Скачать с ютуб How to start a docking project? | 4 Practical tips PART 2 в хорошем качестве

How to start a docking project? | 4 Practical tips PART 2

Molecular docking seems deceivingly simple at first glance, but several computational chemistry factors can influence the quality of the final result. Anyone who is research naive can generate both revolutionary results and artifacts, unrealistic results without realizing. Force field parameters are implemented in Molecular mechanics (MM) methods, as part of Potential energy function and in more simplified ways in docking scoring functions. The total potential, usually does not differ very much from one force field to another. The force fields usually vary between one each other based on the parameterization. However, the potential energies calculated in docking methods, can vary significantly from one method to another, since several approximations are applied. Scoring functions enforced in docking programs make various presumptions and simplifications and so they do not fully account for physical phenomena such as, desolvation upon ligand binding, or entropic effects. In docking, the scoring function attempts to estimate and quantify the fit of a ligand into the binding site. The quantification and the ranking of the predicted ligand conformations is a crucial to be able to interpret the docking results. This process is essential to be able to ultimately differentiate correct poses from incorrect ones, but also to identify correct binders in case of a computational virtual screening. Thus, the development of reliable scoring functions is of central importance. B-factors in PDB files commonly are seen as a measure of (local) mobility in the (macro)molecule, but this value is is strong relation with the correctness of the structure and resolution as well. If you'd like to buy me a coffee... ko-fi.com/scienceaddicted :D Thank you! Affiliate link to equipment used in the video Microphone C1 Behringer: https://amzn.to/2YHbNIm Wacom CTL4100 Intuos Graphics Drawing Tablet: https://amzn.to/3txmFqw Channel Art and Thumbnails are crated with Canva https://www.canva.com/join/qwq-hrf-ntl