Tutorial of CSDU "Protein-ligand docking 101 - running a simulation in GOLD” скачать в хорошем качестве

Tutorial of CSDU "Protein-ligand docking 101 - running a simulation in GOLD”

Learn the basics of protein-ligand docking using the GOLD docking software in this CSDU (self-guided on-demand training) module "Protein-ligand docking 101 - running a simulation in GOLD”. In this tutorial you will see a step-by-step set up of a docking run in GOLD, from importing the protein structure and selecting the ligand and binding site, to visualising and analysing the docking solutions obtained in GOLD. In this GOLD docking demo tutorial we will cover: 00:05 Introduction to the case study: tyrosine kinases - erdafitinib. 00:30 Let's get started! We start with Hermes, the interface we will use for running a docking simulation in GOLD. 00:47 How to import a protein file from the PDB directly from the interface. The PDB code we are using is 5EW8. Editing options. 03:12 Launch the GOLD wizard from the Hermes interface and complete the first step, target selection. 03:50 Protein preparation, including how to add missing hydrogens and check protonation, and how to extract water molecules and the ligand already present in the crystal. 05:34 How to define the binding site in the docking software GOLD (four options available). 06:58 Selection of the ligand, file format and how to import the ligand file. You can also upload a reference ligand. 07:51 How to select the scoring functions in GOLD. For this docking case study we use CHEMPLP. 08:25 Options for the Genetic Algorithm. 09:13 Advanced options for configuring your GOLD run. 12:21 Run the docking calculation in GOLD. 13:13 Analysis of the docking solutions, including visualization tips and tricks, sorting the solutions in the Molecule Explorer, and hydrogen bonds. This video forms part of a short course that introduces scientists – crystallographers, biochemists and cheminformaticians, among others, to the basics of molecular docking simulations with GOLD through videos, demonstrations, guided tutorials, and a test that can be completed at the end to earn a certificate. After watching this video, continue your CSDU module by completing the U Try and U Test parts on our website to earn a completion certificate: https://www.ccdc.cam.ac.uk/Community/... On the website you will also find the slides with the steps from the demonstration in this video. Find the introductory videos in this playlist:    • CSDU: Protein-ligand docking 101 - running...   Note: This module is designed for beginners. Follow us on social media: Instagram: @ccdc_cambridge Twitter: @ccdc_cambridge Facebook: Cambridge Crystallographic Data Centre (CCDC) (ccdc.cambridge)