Creszensci, Goldman, Papadimitriou, Piccolboni, Yannakakis. On the complexity of protein folding. [hardcopy]

P. Clote, L. Gasieniec, R. Kolpakov, E. Kranakis, D. Krizanc, On Realizing Shapes in the theory of RNA neutral networks. Journal of Theoretical Biology. Volume: 236, Issue: 2, September 21, 2005, pp. 216-227. -- Mαρία Λιαζη

Clote, Ferre, Kranakis, Krizanc. RNA has lower folding energy than random RNA on the same dinucleotide frquency. [hardcopy]

κεφάλαιο από το "Intro to Bioinformatics algorithms (Comp. Mo. Bio)". Jones & Pevzner. [Πληροφορική, Copy center στην είσοδο Zωγράφου]

Κεφάλαιο 9-Transformational grammars,  από το βιβλίο Biological sequence analysis, R.Durbin, S.Eddy, A.Krogh, G.Mitchison. -- Χρυσηίδα Γαλανάκη

Structure

Wolfson, Nussinov et al. Multiple docking and structure prediction. International Journal of Robotics Research: 2005, Special Issue on Robotics Techniques Applied to Computational Biology. http://www.ijrr.org/contents/24_02/IJR24_02.html

Guibas et.al. Protein loops and inverse kinematic problem. International Journal of Robotics Research: 2005, Special Issue on Robotics Techniques Applied to Computational Biology. http://www.ijrr.org/contents/24_02/IJR24_02.html

Haliloglu T, Kolinski A, Skolnick J. Use of residual dipolar couplings as restraints in ab initio protein structure prediction. Biopolymers. 2003 Dec;70(4):548-62.

Andrew Leaver-Fay, Yuanxin Liu and Jack Snoeyink, Faster Placement of Hydrogens in Protein Structures by Dynamic Programming. Alenex 2004. (pdf)

Badoui, Demaine, T. Hajiaghayi, Indyk. Low-dim embedding with extra info. SOCG 2004. [hardcopy]

Huan, Wang, Bandyiopadhay, Snoeyinck, Prins, Tropsha. Mining protein family specific residue packing patterns from protein structure groups. RECOMB'04. [hardcopy]

P. Guentert. Automated NMR protein structure prediction. Survey [pdf]

Distances

John W. Raymond and Peter Willett. Similarity Searching in Databases of Flexible 3D Structures using Smoothed Bounded Distance Matrices. J. Chem. Inf. Comput. Sci.; 2003 [pdf]

Porta, Thomas, Ros et.al. A branch-and-prune algorithm for solving systems of distance constraints. IEEE Intern. Conf. Robotics & Automation, 2003. [pdf] -- Μαρκομανώλης

B. Berger, J. Kleinberg, F.T. Leighton. Reconstructing a Three-Dimensional Model with Arbitrary Errors. Proc. 28th ACM Symposium on Theory of Computing, 1996. Final version: J.ACM:46 [pdf] [Postscript].

T. Akutsu, H. Tamaki, T. Tokuyama. ``Distribution of distances and triangles in a point set and algorithms for computing the largest common point sets." SoCG 1997, pp. 314. [pdf].

M. Laurent. Poly-instances of the positive semidefinite and euclidean distance matrix completion problem. SIAM J Matrix analysis, 2000. [hardcopy] -- Zαγωριανάκος

Havel, Distance geometry: theory, algorithms and chemical applications. [hardcopy] Survey.

Algebra

Coutsias, Seok et al. Kinematic view of loop closure, J. Comp.Chemistry, 25(4):2004. Wiley [pdf]. -- Συρσελούδης.

Άρθρο από το: Barnett, ed. Special issue, Int. J. quantum chem. 2006.

Άρθρο από: International Journal of Robotics Research: 2005, Special Issue on Robotics Techniques Applied to Computational Biology http://www.ijrr.org/contents/24_02/IJR24_02.html

M.P. Barnett, T. Decker, W. Krandick. Power series expansion of the roots of a secular equation containing symbolic elements: computer algebra and Moseley's law.  J. Chem. Phys. 114(23):10265-10269, 2001.

Wedemeyer and Scheraga, Exact analytical loop closure in proteins using polynomial equations, J. Comp. Chemistry, 1999 [hardcopy]

Ming Zhang, R. Allen White, Liqun Wang, Ronald Goldman, Lydia Kavraki and Brendan Hassett. Improving conformational searches by geometric screening. Bioinformatics 2005 21(5):624-630; Published by Oxford University Press [pdf]

Donald, Wang. Exact Solutions for Internuclear Vectors and Backbone Dihedral Angles from NH Residual Dipolar Couplings in Two Media, and Their Application in a Systematic Search Algorithm for Determining Protein Backbone Structure, Journal of Biomolecular NMR 2004; 29(3):223-242.  [PDF].

Kεφάλαιο από: Algebraic statistics in computational biology, Pachter και Sturmfels, 2005, δες εδώ. Kεφάλαιο 1 έως και 1.3. Kεφάλαιο 2 έως και 2.3. Kεφάλαιο 5. Κεφάλαιο 11. Κεφάλαιο 19. Ορισμένα απο αυτά εμφανίστηκαν στο: J. Symb. Comput., Special Issue on Computational Algebraic Statistics v. 41, Issue 2,  Pages 123-254 (February 2006).

Geometry

D. Halperin et.al, Dynamic maintenance molecular surfaces under conformational change, ACM Symp. of Comp. Geom.'05

F. Cazals, F. Proust, Revisiting the description of Protein-Protein interfaces. Part I: Algorithms. 2004. [pdf]

Pankaj K. Agarwal. Herbert Edelsbrunner, John Harer, Yusu Wang. Extreme elevation on a 2-manifold. Proceedings of symposium on Computational geometry, 2004. [Pdf (362 KB)] -- Zαφειρακοπουλος

H-M. Will, Fast and efficient computation of additively weighted Voronoi cells for applications in molecular biology [SWAT'98, LNCS 1432, pdf].

α-σχήματα. Kεφάλαιο βιβλίου H. Edelsbrunner [ps.gz]