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Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Protein Families

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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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Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

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Updated: Oct 4, 2025

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

ProtPlat: an efficient pre-training platform for protein classification based on FastText.

Yuan Jin¹, Yang Yang²

¹Department of Computer Science and Engineering, Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai, 200240, China.

BMC Bioinformatics

|February 12, 2022

Summary

This summary is machine-generated.

We developed ProtPlat, a novel pre-training platform for protein sequences, to improve machine learning predictions. This method enhances amino acid representations and boosts classification performance, especially for limited data scenarios.

Keywords:

Pre-training ProtPlat Protein sequence classification Web server

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Area of Science:

Computational Biology
Bioinformatics
Machine Learning

Background:

Machine learning for protein sequence analysis is limited by insufficient labeled data.
Pre-training methods are successful in other fields but underexplored for protein sequences.

Purpose of the Study:

To develop a general pre-training platform for protein sequences to enhance feature representation.
To improve performance on sequence-based classification tasks, particularly with small datasets.

Main Methods:

ProtPlat platform utilizes the Pfam database for large-scale supervised pre-training.
A three-layer neural network and FastText model are employed for efficient learning.
The pre-trained model is fine-tuned on specific downstream task data.

Main Results:

ProtPlat learns effective amino acid representations and achieves efficient classification.
Experiments on three tasks (effector identification, localization, signal peptide recognition) show performance enhancement.
ProtPlat is competitive with state-of-the-art predictors, outperforming them on small datasets.

Conclusions:

ProtPlat effectively enhances feature representation for protein amino acid sequences.
The platform improves performance in sequence-based classification tasks.
ProtPlat is a valuable tool for protein sequence analysis, accessible as a public web service.