Dear Andrzej,

The following text was taken from a recent review (see attached file) which summarizes the methods used in your case:

Docking methods are used to predict the preferred orientation of one molecule to a protein when bound to each other to form a stable complex. Depending on the method, there are different considerations of the flexibility of either the ligand or the protein during the docking process. The most commonly used method considers the ligand flexible, while the protein docking site is held rigid, usually pre-treated with molecular dynamics force fields. Several software packages are available for docking, such as Gold, Autodock, AutoDock Vina, DOCK, GLIDE, SURFLEX and others. The docking score is an evaluation of the energetic affinity of the complex, calculated by scoring functions. These scoring functions can be molecular mechanics-based, empirical, knowledge-based, or consensus-based functions. For example, DOCK uses the AMBER force field for evaluating the energetics of binding, while SURFLEX uses an empirical function. Consensus scoring is a method whereby the binding affinities of compounds for a particular target are predicted by using more than one scoring algorithm and is a frequently studied method. In such a study, Tuchinardi et al. evaluated the consensus docking and scoring of several different algorithms along 83 ligand-receptor X-ray structures.

Another widely used method for evaluating the probability of molecule binding to protein binding sites is pharmacophore modeling. A pharmacophore is the ensemble of steric and electronic features that is necessary to ensure the optimal supramolecular interactions with a specific biological target structure. By mapping the interaction of an active compound bound to its target protein, a pharmacophore can represent the geometrical and chemical properties using pharmacophore features, which include hydrogen bond acceptors and donors, basic and acidic groups, partial charge, aliphatic and aromatic hydrophobic moieties. This representation can be used for virtual screening projects, in order to identify potential binders based on this interaction. Several software packages have been developed towards pharmacophore modeling, Ligandscout and The Pocket v.2 use algorithms in protein-ligand complex data to map interactions between ligand and target.

For more information, please see attached review article entitled "Computational approaches in target identification and drug discovery " by Theodora Katsila et al. published in Comput Struct Biotechnol J. 2016; 14: 177–184.

Hoping this will be helpful,

Rafik

Dear Rafik,

many thanks for a large, substantial answer and for an article containing many information which is important for me to start planned conputational research.

Best regards,                                                                                                                                    Andrzej 

Dear Andrzej,

Pharmacophore modeling and docking studies are the most widely used computational techniques for the drug-receptor interactions. Moreover, to find the list of software's for the same following link may be helpful:http://www.click2drug.org/

All the best.

Dear Mohsin,

Thanks a lot of valuable information.

Regards,                                                                                                                                            Andrzej

On the practical side, for a quick start, I would suggest to download and install Chimera, a molecular modeling freeware, which has a toolkit to prepare input file for popular free docking engines, such as, DOCK or Autodock Vina.

Dear Dmitri,

Thanks for valuable information.

Regards,                                                                                                                                            Andrzej