Abstract
The design of new computational procedures to predict molecular complexes is a fast developing area stimulated by the growing demands of researchers working in various fields of molecular biology and looking for more powerful tools for their investigations. The problem for molecular recognition (docking) approaches may be shortly formulated as following: how to match two molecules with known 3D structures in order to predict the configuration of their complex? In the general case, no additional prior knowledge on binding sites is assumed to be available.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Kuntz, I.D., Meng, E.C., and Shoichet, B.K., 1994, Structure-based molecular design, Acc. Chem. Res. 27: 117–123.
Kollman, P.A., 1994, Theory of macromolecule-ligand interactions, Curr. Opin. Struct. Biol. 4: 240–245.
Blaney, J.M., and Dixon, J.S., 1993, A good ligand is hard to find: automated docking methods, Perspec. Drug Disc. Des. 1: 301–319.
Cherfils, J., and Janin, J., 1993, Protein docking algorithms: simulating molecular recognition, Curr. Opin. Struct. Biol. 3: 265–269.
Goodford, P.J., 1985, A computational procedure for determining energetically favorable binding sites on biologically important macromolecules, J. Med. Chem. 28: 849–857.
Warwicker, J., 1989, Investigating protein-protein interaction surfaces using a reduced stereochemical and electrostatic model, J. Mol. Biol. 206: 381–395.
Goodsell, D.S., and Olson, A.J., 1990, Automated docking of substrates to proteins by simulated annealing, Proteins 8: 195–202.
Yue, S.-Y., 1990, Distance-constrained molecular docking by simulated annealing, Protein Engng. 4: 177–184.
Caflisch, A., Niederer, P., and Anliker, M., 1992, Monte Carlo docking of oligopeptides to proteins, Pmteins 13: 223–230.
Hart, T.N., and Read, R.J., 1992, A multiple-start Monte Carlo docking method, Proteins 13: 206–222.
Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R., and Ferrin, T.E., 1982, A geometric approach to macromolecule-ligand interactions, J. Mol. Biol. 161: 269–288.
Connolly, M.L., 1986, Shape complementarity at the hemoglobin alphal-betal subunit interface, Biopolymers 25: 1229–1247.
DesJarlais, R.L., Sheridan, R.P., Seibel, G.L., Dixon, J.S., Kuntz, I.D., and Venkataraghavan, R., 1988, Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure, J. Med. Chem. 31: 722–729.
Jiang, F., and Kim, S.H., 1991, “Soft docking”: matching of molecular surface cubes, J. Mol. Biol. 219: 79–102.
Nord, R., Fischer, D., Wolfson, H.J., and Nussinov, R., 1994, Molecular surface recognition by a computer vision-based technique, Protein Engng. 7: 39–46.
Shoichet, B.K., and Kuntz, I.D., 1991, Protein docking and complementarity, J. Mol. Biol. 221: 327–346.
Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C., and Vakser, I.A., 1992, Molecular surface recognition: determination of of geometric fit between proteins and their ligands by correlation techniques, Proc. Natl. Acad. Sci. U.S.A. 89: 2195–2199.
Helmer-Citterich, M., and Tramontano, A., 1994, PUZZLE: a new method for automated protein docking based on surface shape complementarity, J. Mol. Biol. 235: 1021–1031.
Ho, C.M.W., and Marshall, G.R., 1993, SPLICE: a program to assemble partial query solutions from three-dimensional database searches into novel ligands, J. Comput. Aided Mol. Des. 7: 623–647.
Shoichet, B.K., and Kuntz, I.D., 1993, Matching chemistry and shape in molecular docking, Protein Engng. 6: 723–732.
Vakser, I.A., and Aflalo, C., Hydrophobic docking: a proposed enhancement to molecular recognition techniques, Proteins,in press.
Wodak, S.J., and Janin, J., 1978, Computer analysis of protein-protein interaction, J. Mol. Biol. 124: 323–342.
Janin, J., and Chothia, C., 1990, The structure of protein-protein recognition sites, J. Biol. Chem. 265: 16027–16030.
Marshall, G.R., 1992, 3D structure of peptide-protein complexes: implications for recognition, Curr. Opin. Struct. Biol. 2: 904–919.
Leach, A.R., 1994, Ligand docking to proteins with discrete side-chain flexibility, J. Mol. Biol. 235: 345–356.
Tello, D., Goldbaum, F.A., Mariuzza, R A, Ysern, X., Schwarz, F.P., and Poljak, R.J., 1993, Tree-dimensional structure and thermodynamics of antigen binding by anti-lysozyme antibodies, Biochem. Soc. Trans. 21: 943–946.
Lawrence, M.C., and Colman, P.M., 1993, Shape complementarity at protein/protein interfaces, J. Mol. Biol. 234: 946–950.
Vakser, I.A., 1995, Protein docking for low-resolution structures, Protein Engng. 8: 371–377.
Abola, E.E., Bernsein, F.C., Bryant, S.H., Koetzle, T.L., and Weng, J., 1987, Protein Databank, in: Crystallographic Databases–Information Content, Software Systems, Scientific Applications. Allen, F.H., Bergerhoff, G., and Sievers, R. eds., Data Commission of the International Union of Crystallography, Bonn, pp 107–132.
Fermi, G., Perutz, M.F., Shaanan, B., and Fourme, R., 1984, The crystal structure of human deoxyhaemoglobin at 1.74 A resolution, J. Mol. Biol. 175: 159–174.
Ladner, R.C., Heidner, E.G., and Perutz, M.F., 1977, The structure of horse methaemoglobin at 2.0 angstroms resolution, J. Mol. Biol. 114: 385–414.
Marquart, M., Walter, J., Deisenhofer, J., Bode, W., and Huber, R., 1983, The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors, Acta Crystallog., Sect. B 39: 480–490.
Fujinaga, M., Sielecki, A.R., Read, R.J., Ardelt, W., Laskowski, M. Jr, and James, M.N.G., 1987, Crystal and molecular structures of the complex of aplpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 angstroms resolution, J. Mol. Biol. 195: 397–418.
McPhalen, C.A., and James, M.N.G., 1988, Structural comparison of two serine proteinase-protein inhibitor complexes: eglin-c-subtilisin Carlsberg and CI-2-subtilisin Novo, Biochemistry 27: 6582–6598.
Suguna, K., Bott, R.R., Padlan, E.A., Subramanian, E., Sheriff, S., Cohen, G.H., and Davies, D.R., 1987, Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis, J. Mol. Biol. 196: 877–900.
Brick, P., Bhat, T.N., and Blow, D.M., 1989, Structure of tyrosyl-tRNA synthetase refined at 2.3 angstroms resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate, J. Mol. Biol. 208: 83–98.
Madden, D.R., Gorga, J.C., Strominger, J.L., and Wiley, D.C., 1992, The three-dimensional structure of HLA-B27 at 2.1 angstroms resolution suggests a general mechanism for tight peptide binding to MHC, Cell 70: 1035–1048.
Sheriff, S., Silverton, E.W., Padlan, E.A., Cohen, G.H., Smith-Gill, S.J., Finzel, B.C., and Davies, D.R., 1987, Three-dimensional structure of an antibody-antigen complex, Proc. Natl. Acad. Sci. U.S.A. 84: 8075–8079.
Rini, J.M., Stanfield, R.L., Stura, E.A., Salinas, P.A., Profy, A.T., and Wilson, I.A., 1993, Crystal structure of an HIV-1 neutralizing antibody 50.1 in complex with its V3 loop peptide antigen, Proc. Natl. Acad. Sci. U.S.A. 90: 6325–6329.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1995 Springer Science+Business Media New York
About this chapter
Cite this chapter
Vakser, I.A., Nikiforovich, G.V. (1995). Protein Docking in the Absence of Detailed Molecular Structures. In: Atassi, M.Z., Appella, E. (eds) Methods in Protein Structure Analysis. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-1031-8_46
Download citation
DOI: https://doi.org/10.1007/978-1-4899-1031-8_46
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4899-1033-2
Online ISBN: 978-1-4899-1031-8
eBook Packages: Springer Book Archive