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Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Protein-protein interactions: scoring schemes and binding affinity.

M Michael Gromiha¹, K Yugandhar¹, Sherlyn Jemimah¹

¹Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India.

Current Opinion in Structural Biology

|November 21, 2016

Summary

This summary is machine-generated.

This review explores computational methods for predicting protein-protein complex structures and binding affinities. It covers protein-protein docking, interaction thermodynamics, and available resources for studying these interactions.

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Computational biology
Structural biology
Biophysics

Background:

Protein-protein interactions (PPIs) are crucial for cellular functions.
Understanding PPIs requires knowledge of complex structures and binding affinities.
Computational approaches are vital for predicting these properties.

Purpose of the Study:

To review computational methods for predicting protein-protein complex structures.
To explore computational strategies for determining protein-protein binding affinities.
To highlight recent advancements and available resources in PPI research.

Main Methods:

Protein-protein docking simulations.
Conformational searching and scoring functions.
Thermodynamic analysis of binding affinities.
Prediction methods using 3D structures or amino acid sequences.
Analysis of binding affinity changes upon mutation.

Main Results:

Detailed overview of protein-protein docking techniques.
Discussion of databases for binding affinities and thermodynamic parameters.
Evaluation of computational methods for predicting binding affinity.
Insights into the impact of mutations on binding affinity.

Conclusions:

Computational methods are essential for predicting protein-protein complex structures and binding affinities.
Advancements in docking and affinity prediction offer valuable tools for biological research.
Accessible computational resources aid in understanding complex protein-protein interactions.