Computational Drug Discovery and Design
the distance slider allows the user to set the desired distance for a given constraint. It is possible to sequentially add multi ...
button allows you to pause the simulation while looking at real- time results in the PyMOL viewer. The “Stop” and “Abort” button ...
this specific case easily when this protocol is used (seeNote 33). Both the specific interactions (H_BONDS in the PyMOL viewer o ...
Linux Open up a terminal and move to the directory in which you downloaded the archive NRGsuite_2.48i_Linux<32/64>.tar, an ...
The NRGsuite is developed to allow molecular docking simu- lations involving any biological target. Although this tutorial will ...
deeply buried cavities. Thus, clefts generated with a lower minimum are larger. The NRGsuite uses a string representation to id ...
The NRGsuite has been designed to load and save files in the project directory initially defined by the user upon installation. ...
undetermined or when multiple allosteric sites need to be queried altogether. It is possible to import multiple clefts at once b ...
orange. Clicking on the two atoms that define the flexible bond will render this bond as flexible during the docking simulation. ...
Scoring Cfg. You can modify the parameters of the genetic algorithms and still be able to continue a simulation. Docking is an ...
Mobley DL, Dill KA (2009) Binding of small- molecule ligands to proteins: “what you see” is not always “what you get”. Structur ...
Varghese JN, Laver WG, Colman PM (1983) Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 A ̊ resoluti ...
Chapter 19 Calculation of Thermodynamic Properties of Bound Water Molecules Ying Yang, Amr H. A. Abdallah, and Markus A. Lill Ab ...
the entropic loss for immobilizing the water involved [10]. Thus, the thermodynamics of water molecules in protein active sites ...
directory ($HOME). WATsite plugin can be installed using “Plugin Manager” under Plugin menu, and choose the fileWATsite.py under ...
trajectory with WATsite. Water thermodynamics with (6) and with- out (7) the presence of ligand can be calculated. We will then ...
Fig. 3 Step 2of WATsite procedure to prepare the protein or protein–ligand system Calculation of Water Thermodynamics 393 ...
and ligand-bound (holo) protein structures (seeNote 6). If the user intends to predict hydration sites at the interface between ...
Using the default settings for the simulation, the system will first be energy minimized until convergence with a tolerance of 1 ...
During the WATsite analysis step, the production trajectory will first be aligned to the reference which is the user input prote ...
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