Molecular modelling and computational biology 1 1000-715MM1

From protein sequence and structure to protein dynamics and function. Overview of basic methods for analysing protein sequences and structures. Protein structure prediction using homology modelling methods. Fundamentals of molecular mechanics and molecular dynamics methods, and their applications in studies of structure and dynamics using popular molecular modelling packages. Physics of protein interactions with low-molecular-weight ligands. Use of a selected, widely used modelling package in docking procedures. During the practical classes, publicly available packages such as NAMD/VMD and AutoDock will be used, as well as commercial software packages: MOE and/or Schrödinger, Molecular Conceptor, Accelrys and/or Tripos.

Course coordinators

Krystiana Krzyśko

Type of course

optional courses

Mode

Classroom

Prerequisites (description)

Scope of Linux knowledge considered basic by the instructor: familiarity with the vi or vim editor; basic shell commands, including: metacharacters (*, ? and [...], and pathname expansion); regular expressions (the dot character, the symbols $, ^, *, [] and [^], {m,n}, (...), and extended operators in egrep and awk); filters (grep, egrep, fgrep, cut, sort, uniq, tr, the sed stream editor, and the awk text filter); input/output redirection operators (>, <, >>, <<[-]delimiter, 2>, 2>&1, and the noclobber variable); pipes, including the tee command; as well as ssh and scp. Materials are available at www.bioexploratorium.pl/wiki. Scope of knowledge concerning the structure and properties of the basic amino acids — recommended book: Biochemistry by L. Stryer.

Learning outcomes

Students learn the basics of mathematical modeling and computer biomolecular systems, dynamics and simulation of selected regulatory processes using the methods of mechanic and molecular dynamics, Monte-Carlo methods, molecular models, and the basics of systems theory. Students become familiar with well-known and popular molecular modeling and design packages as well as the virtual reality technology. The lecture and exercises prepare students for independent modeling of biomolecular systems and designing of enzyme inhibitors – potential drugs.

Assessment criteria

The lecture concludes with a graded examination, which takes place during the final class. Any student who has received credit for the first report and has passed the quizzes from the practical classes may take the examination (maximum of 5 quizzes). The examination is in the form of a test. The test questions are open-ended, and the number of questions depends on their level of difficulty. The maximum score for the test is 100 points. A score of more than 50% is required to pass.

Receiving a final course grade is conditional upon submitting all three reports from the practical classes, correctly written. The grade is entered once the reports have been submitted, but no later than the end of the semester.

The practical classes are conducted in a hands-on format and are integrated with the lecture content. A report must be submitted after each practical class. Reports are graded on a scale from 2 to 6. Reports should be sent to the instructor’s e-mail address, with the subject line “Report X” where X = 1, 2, 3 or I, II, III. After checking the report, the instructor sends a message confirming that the report has been accepted, including the grade, or indicating that it must be corrected, with a list of errors.

The first correction of a report does not affect the report grade. The corrected report is then assessed. The deadline for submitting the report is set by the instructor. Failure to submit a report by the deadline results in the grade being lowered by one grade for each full week of delay. Students have two weeks to correct a report.

If a student receives no more than one grade of 4 for the reports, and grades of 5 or 6 for the remaining reports, the final course grade will be raised by one grade. If a student receives only one grade of 2 for a report, they will have to pass the part of the material covered by that report. This assessment is practical in form. If a student receives more than one grade of 2 for the reports, the assessment will cover the entire material. These assessments take place during the examination session.

The instructor requires knowledge of basic Linux skills and assumes that students possess this knowledge.

Students may expect short quizzes during the practical classes, covering lecture material and completed practical exercises. The quizzes will be announced in advance. The first quiz always takes place during the third practical class and concerns knowledge of the structure and properties of the basic amino acids. The quizzes are pass/fail rather than graded, and passing them is a condition for admission to the final examination in the course.

Bibliography

MOE tutorial (file:///c:/program%20files/moe/html/tutorials/moetour.html)
VMD and NAMD tutorial (http://www.ks.uiuc.edu/Training/Tutorials/)
YASARA tutorial (available in the program)
Lecture materials (available on Kampus)
Molecular Conceptor lectures — available on the computers in the laboratory.