Recommended Reading and full list of references
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Introduction - Preliminaries on macromolecular structure
in general and protein structure in particular:
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Branden and Tooze, "Introduction to protein structure" - book. Garland
Pub., 1991 (copies of this book are available in the library of Life Sciences
and Medicine, book no. 572.633 BRA).
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A.M. Lesk, "Protein Architecture: A Practical Approach",
Oxford Univ. Press, 1991.
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M.S. Waterman, "Introduction to Computational Biology",
Chapman & Hall, 1995.
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Computational analysis of DNA and protein sequences,
in particular biological sequence alignments, multiple sequence alignments,
and large data base searches:
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Dan Gusfield, Algorithms on Strings, Trees, and Sequences : Computer Science
and Computational Biology, Cambridge University Press, 1997 (copies of
this book are available in the library of Exact Sciences and Engineering,
book no. 519.93 GUS).
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Setubal - Introduction to computational biology - book (copies of
this book are available in the library of Exact Sciences and Engineering,
book no. 519.93 SET).
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Protein Structural Alignment - rigid:
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Dynamic Programming methods (sequence order dependent):
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Taylor, W. R. and Orengo, C. A., Protein Structure Alignment, Journal of
Molecular Biology, vol. 208, pp.1-22, (1989).
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Fragment alignment (semi sequence order dependent) :
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Vriend, G. and Sander, C., Detection of Common Three-Dimensional Substructures
in Proteins, PROTEINS, vol. 11, pp. 52-58", (1991).
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Geometric Hashing (sequence order independent) :
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Lamdan, Y. and Wolfson, H. J., Geometric Hashing: A General and Efficient
Model-Based Recognition Scheme, Proc. of the Second Int. Conf. on Computer
Vision, Tampa, Florida, pp. 238-249, IEEE Press, (1988).
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Nussinov, R. and Wolfson, H.J., Efficient detection of three-dimensional
motifs in biological macromolecules by computer vision techniques, Proc.
of the National Academy of Science, USA, vol. 88, pp. 10495-10499, (1991).
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Fischer, D., Nussinov, R. and Wolfson, H. J., "3-D Substructure Matching
in Protein Molecules", Proceedings of the Third Symposium on Combinatorial
Pattern Matching, Lecture Notes in Computer Science, vol. 644, Springer-Verlag,
pp. 136-150, (1992).
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Holm, L., and Sander, C., Searching protein structure databases has come
of age, PROTEINS, vol. 19, pp. 165--173, (1994).
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Protein Secondary Structure Alignment :
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Mitchell, E.M., Artymiuk, P.J. , Rice, D.W., and Willet, P., Use of Techniques
Derived from Graph Theory to Compare Secondary Structure Motifs in Proteins,
J. Mol. Bio., vol. 212, pp. 151-166, (1989).
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V. Alesker, R. Nussinov, H.J. Wolfson", Identification of Non-Topological
Motifs in Protein Structures, "Protein Engineering, vol. 9(12), pp. 1103-1119,
(1996).
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Koch, I., Lengauer, T., and Wanke, E., An Algorithm for Finding Maximal
Common Subtopologies in a set of Protein Structures, Journal of Computational
Biology, vol. 3(2), pp. 289--306, (1996).
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Flexible Protein Structure Alignment :
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Wolfson, H. J., Generalizing the Generalized Hough Transform, Pattern Recognition
Letters, vol. 12(9), pp. 565 - 573, (1991).
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Verbitsky, G., Nussinov, R., and Wolfson, H.J., Structural Comparison Allowing
Hinge Bending, Swiveling Motions, PROTEINS, vol. 34, pp. 232--254, (1999).
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Molecular Surface Representation :
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Connolly, M.L., Solvent-Accessible Surfaces of Proteins and Nucleic Acids,
Science, vol. 221, pp. 709-713, (1983).
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Connolly, M.L., Analytical Molecular Surface Calculation, J. Appl. Cryst.,
vol. 16, pp. 548-558, (1983).
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Lin, S. L., Nussinov, R., Fischer, D., and Wolfson, H.J., Molecular Surface
Representation by Sparse Critical Points, PROTEINS, vol. 18, pp. 94-101,
(1994).
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Docking - rigid :
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Review paper :
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T. Lengauer and M. Rarey, Computational Methods for Biomolecular Docking,
Current Opinion in Structural Biology, vol. 6, pp. 402-406, (1996).
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Various methods :
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Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R., Ferrin, T.E., A
Geometric Approach to Macromolecule-Ligand Interactions, J. of Mol. Bio.,
vol. 161, pp. 269-288, (1982).
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Shoichet, B.K. and Kuntz, I.D., Protein Docking and Complementarity, J.
of Mol. Bio., vol. 221, pp. 327-346, (1991).
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Jiang, F. and Kim, S.H., Soft Docking : Matching of Molecular Surface Cubes,
J. of Mol. Bio., vol. 219, pp. 79-102, (1991).
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Katchalski-Katzir, E., Shariv, I. , Eisenstein, M., Friesem, A.A., Aflalo,
C., Vakser, I.A., Molecular Surface Recognition: Determination of Geometric
Fit between Protein and their Ligands by Correlation Techniques", Proc.
of the Nat. Acad. Sc., USA, vol. 89, pp. 2195-2199, (1992).
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Fischer, D. Lin, S. L., Wolfson, H.J. , Nussinov, R., A Geometry-based
Suite of Molecular Docking Processes, J. of Mol. Bio., vol. 248, pp. 459-477,
(1995).
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Fischer, D., Norel, R., Nussinov, R., Wolfson, H. J., 3-D Docking of Protein
Molecules, Proc. of the Fourth Symposium on Combinatorial Pattern Matching,
Padova, Italy, Springer Verlag Lecture Notes in Computer Science No. 684,
pp. 20-34, (1993).
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Norel, R., Lin, S. L., Wolfson, H.J., Nussinov, R., Molecular Surface Complementarity
at Protein-Protein Interfaces: The Critical Role Played by Surface Normals
at Well Placed, Sparse Points in Docking, J. of Mol. Bio., vol. 252, pp.
263-273, (1995).
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Docking - flexible :
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DesJarlais, R.L., Sheridan, R.P., Dixon, J.S., Kuntz, I.D., Venkataraghavan,
R., Docking Flexible Ligands to Macromolecular Receptors by Molecular Shape",
J. Med. Chem., vol. 29, pp. 2149-2153, (1986).
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Sandak, B., Nussinov, R., Wolfson, H.J., Docking of Conformationally Flexible
Molecules, Proc. Seventh Symposium on Combinatorial Pattern Matching, CPM
96, Laguna Beach, California", Springer Verlag Lecture Notes in Computer
Science No. 1075, pp. 271-287, (1996).
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Sandak, B., Wolfson, H.J., Nussinov, R., Flexible Docking Allowing Induced
Fit in Proteins, PROTEINS, vol. 32, pp. 159-174, (1998).
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Rarey, M., Kramer, B., Lengauer, T. , Klebe, G.", A fast flexible docking
method using incremental construction algorithm, J. Mol. Bio., vol. 261,
pp. 470-489, (1996).
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Folding :
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Bowie, J. V., Luthy, R., Eisenberg, D., Method to identify protein sequences
that fold into a known three-dimensional structure, Science, vol. 253,
pp. 164-170, (1991).
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Michael Levitt's lecture notes : http://csb.stanford.edu/levitt/Folding_Lecture.html