Summary
A software package is described that operates on small molecules observed in the PDB collection of protein structures. Molecular topology files for many molecular modeling programs can be generated automatically. The three-dimensional coordinates of small molecules can be converted to molecular descriptor strings that encode them uniquely in order to enable small-molecule recognition, despite high variability in atom and molecule nomenclature. From this descriptor a plausible 3D structure can be regenerated using energy minimisation. Alternatively, an ensemble of structures can be generated using a distance-geometry-based algorithm.
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Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M., J. Mol. Biol., 112 (1977) 535.
Vriend, G., J. Mol. Graph., 8 (1990) 52.
Van Gunsteren, W.F. and Berendsen, H.J.C., BIOMOS, Biomolecular Software, Laboratory of Physical Chemistry, University of Groningen, Groningen, The Netherlands.
SYBYL Molecular Modelling Software, Tripos Associates, St. Louis, MO, 1991.
VanGunsteren, W.F. and Berendsen, H.J.C., Angew. Chem., Int. Ed. Engl., 29 (1990) 992.
Meng, E.C. and Lewis, R.A., J. Comput. Chem., 12 (1991) 891.
Baber, J.C. and Hodgkin, E.E., J. Chem. Inf. Comput. Sci., 32 (1992) 401.
Weast, R.C. (Ed.) Handbook of Chemistry and Physics, Chemical Rubber Co., Cleveland, OH, 1964.
Kier, L.B. and Hall, L.H., Molecular Connectivity in Chemistry and Drug Research, Academic Press, New York, NY, 1976.
Weininger, D., J. Chem. Inf. Comput. Sci., 28 (1988) 31.
Weininger, D., Weininger, A. and Weininger, J.L., J. Chem. Inf. Comput. Sci., 29 (1989) 97.
Weininger, D., J. Chem. Inf. Comput. Sci., 30 (1990) 237.
Ryckaert, J.P., Cicotti, G. and Berendsen, H.J.C., J. Comput. Phys., 23 (1977) 327.
Crippen, G.M., J. Comput. Chem., 24 (1977) 96.
Converter: Biosym Techonologies Inc., San Diego, CA, 1992.
James, M.N.G., Sielecki, A.R., Hayakawa, K., Gelb, M.H., Biochemistry, 31 (1992) 3872.
Xu, Z.H., Bernlohr, D.A. and Banaszak, L.J., J. Biol. Chem., 268 (1993) 7874.
Arevalo, J.H., Stura, E.A., Taussig, M.J. and Wilson, I.A., J. Mol. Biol., 231 (1993) 103.
Boles, J.O., Lewinski, K., Kunkle, M.G., Hatada, M., Lebioda, L., Dunlap, R.J. and Odom, J.D., Acta Crystallogr. D., 51 (1995) 731.
Ricketts, E.M., Bradshwa, J., Hann, M., Hayes, F., Tanna, N. and Ricketts, D.M., J. Chem. Inf. Comput. Sci., 33 (1993) 905.
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The program PRODRG is freely available by writing to D.M.F. van Aalten. In addition, structures can be submitted to the WWW server http://swift.embl-heidelberg.de/prodrg serv, which will return a MOLDES and three molecular topologies.
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van Aalten, D.M.F., Bywater, R., Findlay, J.B.C. et al. PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. Journal of Computer-Aided Molecular Design 10, 255–262 (1996). https://doi.org/10.1007/BF00355047
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DOI: https://doi.org/10.1007/BF00355047