TY - JOUR
KW - Models, Molecular
KW - Crystallography, X-Ray
KW - Humans
KW - Algorithms
KW - HIV Protease Inhibitors
KW - Protein Binding
KW - Protein Conformation
KW - Binding Sites
KW - Ligands
KW - Estrogen Receptor beta
KW - Receptors, Estrogen
KW - Thrombin
AU - M. Cecchini
AU - P. Kolb
AU - N. Majeux
AU - A. Caflisch
AB - <p>An improved version of the fragment-based flexible ligand docking approach SEED-FFLD is tested on inhibitors of human immunodeficiency virus type 1 protease, human &alpha;-thrombin and the estrogen receptor &beta;. The docking results indicate that it is possible to correctly reproduce the binding mode of inhibitors with more than ten rotatable bonds if the strain in their covalent geometry upon binding is not large. A high degree of convergence towards a unique binding mode in multiple runs of the genetic algorithm is proposed as a necessary condition for successful docking.</p>
BT - Journal of Computational Chemistry
C1 - 0054
DA - 2004 Feb
DO - 10.1002/jcc.10384
IS - 3
J2 - J Comput Chem
LA - eng
M3 - Research Article
N2 - <p>An improved version of the fragment-based flexible ligand docking approach SEED-FFLD is tested on inhibitors of human immunodeficiency virus type 1 protease, human &alpha;-thrombin and the estrogen receptor &beta;. The docking results indicate that it is possible to correctly reproduce the binding mode of inhibitors with more than ten rotatable bonds if the strain in their covalent geometry upon binding is not large. A high degree of convergence towards a unique binding mode in multiple runs of the genetic algorithm is proposed as a necessary condition for successful docking.</p>
PY - 2004
SP - 412
EP - 422
T2 - Journal of Computational Chemistry
TI - Automated docking of highly flexible ligands by genetic algorithms: A critical assessment
VL - 25
SN - 0192-8651
ER -