160:544 Special Topics in Biological Chemistry (3 credits)
Mathematical & Computational Methods in Biological Research
Faculty & Staff Contacts:
Professor Ronald M. Levy - Wright-Rieman Labs, Rm A205; 445-3947; ronlevy@lutece.rutgers.edu
Professor Wilma K. Olson - Wright-Rieman Labs, Rm A209; 445-3993; olson@rutchem.rutgers.edu
Dr. Emilio Gallicchio - Wright-Rieman Labs, Rm 205; 445-5157; emilio@hpcp.rutgers.edu
Dr. A. R. Srinivasan - Wright-Rieman Labs, Rm A209; 445-4619; srini@rutchem.rutgers.edu
Time & Location:
Tuesdays and Thursdays, 3:00-4:30 PM, Wright-Rieman Laboratories, Room 260
Requirements:
Assigned computational exercises and special project
Course Outline (approximate timetable):
Introduction; statistical mechanical foundations (January 16)
Assessment of conformational freedom (January 18-February 8)
Conformational energy functions
Internal chemical parameters and their direct control
Implicit solvation models
Regular helical structures and virtual bond representations
Computational exercises:
energy surfaces of the alanine dipeptide and regular polyalanine helices in vacuo and in solution
Computation of protein-ligand binding interactions (February 13-15)
Energy minimization
Computational exercises:
To be announced
Sequence similarities and structural similarities (February 20-March 6)
Sequence alignment algorithms, e.g., Smith-Waterman, etc.
Measures of global folding, e.g., distance plots, writhing number, etc.
Computational exercises:
To be announced
Molecular dynamics simulations of DNA and proteins (March 20-April 17)
Molecular dynamics
Base-pair parameters
Harmonic analysis
Elastic models
Computational exercises:
To be announced
Special projects (April 24-May 3)
Special Workshops:
March 8-9 - DIMACS Workshop Protein Structure & Structural Genomics: Prediction, Determination, Technology and Algorithms; URL: http://dimacs.rutgers.edu/Workshops/ProteinStructure2/
April 19-20 - DIMACS Workshop on DNA Sequence & Topology; URL: http://dimacs.rutgers.edu/Workshops/TopologyIII/
SYLLABUS (Topic):
1 January 16-18
Introduction; statistical mechanical foundations
Conformational energy functions;
2 January 23-25
Dipeptide computations in vacuo
Internal chemical parameters and their control
3 January 30-February 1
Helical representations
Helical computations in vacuo
4 February 6-8
Solvation models
Dipeptide and helical calculations in solution
5 February 13-15
Energy minimization
Computation of protein-ligand binding interactions
6 February 20-22
Sequence alignment algorithms
7 February 27-March 1
Measures and comparisons of global folding
8 March 6
Decoy protein folds and their analysis
March 8-9
DIMACS Workshop Protein Structure & Structural Genomics: Prediction, Determination, Technology and Algorithms
March 13-15
Spring Break
9 March 20-22
Molecular dynamics
Simulation of DNA and protein motions
10 March 27-29
Base-pair parameters and DNA analysis
11 April 3-5
Harmonic analysis in Cartesian and base-pair parameter space
12 April 10-12
Elastic modeling of spatially constrained DNA
13 April 19-20
DIMACS Workshop on DNA Sequence & Topology
14 April 24-26
Special project
15 May 3
Special project due
The following graduate students are pre-approved for enrollment:
Student E-mail address Faculty Advisor
1. Sreekala Balasubramanian balasubr@rutchem.rutgers.edu W. Olson
2. Yoav Biton yoavbi@yahoo.com B. Coleman
3. Heather E. Burden hburden@rutchem.rutgers.edu W. Olson
4. Pei-Ying (Elfin) Chu chup@rutchem.rutgers.edu W. Olson
5. Andrew Colasanti andrewc@rutchem.rutgers.edu W. Olson
6. Peicheng Du piecheng@lutece.rutgers.edu R. Levy
7. Wei (Julius) Ge wge@rutchem.rutgers.edu W. Olson
8. Jennifer Knight jknight@rutchem.rutgers.edu 1st year
9. Yun Li yunli@rutchem.rutgers.edu W. Olson
10. Charles Lu charlu76@yahoo.com M. Driscoll
11. Kevin J. Maurice kmaurice@hotmail.com R. Levy
12. William McLaughlin billme@rci.rutgers.edu H. Berman
13. Kiyean Nam kiyean.nam@pharma.novartis.com J. Dougherty (UMDNJ)
W. Cornell (Novartis)
14. Yang Su yangsu@rutchem.rutgers.edu R. Levy
15. Fei Xu feixu@eden.rutgers.edu 1st year
16. Sukjoon Yoon sukjoon@lutece.rutgers.edu R. Levy
160:544 Special Topics in Biological Chemistry (3 credits)
Mathematical & Computational Methods in Biological Research
Tuesdays and Thursdays, 3:00-4:30 PM
Wright-Rieman Laboratories, Rooms 260/308
160:544 Special Topics in Biological Chemistry (3 credits)
Mathematical & Computational Methods in Biological Research
Tuesdays and Thursdays, 3:00-4:30 PM
Wright-Rieman Laboratories, Rooms 260 and 308