Molecular Modeling

In general, molecular modeling systems are computer programs which allow: building molecules from fragments (e.g., residues) and groups; displaying different graphic representations of molecules; translation and rotation of molecular objects on the screen; modifying molecular models by changing distances, angles and replacing/adding atoms and groups; refining geometry of molecules by molecular mechanics or similar methods; superimposing and comparing molecular objects; computation and display of molecular volumes, surfaces, electrostatic potentials and other properties; and preparing plots on various hardcopy devices. Molecular modeling systems also incorporate, or help in preparing, input data for specialized programs like molecular mechanics, dynamics, conformational searches, quantum methods, databases of chemical information, etc. They also provide means for the analysis and visualization of results from other specialized programs.