Recommended Reading and full list of references

  1. Introduction - Preliminaries on macromolecular structure in general and protein structure in particular:
    1. 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).
    2. A.M. Lesk, "Protein Architecture: A Practical Approach", Oxford Univ. Press, 1991.
    3. M.S. Waterman, "Introduction to Computational Biology", Chapman & Hall, 1995.
  2. Computational analysis of DNA and protein sequences, in particular biological sequence alignments, multiple sequence alignments, and large data base searches:
    1. 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).
    2. 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).
  3. Protein Structural Alignment - rigid:
    1. Dynamic Programming methods (sequence order dependent):
      1. Taylor, W. R. and Orengo, C. A., Protein Structure Alignment, Journal of Molecular Biology, vol. 208, pp.1-22, (1989).
    2. Fragment alignment (semi sequence order dependent) :
      1. Vriend, G. and Sander, C., Detection of Common Three-Dimensional Substructures in Proteins, PROTEINS, vol. 11, pp. 52-58", (1991).
    3. Geometric Hashing (sequence order independent) :
      1. 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).
      2. 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).
      3. 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).
      4. Holm, L., and Sander, C., Searching protein structure databases has come of age, PROTEINS, vol. 19, pp. 165--173, (1994).
  4. Protein Secondary Structure Alignment :
    1. 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).
    2. V. Alesker, R. Nussinov, H.J. Wolfson", Identification of Non-Topological Motifs in Protein Structures, "Protein Engineering, vol. 9(12), pp. 1103-1119, (1996).
    3. 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).
  5.  Flexible Protein Structure Alignment :
    1. Wolfson, H. J., Generalizing the Generalized Hough Transform, Pattern Recognition Letters, vol. 12(9), pp. 565 - 573, (1991).
    2. Verbitsky, G., Nussinov, R., and Wolfson, H.J., Structural Comparison Allowing Hinge Bending, Swiveling Motions, PROTEINS, vol. 34, pp. 232--254, (1999).
  6. Molecular Surface Representation :
    1. Connolly, M.L., Solvent-Accessible Surfaces of Proteins and Nucleic Acids, Science, vol. 221, pp. 709-713, (1983).
    2. Connolly, M.L., Analytical Molecular Surface Calculation, J. Appl. Cryst., vol. 16, pp. 548-558, (1983).
    3. 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).
  7. Docking - rigid :
    1. Review paper :
      1. T. Lengauer and M. Rarey, Computational Methods for Biomolecular Docking, Current Opinion in Structural Biology, vol. 6, pp. 402-406, (1996).
    2. Various methods :
      1. 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).
      2. Shoichet, B.K. and Kuntz, I.D., Protein Docking and Complementarity, J. of Mol. Bio., vol. 221, pp. 327-346, (1991).
      3. Jiang, F. and Kim, S.H., Soft Docking : Matching of Molecular Surface Cubes, J. of Mol. Bio., vol. 219, pp. 79-102, (1991).
      4. 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).
      5. 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).
      6. 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).
      7. 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).
  8. Docking - flexible :
    1. 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).
    2. 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).
    3. Sandak, B., Wolfson, H.J., Nussinov, R., Flexible Docking Allowing Induced Fit in Proteins, PROTEINS, vol. 32, pp. 159-174, (1998).
    4. 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).
  9. Folding :
    1. 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).
    2. Michael Levitt's lecture notes :