I did docking and this was a question that has really been in my mind and after searching, I still did not have an answer which is really satisfactory. Please I will be really grateful if anyone can help me out. Thanks in advance.
Line has one dimension (length), surface has two dimensions (length and width), and body has three dimensions (length, width, and depth). Molecule is a body.
Interesting question. I think it can be addressed by asking the question: can we go below or beyond three dimensions in molecular docking? While representing docking results, we can definitely go below three dimensions. We often portray interactions in 2D projections. But can we do the search in 1D/2D or 4D? I would say, if the system permits. If we have a system (target and ligand) that can be defined in 2D space, we can definitely do a search in two dimensions. For example, metal porphyrin is such a system. If we want to dock a metal ion into the central cavity of porphyrin, we can define a 2D search. Similarly, if we want to study the interactions of two dipoles, 1D search maybe sufficient. Now, what about going beyond 3D? If we consider time as a fourth dimension, we can take an ensemble of structures sampled in time dimension and do the docking with that ensemble. So, it's not necessarily be 3D. Generally, people use protein and DNA as targets and complex small molecules as ligands which cannot be defined in 2 dimensions; that's why we use 3D for such systems.
If you are wondering, must we need optimized 3D geometries of ligands for input in molecular docking, then the answer is no. Several molecular docking programs can take 2D sketches (such as ChemDraw drawings) and SMILES (one dimensional string of characters such as: CC(=O)NC1=CC=C(C=C1)O) of ligands as input for docking. Of course, these are converted internally into 3D geometries for the reasons stated in my previous comment.
Dear
Certainly, we can perform 1D, 2D, 3D, 4D,5D...... simulation, but it depends on what type of pigment is focused on. For example, if you wanna perform docking in-between dots in a straight line 1D is sufficient, 2D will be sufficient for dots in a plane, but for solvent-protein docking analysis (as they reside in 3D condition) we need 3D docking at least. If 4D docking is performed (where time is another dimension) that will be more amazing.
regards
Marzan
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