Algorithmic Problems in Computational Structural Biology
Instructors : firstname.lastname@example.org, email@example.com
This class covers topics at the cross-roads of computational geometry,
computational topology, graph theory, combinatorial algorithms, and
structural biology - biophysics. Each lecture consists of two sessions
- Lecture 1: fundamental geometric constructions for collections of balls
- Delaunay triangulations and Voronoi diagrams [G-BY,G-E1]
- alpha-shapes [G-E2,G-E3]
- Lecture 2: Molecular surfaces, volumes, and interfaces
- Collections of balls and space-filling diagrams [G-E3]
- Unions of balls: surfaces and volumes [G-C1]
- Modeling macro-molecular interfaces [G-C2,P-JBC]
- Lecture 3: Introduction to protein structure
- Structural biology: the structure-function-dynamics paradigm [P-F]
- Modeling protein structures: the static setting [P-F]
- Modeling protein structures: the dynamic setting [P-FS,P-W]
- Lecture 4: Practical with Visual Molecular Dynamics and the Structural Bioinformatics Library
- Proteins and their hierarchical structure [P-BT]
- The PDB file format
- Elementary analysis under VMD: static structures
- Elementary analysis under VMD: trajectories
- Lecture 5: Graphs and algorithms--introduction
- Modeling and graph problems (chapter 1 of [C-1])
- Algorithms and complexity of algorithms (chapter 8 of [C-1])
- Application to structural biology ([C-3] and [C-4])
- Lecture 6: Graphs, combinatorial problems, and complexity theory
- Some complexity classes: P, NP... (chapter 15 and chapter 16 of [C-1])
- Approximability and hardness of approximation ([C-2] and chapter 17 of [C-1])
- Applications in structural biology ([C-3] and [C-4])
- Lecture 7: Graphs and algorithmic techniques
- Decomposition of graphs for dynamic programming (chapter 18 of [C-1])
- Exponential algorithm (e.g. Branch & Bound) (chapter 18 of [C-1])
- Mathematical programs (e.g. linear programming) (chapter 2 and chapter 13 of [C-1])
- Application to structural biology, continued ([C-3] and [C-4])
- Lecture 8: Exam
References sorted by topic
Geometric and topological modeling
- [G-BY] Algorithmic Geometry, J-D. Boissonnat and M. Yvinec, Cambridge University Press, 1998.
- [G-E1] Geometry and topology for mesh generation, volume 7 of Cambridge
Monographs on Applied and Computational Mathematics,
H. Edelsbrunner, Cambridge, 2001.
H. Edelsbrunner; Weighted alpha shapes; Technical Report
UIUCDCS-R-92-1760, Univ Illinois; 1992.
[G-E3] H. Edelsbrunner; The union of balls and its dual shape;
Discrete Comput. Geom. 13; 1995.
F. Cazals and H. Kanhere and S. Loriot;
Computing the Volume of Union of Balls: a Certified Algorithm;
ACM Transactions on Mathematical Software; 38 (1); 2011.
- [G-C2] F. Cazals;
Revisiting the Voronoi description of Protein-Protein interfaces: Algorithms;
IPAR International Conference on Pattern Recognition in
- [P-F] A. Fersht, Structure and mechanism in protein science: a guide to enzyme
catalysis and protein folding, Freeman, 1999.
- [P-BT] C. Branden and J. Tooze, Introduction to Protein Structure (2nd
Ed.), Garland publishing, 1999.
- [P-FW] D. Frankel and B. Smit, Understanding molecular simulation, Academic press, 2002.
- [P-W] D.J. Wales, Energy Landscapes, Cambridge University Press, 2003.
J. Janin and R. P. Bahadur and P. Chakrabarti;
Protein-protein interaction and quaternary structure;
Quarterly reviews of biophysics 41 (2); 2008.
[C-1] Combinatorial optimization: algorithms and complexity
C. H. Papadimitriou, and K. Steiglitz
Courier Corporation. 1982 (new versions available).
[C-2] Approximation algorithms,
V. V. Vazirani,
College of Computing, Georgia Institute of Technology, 1997 (new versions available).
[C-3] Unveiling Contacts within Macro-molecular assemblies by solving Minimum Weight Connectivity Inference Problems,
D. Agarwal, C. Caillouet, D. Coudert, and F. Cazals,
Molecular and Cellular Proteomics, 14, 2015.
[C-4] Protein Structure Comparison: From Contact Map Overlap Maximisation to Distance-based Alignment Search Tool,
PhD thesis, Univ. Rennes 1, 2010.
The final grade will be the weighted average of the class
participation (1/5) and the mark of a 2h written exam (4/5).