Syllabus

Structural Bioinformatics

I619 - Spring 2008 - class ID 28329

 

Class Meets

Time: Mondays and Wednesdays, 9:30am-10:45am

Place: PY109 (Psychology Building) Campus map.

 

Instructor

Predrag Radivojac

Office: Eigenmann 1005 (during Fall 2007, should move to I219 during Spring 2008)

Email:.predrag@indiana.edu.

Web: http://www.informatics.indiana.edu/predrag

 

Office Hours

By appointment.

 

Course Objective

The course will cover informatics approaches, based on the sequence and 3D structure of biological macromolecules, whose objective is to improve our understanding of the function of these molecules.

 

Prerequisites

Graduate student standing or permission of the instructor.

 

Textbooks

Required

Structural Bioinformatics (Methods of Biochemical Analysis, V. 44) - by Philip E. Bourne (Editor), Helge Weissig (Editor), 2000.

 

Recommended

Introduction to Protein Structure - by Carl-Ivar Branden and John Tooze

Understanding DNA - by Chris Calladine, Horace Drew, Ben Luisi, and Andrew Travers

 

Supplementary material, especially recent research papers, will be provided in class.

 

Topics

▪  Introduction to structural bioinformatics

▫  structural basis of biological phenomena

▫  challenges in computing with structural data 

▪  Fundamental principles of protein/DNA/RNA structure

▫  chemical structure of proteins

▫  protein secondary and tertiary structure

▫  protein domains and folds

▫  sequence-to-structure-to-function paradigm

▫  chemical structure of nucleic acids

▫  structure of nucleic acids

▪  Molecular visualization

▫  visualization styles and software

▪  Experimental methods for structure determination

▫  basic principles of X-ray crystallography

▫  basic principles of NMR spectroscopy

▫  other methods for direct and indirect determination of structure of biopolymers

▫  structural/functional genomics initiative and high-throughput techniques

▫  structural quality assurance

▪  Structure-based databases

▫  Protein Data Bank

▫  SCOP and CATH classifications

▫  RNABase

▫  other sources

▪  Structure comparison and alignment

▫  automated assignment of secondary structure

▫  structural similarity measures

▫  structural alignment algorithms

▪  Prediction of structure of biopolymers

▫  prediction of protein structure (prediction of secondary structure, homology modeling, fold recognition and ab initio methods)

▫  membrane proteins

▫  prediction of RNA structure

▫  prediction of DNA curvature

▪  Prediction of protein function from structure and other types of data

▫  definition of protein function and gene ontology

▫  enzyme classification and functional site identification

▫  relationship between structure and function

▫  prediction of protein-ligand interactions

▪  Principles of molecular recognition and docking

▫  protein-small molecule interactions

▫  macromolecular docking and protein-protein interactions

▫  structural bioinformatics in drug discovery

▪  Intrinsically disordered (unstructured) proteins

▫  sequence-to-disordered ensemble-to-function paradigm

▫  functional characterization of disordered proteins

▫  prediction of disordered proteins

 

Expected Guest Speakers

Prof. Vladimir Uversky, School of Medicine

Prof. Sean Mooney, School of Medicine

 

Grading

Midterm exam: 20% (week 9, in class exam)

Final project: 30% (will include presentation at the end of semester)

Homework assignments: 40% (critical reading of research papers, 1 page summaries for each paper, small presentations)

Class participation: 10% (based on attendance and activity)

 

Late Policy and Academic Honesty

The homework assignments are due in class, on the specified due date. No late assignments will be accepted unless there are legitimate circumstances. All assignments are individual, except when collaboration is explicitly allowed. All the sources used for problem solution must be acknowledged, e.g. web sites, books, research papers, personal communication with people, etc. Academic honesty is taken seriously; for detailed information see Indiana University Code of Student Rights, Responsibilities, and Conduct.

Last updated: 01/01/2008