Computer Modeling of Macromolecular Structure and Function

HBCG 6338: Computer Modeling of Macromolecular Structure and Function
HBCG 6206: Bioinformatics on the Web

Time: Monday 9:30 am - 11:15 am, Thursday 9:30 am - 11:15 am

Location: Clay Hall, Conference room 2.130

Textbooks: - Gibas, Jambeck
Developing Bioinformatics Computer Skill, O’Reilly & Assoc., Inc. Sebastopol, CA

                         Durbin, Eddy, Krogh, Mitchison
                                     Biological sequence analysis Cambridge University Press

      Course Director: Werner Braun, Ph.D., Professor, Biochemistry and Molecular Biology,
                                        202 Clay Hall, webraun@utmb.edu, (409) 747-6810

            Course Description: Introduction to computational modeling methods for protein and nucleic
               acid structure and function. Topics include molecular dynamics, homology modeling and
               sequence and genomic analysis methods.

Useful Links for the Course
Click Here

         Mon Jan 7 (W. Braun)
                Overview of Bioinformatics
                Probabilities and Probabilistic Models
                Bayes Theorem
                Basics of sequence alignment, Substitution Matrices
- Lecture Notes
      - Homework 1

         Thu Jan 10 (W. Braun/D. Power)
                Selection of Student Projects
                UNIX OS Systems, Files and Directories, UNIX Shell Scripts Communication
                Gibas, Chap. 3-5
                - Lectures Notes

         Mon Jan 14 (D. Power/W. Braun)
                I. Perl Scripts, Bioperl
                Gibas, Chap. 12
                 - Lectures Notes
                 - Homework 2
                      - Example Solution (simple)
                      - Example Solution (prompts user for PDB and OUT file names)
                      - Output (output is identical for both Example Solutions)

            II. Molecular Mechanics: Nature of Forces
                Estimation of parameters, calculation of energies
                - Lecture Notes

         Thu Jan 17 (W. Braun/N. Oezguen)
                Retrieval and Visualization of Protein Structures, the Protein Data Bank (PDB)
                Practical Excercise with MolMol
                Gibas, Chap. 9
   - Lecture Notes
   - Homework 3

Mon Jan 21 Martin Luther King Day (UTMB Holiday)

         Thu Jan 24 (C.H. Schein)
                Practical Aspects of Sequence Alignment
                FASTA, BLAST, CLUSTAL_W, DALI, PCPMer
                Motif Search, PROSITE Patterns
                - Lecture Notes
                    - Related Sequence File (MS Word file)
                    - CLUSTAL W 2.0 multiple sequence alignment files
                          - 6 sequences (*.aln file) can be opened in a text editor
                          - Page 1: 4 sequence alignment, Page 2: 6 sequences from above (MS Word file)
                             (in both case, residue labels are colored by type)
        - Anthrax Lethal Factor Movie
               - Homework 4

         Mon Jan 28 (W. Braun)
                Theory and Procedures of Dynamic Programming
                Needleman-Wunsch algorithm
                Significance of Scores
                Chap. 2, Durbin, Eddy, Krogh, Mitchison
- Lecture Notes

        Thu Jan 31 (W. Braun)
                Motif and Profile Search
                Markov Chains and Hidden Markov Models
                Chap. 3, Durbin, Eddy, Krogh, Mitchison
                - Lecture Notes
                - Homework 5

         Mon Feb 4 (O. Ivanciuc)
                Basics of Homology Modeling, MPACK
              Fold Recognition Servers
                - Lecture Notes
                    - Homology Modeling
                    - Geometry Optimization with Molecular Mechanics

         Thu Feb 7 (N. Oezguen)
                Practical exercise with fold recognition servers
                - Lecture Notes

Mon Feb 11 (W. Braun/D. Power/C.H. Schein/O. Ivanciuc/N. Oezguen)
Practical exercises with Molecular Modeling and Empirical Energy Calculations

         Thu Feb 14 (W. Braun/D. Power/C.H. Schein/O. Ivanciuc/N. Oezguen)
              Practical Exercise on student projects (BSCB students)

         Mon Feb 18 President’s Day (UTMB Holiday)

Thu Feb 21 (W. Braun/D. Power/C.H. Schein/O. Ivanciuc/N. Oezguen)
Practical Exercise on student projects (BSCB students)

Mon Feb 25 (W. Braun/D. Power/C.H. Schein/O. Ivanciuc/N. Oezguen)
Practical Exercise on student projects (BSCB students)

Thu Feb 28 (W. Braun/D. Power/C.H. Schein/O. Ivanciuc/N. Oezguen)
Student Presentations

Additional Lectures HBCG 6338:
------------All Classes Will Now Occur EVERY TUESDAY and at a different LOCATION--------------

Tues March 4 (B. Luxon/H. Spratt)
Basic Probability and Statistics Including Non-Parametric Methods

            Tues March 11 (B. Luxon/H. Spratt)
                Application of basic statistics including construction of boxplots, QQ plots, etc.
                Data analytical methods including t-tests, one-way and two-way ANOVA, etc.

Tues March 18 (B. Luxon/H. Spratt)
Hierarchical clustering and principle component analysis (PCA)

            Tues March 25 (B. Luxon/H. Spratt)
                Basic genomics data analysis of microarrays with software laboratory using the
                 Spotfire DecisionSite data mining software suite.

            Tues April 1 (B. Luxon/H. Spratt)
                Basic proteomics analysis and 2D gel image analysis.
                Introduction to the Ingenuity Pathways Analysis software suite.

           Grades:
       Grades will be calculated based on the performance of the following:

                            Five homework problems (40%)
                            Final project and presentation (50%)
                            Class Participation (10%)

The grading may be subject to change at the discretion of the co-directors, but final course grades
will be determined using GSBS grading scale:

               *** Student end-of-course evaluations are required for all A/B/C/F-graded GSBS courses.
               Students are required to fill out the evaluations to receive a grade in the course. If the specified
               evaluation form is not received, an "I" (Incomplete) grade will be reported to the Office of
               Enrollment Services. If the course requirements are not completed within 30 days, the grade
               automatically converts to an "F" (Failure) grade. The evaluations are anonymous and will be
               available to course directors only after grades are assigned.

           Examinations/Evaluations:
       Each student will be given a project to work through during the course. At the end of
               the course, the students have to present the results of their projects in a PowerPoint presentation.

           Excused Absences:
       Since the course is highly interactive, attendance and participation are required. Students
               can be excused from graded assignments without penalty to their grade if an excused letter is
               obtained from Dr. Lillian Chan, Director of BMB Graduate Program, or Dr. Wayne Bolden,
               Director of BSCB Educational Track, in advance. If absences are excused, appropriate make-up
               work will be provided for students at the discretion of the co-directors.

           Important Dates:
       No GSBS Classes: [these dates are also noted (vida supra) in the course schedule]
               Monday, January 21: Martin Luther King Day
               Monday, February 18: President's Day

90	-	100	=	A
80	-	89	=	B
70	-	79	=	C
69	or	below	=	F