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CHEM 337 - Computational Structural And Chemical Biology

Theoretical and practical aspects of protein sequence alignments,
secondary structure prediction, comparative modeling, protein-protein
and protein-ligand docking. Structure-based drug design, virtual
quantitative structure activity relations, cheminformatics, and
screening, pharmacophore mapping in therapeutic development.
This course includes a laboratory section.

Syllabus: pdf-download

Course Materials
Lecture Slides Materials for lab following lecture
To decompress myfile.tgz, type tar -xzvf myfile.tgz from a linux terminal
1: Course Overview and Introduction to Protein Structure pdf-download
2: Sequence-Sequence Alignment Methods pdf-download Intro to Linux: tar-download
3: Sequence Based Secondary Structure Prediction pdf-download
4: Protein Family Classification through Hidden Markov Models pdf-download Sequence-sequence alignment: tar-download
Secondary structure prediction: tar-download
Homework: tar-download
5: Fold Recognition & Sequence-Structure Alignment (Threading) pdf-download
6: Comparative Modelling and the Loop Closure Problem pdf-download Fold Recognition and Threading: tar-download
7: De-Novo Structure Prediction pdf-download
8: Modeling Protein Side Chains from Rotamer Libraries pdf-download Comparative Modelling/Loops: tar-download
9: Protein Structure Determination from Limited Experimental Datasets pdf-download
10: Protein Design pdf-download De Novo Structure Prediction: tar-download
10.5: Topic Overflow, Summary, First Exam Preparation Rotamer Library: tar-download
11: Structure-Structure Alignment Techniques and Fold Classification pdf-download tar-download
12: Protein-Protein Docking pdf-download
13: Protein-Ligand Docking pdf-download Docking: tar-download
14: Structure-based Virtual Screening & Drug Design pdf-download
15: Constitution, Configuration, & Conformation pdf-download Structure-Based Virtual Screening: tar-download
16: Structure Generators pdf-download Ligand-Based Virtual Screening: tar-download
17: Molecular Descriptors pdf-download
18: QSAR, Ligand-based Virtual Screening, and Pharmacophore Mapping pdf-download Pharmacophore Mapping: tar-download


Michael Müller, Kerstin Gräbe, Jens Meiler

Organochemical Pathways is a systematic review on typical reactions in organic chemistry on a poster and as a program running on windows 95/98/NT

File and hi-resolution poster: pathways.zip pdf-download

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