Elzu's micro notes

AutoDock AutoDock  is the first docking package to model the ligand with full conformational flexibility . AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure . Over the years, it has been modified and improved to add new functionalities, and multiple engines have been developed. The package consists of two sequentially applied programs , AutoGrid and AutoDock. AutoGrid is initially used to calculate the noncovalent energy of interaction between the rigid part of the receptor and a probe atom that is located at various grid points of the lattice . Furthermore,   AutoGrid generates an electrostatic potential grid map and a desolvation map. The full set of grid maps and the flexible part of the receptor are used by AutoDock to guide the docking process of the selected ligands .   AutoDock's main strengths are (i)    ...

Scoring Function There are three important applications of scoring functions in molecular docking. The first of these is the determination of the binding mode and site of a ligand on a protein. Given a protein target, molecular docking generates hundreds of thousands of putative ligand binding orientations/conformations at the active site around the protein. A scoring function is used to rank these ligand orientations/conformations by evaluating the binding tightness of each of the putative complexes . An ideal scoring function would rank the experimentally determined binding mode most highly . Given the determined binding mode of a ligand, scientists would be able to gain a deep understanding of the molecular mechanism of ligand binding and to further design an efficient drug by modifying the protein or ligand . The second application of a scoring function , which is related to the first application, is to predict the absolute binding affinity between protein and ligand. This is p...

  Search Algorithms In the conformational search, structural parameters of the ligands, such as torsional (dihedral), translational and rotational degrees of freedom, are incrementally modified. Conformational search algorithms perform this task by applying different methods. The identification of molecular features and modifications in compounds, in order to improve the potency are the difficult issues to understand. The docking process may be regarded as a multi-step process in which each step introduces one or more additional degrees of complication. Accurate structural modeling and correct prediction of activity are the aspirants of docking studies. The search algorithms used to predict plausible conformations of the complex are defined by a set of rules and parameters. In terms of the flexibility of the ligand and/or the receptor, docking algorithms can be categorized in two large sets: rigid-body and flexible docking which are based on different types of algorithms. ...

  Molecular Docking Molecular recognition is the ability of biomolecules to recognize other biomolecules and selectively interact with them in order to promote fundamental biological events such as transcription, translation, signal transduction, transport, regulation, enzymatic catalysis, viral and bacterial infection and immune response. Molecular docking is the process that involves placing molecules in appropriate configurations to interact with a receptor. Molecular docking is  a key tool in structural molecular biology and computer-assisted drug design . Docking is computational simulation of a candidate ligand binding to a receptor. In molecular modeling the term “molecular docking” refers to the study of how two or more molecular structures fit together. Molecular docking is the process that involves placing molecules in appropriate configurations to interact with a receptor. Molecular docking is a natural process which occurs within seconds in a cell when boun...