

1 Linux (pdf, 444 KB)
2 Chimera (pdf, 1.1 MB)
3 Modelling (pdf, 151 KB)
4 Revision (pdf, 309 KB)

67-102 Vorlesung Bioinformatik

1 Sequence alignments (pdf, 2.7 MB)
2 Multiple sequence alignments similarity without sequence similarity (pdf, 3.2 MB)

67-123 Übungen zu Struktur und Simulation

1 Calculating gradients and forces (pdf, 156 KB)
2 Statistical Mechanics and Simple Monte Carlo Integration (pdf, 125 KB)
3 Metropolis Monte Carlo (pdf, 106 KB)
4 A Molecular Dynamics Program (pdf, 110 KB)
5 Revision: Force Fields for Monte Carlo and Molecular Dynamics (pdf, 101 KB)
6 Molecular dynamics simulation of a protein (pdf, 124 KB)
7 Revision (pdf, 111 KB)

67-122 Vorlesung Struktur und Simulation

1 Atomistic models (pdf, 1.0 MB)
2 Simulations / statistical mechanics / ... (pdf, 559 KB)
3 Monte Carlo and MD simulations (pdf, 845 KB)
4 Applications - MD / MC (pdf, 745 KB)
5 Modern Monte Carlo (pdf, 704 KB)
6 Water models / solvation (pdf, 612 KB)
7 Coarse grain models (continuous) ... potentials of mean force (pdf, 1.6 MB)
8 Lattice Models (pdf, 1.2 MB)
9 Molecular Evolution (pdf, 732 KB)

62-455.2 Seminar zur Biochemie der RNA

62-455.1 Biochemie der RNA

0 Vorbesprechung (pdf, 626 KB)
1 RNA structure (pdf, 4.3 MB)
2 The RNA world (pdf, 2.8 MB)