A fast and efficient method to generate biologically relevant conformations

J Comput Aided Mol Des. 1994 Oct;8(5):583-606. doi: 10.1007/BF00123667.


Mutual binding between a ligand of low molecular weight and its macromolecular receptor demands structural complementarity of both species at the recognition site. To predict binding properties of new molecules before synthesis, information about possible conformations of drug molecules at the active site is required, especially if the 3D structure of the receptor is not known. The statistical analysis of small-molecule crystal data allows one to elucidate conformational preferences of molecular fragments and accordingly to compile libraries of putative ligand conformations. A comparison of geometries adopted by corresponding fragments in ligands bound to proteins shows similar distributions in conformations space. We have developed an automatic procedure that generates different conformers of a given ligand. The entire molecule is decomposed into its individual ring and open-chain torsional fragments, each used in a variety of favorable conformations. The latter ones are produced according to the library information about conformational preferences. During this building process, an extensive energy ranking is applied. Conformers ranked as energetically favorable are subjected to an optimization in torsion angle space. During minimization, unfavorable van der Waals interactions are removed while keeping the open-chain torsion angles as close as possible to the experimentally most frequently observed values. In order to assess how well the generated conformers map conformation space, a comparison with experimental data has been performed. This comparison gives some confidence in the efficiency and completeness of this approach. For some ligands that had been structurally characterized by protein crystallography the program was used to generate sets of some 10 to 100 conformers. Among these, geometries are found that fall convincingly close to the conformations actually adopted by these ligands at the binding site.

MeSH terms

  • Adenosine Monophosphate / chemistry
  • Binding Sites
  • Computer-Aided Design
  • Databases, Factual
  • Drug Design
  • Ligands
  • Macromolecular Substances
  • Models, Molecular
  • Molecular Conformation*
  • Molecular Structure
  • Peptides / chemistry
  • Software
  • Thermodynamics


  • Ligands
  • Macromolecular Substances
  • Peptides
  • Adenosine Monophosphate