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Protein-protein Interfaces

Protein-protein Interfaces

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...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Protein Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...

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Related Experiment Video

Updated: Jul 8, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction.

Pascal Notin¹, Aaron W Kollasch², Daniel Ritter²

¹Computer Science, University of Oxford.

Biorxiv : the Preprint Server for Biology

|December 18, 2023

Summary

This summary is machine-generated.

ProteinGym provides a large-scale benchmark for assessing machine learning models in protein fitness prediction and design. This resource aims to standardize evaluation across diverse protein families and experimental data, improving model development for applications in health and agriculture.

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A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

Area of Science:

Computational Biology
Protein Engineering
Machine Learning

Background:

Predicting protein mutation effects is crucial for understanding genetic diseases and designing novel proteins for climate, agriculture, and healthcare.
Current machine learning models for protein analysis face challenges due to varied datasets and inconsistent performance across protein families.

Conclusions:

ProteinGym offers a scalable and holistic solution for benchmarking protein fitness prediction and design models.
The open-sourced codebase, datasets, and user-friendly website facilitate broader research and development in protein engineering.
Standardized evaluation is essential for advancing machine learning applications in protein science.