Conflict of interest

are docked one by one to form dimer, trimer, tetramer, and pentamer

blies to be built.

Figure 8.

Molecular Docking and Molecular Dynamics

4. Conclusions

74

(Figure 7). The resulting pentamer is only 0.73 Å away from the X-ray structure, 1I9B. The electric field maps during the building process are shown in Figure 8. From the field map of the monomer, we can see the most positive field is at the top-right area and the most negative field is at the bottom-left area. A dimer is formed by matching the positive area of the second monomer with the negative area of the first one. The third monomer's positive area fits into the most negative area of the dimer to form the trimer. Similarly, the fourth and fifth monomers are docked to form the tetramer and pentamer. The map interaction limits the way of docking monomers and allows correct assem-

Electric field map at each docking stage to build the pentamer of acetylcholine binding protein (AChBP).

Map objects cannot only be used to model rigid proteins [17], they can also be used for targeted conformational search such as flexible fitting and restrained molecular dynamics [18, 19]. Map objects provide an efficient bridge from molecu-

This work designed and developed a computational tool to manipulate map information for molecular modeling studies. Protein–protein docking can be efficiently performed with map objects. This tool is implemented into CHARMM, as a module, EMAP, and into AMBER in its SANDER program. Our design and implementation make it very flexible and efficient to perform various manipulations of map objects and to perform some routine task related to map data. This module enables user to construct macromolecular assemblies by docking high-resolution X-ray or NMR structures to low-resolution cryo-electron microscopy maps. And

when there is no EM map available, this module allows user to search for

lar systems to large-scale bodies such as cells and organelles.

The authors declare there is no conflict of interest in publishing this work.
