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Molecular Docking Presentation

The document provides an overview of molecular docking strategies, focusing on flexibility and binding site considerations. It outlines various types of docking, including rigid and flexible docking, as well as blind and targeted docking, and describes the docking process, search algorithms, scoring functions, and the AutoDock workflow. Key input files for AutoDock and steps for protein and ligand preparation are also highlighted.

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34 views8 pages

Molecular Docking Presentation

The document provides an overview of molecular docking strategies, focusing on flexibility and binding site considerations. It outlines various types of docking, including rigid and flexible docking, as well as blind and targeted docking, and describes the docking process, search algorithms, scoring functions, and the AutoDock workflow. Key input files for AutoDock and steps for protein and ligand preparation are also highlighted.

Uploaded by

prosenjitdutta771
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPTX, PDF, TXT or read online on Scribd
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Molecular Docking: Flexibility &

Binding Site Considerations


An Overview of Docking Strategies,
Algorithms, and AutoDock Workflow
Types of Docking Based on
Flexibility
• - Rigid Docking (Both Receptor & Ligand Rigid):
Fast, useful for high-throughput screening, but
less accurate.
• - Rigid Receptor & Flexible Ligand Docking:
Allows ligand rotation, more accurate but
computationally demanding.
• - Flexible Docking: Allows receptor and ligand
flexibility, backbone atoms can be made
flexible (Induced Fit Docking).
Types of Docking Based on Binding
Site Knowledge
• - Blind Docking: Used when the active site is
unknown, computationally expensive, may
find potential binding sites.
• - Targeted Docking: Pre-defined active site,
faster, more accurate.
Docking Process
• - Ligand Binding Search: Ligands fitted in
multiple positions, conformations generated
using search algorithms.
• - Pose Selection & Ranking: Multiple
orientations are scored, ligands ranked based
on scores.
Search Algorithms in Docking
• - Systematic Search: Used for rigid-body
docking, time-consuming.
• - Stochastic Methods: Faster, uses random
sampling (Monte Carlo, Simulated Annealing,
Genetic Algorithms).
• - Molecular Dynamics Simulations: Refines
docking results, helps analyze binding stability.
Scoring Functions in Docking
• - Force-Field Based: Uses classical mechanics
force fields.
• - Knowledge-Based: Uses structural data from
molecular databases.
• - Empirical-Based: Uses interaction terms
calibrated with experimental data.
Input Files for AutoDock Docking
• - PDB: Protein Data Bank File.
• - PDBQT: PDB + Partial Charge (Q) & Type (T).
• - GPF: Grid Parameter File.
• - GLG: Grid Log File.
• - DPF: Docking Parameter File.
• - DLG: Docking Log File.
AutoDock Workflow
• - Protein Preparation: Remove water, add
polar hydrogens, assign charges.
• - Ligand Preparation: Define rotatable bonds,
assign charges.
• - Define Binding Site: Generate grid maps
using AutoGrid.exe.
• - Docking Execution: Run AutoDock.exe,
analyze docking score and interactions.

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