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Protein Modeling and Docking Techniques

Unit IV covers protein modeling and structure prediction, including protein structures, visualization, and major non-covalent interactions essential for stability. It also discusses molecular docking and dynamics simulations, focusing on protein-ligand interactions, pose and affinity prediction, as well as various docking methodologies. The unit concludes with an introduction to molecular simulation methods and the concepts of force fields.

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10 views2 pages

Protein Modeling and Docking Techniques

Unit IV covers protein modeling and structure prediction, including protein structures, visualization, and major non-covalent interactions essential for stability. It also discusses molecular docking and dynamics simulations, focusing on protein-ligand interactions, pose and affinity prediction, as well as various docking methodologies. The unit concludes with an introduction to molecular simulation methods and the concepts of force fields.

Uploaded by

aastha.220403
Copyright
© All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd

Unit IV

Protein modelling and Protein structure prediction: Introduction to Protein Structures, Protein
Data Bank (PDB), and PDB Flat File Format. Basics of Protein Structure Visualization:
Major Non-Covalent Interactions for Protein Stability ( Hydrogen Bonds, Hydrophobic
Forces, van der Waals Interactions, Pi-Stacking, and Salt Bridges). Mapping Properties onto
Protein Surfaces, Fitting Monomers, Concepts and application of RMSD.
Concepts in Structure Predictions: The logic of Structure Predictions, Secondary Structure
Prediction, Fold Recognition, Homology Modeling, Ab Initio Structure Prediction.

Protein modelling

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Concepts in Structure Predictions:

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Unit IV
Molecular Docking and molecular dynamics simulations:
Structure-Based Drug Design Introduction: Modelling Protein-Ligand Interactions. Pose
Prediction and Affinity Prediction.
Rigid Body Docking: Concept, Relevant Software, and Limitations.
Flexible Ligand Docking:
a. Systematic Methods (Conformational Search, Fragmentation, and Database Methods).
Types of Systematic Methods 1. Conformational Search Methodology, Advantages, and
Disadvantages. 2. The Fragmentation Method, Place and Join Algorithm and Incremental
Construction Algorithm. 3. Database method.
b. Random/ Stochastic Methods: Monte Carlo Method, Genetic Algorithm, and Tabu Search.
Concepts in affinity prediction: Challenge in Affinity Prediction, Scoring Functions, Force
Field-Based, Empirical, and Knowledge-Based.
Introduction to Molecular Simulation Methods: Need for Studying Molecular Dynamics
(MD) Simulations, Concept, Types. All-Atom and Coarse-Grain MD Simulations.
Conventional and Steered MD Simulations. Hamiltonian Equations in MD Simulations :
Derivation, Practical Drawbacks of Hamiltonian Equations, Taylor Expansion in MD
Simulations. Derivation of the Velocity Verlet Algorithm.
Initial Conditions and Maxwell-Boltzmann Distribution: Initial Velocities assignment.
Maxwell-Boltzmann Theory in Velocity Assignment.
Force Fields: The Concepts and Examples of Force Fields, Detailed Explanation of Terms
within the CHARMM Force Field.

Molecular Docking

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Molecular Dynamics

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