Docking procedures

The conformational and dynamic behaviour of oligomannosides71 has also been investigated and their recognition by banana lectin has been evaluated by STD NMR methods and docking procedures, providing a preliminary view of their putative interaction mode. 

To prepare the protein for a docking procedure, the following considerations are usually taken into account ... 

Docking programs routinely incorporate compound flexibility. However, incorporating receptor flexibility in docking procedures is still a major hurdle (61). Of late, several attempts have been made for this purpose (cf (46, 62) for review). 

Some force fields and docking procedures work with the concept of essential hydrogens, i.e., hydrogens bonded to heteroatoms or hydrogens that could be involved in formation of a hydrogen bond. It is important to adhere to the procedure used to calibrate the docking program and to apply the correct method of protonation. 

However, it is normally assumed that the conformers that bind to target sites will be those with a minimum potential energy. Since molecules may have large numbers of such metastable conformers a number of techniques, such as the Metropolis Monte Carlo method and comparative molecular field analysis (CoMFA), have been developed to determine the effect of conformational changes on the effectiveness of docking procedures. 

The final output of the docking procedure is a set of solutions ranked according to the corresponding scoring function values, each defined by the 3D coordinates of its atoms and expressed as a PDB file. 

Sciabola, S., Baroni, M., Carosati, E., Cruciani, G. Recent improvements in the GRID force field. 1. The docking procedure GLUE, poster presented at the 15 Eur. Symp. QSAR Molecular Modelling, Istanbul, Turkey 2004. 

To further validate the results obtained by the automated docking procedure, the receptor binding pocket was analyzed using program GRID [41]. The hydroxy. 

It is important to stress that the method highlighted here requires neither training nor docking procedures and associated scoring functions, nor 2D or 3D QSAR models. The only experimental information used as input is the 3D structure of the human cytochromes. From the 3D CYP structures, GRID provides all the flexible molecular interaction fields, which in turn form the basis of the remaining calculations. 

To provide new insights in the biological context of biomolecules, obtaining structural information is frequently essential. The tertiary structure of molecules with accuracy at the atom level can be calculated using NMR-derived data on intra-molecular atom distances and angles. Many biomolecules form complexes with each other, and the nature of these complex formations can be deduced from intermolecular distances and determination of the interaction surfaces in combination with computational docking procedures to determine their global structure. 

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