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Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Updated: Jun 29, 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

Graphormer supervised de novo protein design method and function validation.

Junxi Mu^1,2, Zhengxin Li¹, Bo Zhang¹

¹State Key Laboratory of Microbial metabolism, Joint International Research Laboratory of Metabolic Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.

Briefings in Bioinformatics

|April 1, 2024

Summary

This summary is machine-generated.

The Graphormer-based Protein Design (GPD) model enhances protein sequence design, improving enzyme catalytic activity and substrate selectivity. This novel method offers greater sequence diversity than existing approaches for creating functional proteins.

Keywords:

GPD model Graphormer architecture function validation protein sequence design

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Last Updated: Jun 29, 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

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

Identification of Functional Protein Regions Through Chimeric Protein Construction

Identification of Functional Protein Regions Through Chimeric Protein Construction

Published on: January 8, 2019

Area of Science:

Protein Engineering
Computational Biology
Biotechnology

Background:

Protein design is crucial for creating novel proteins with enhanced biological functions, like improved enzyme catalytic efficiency.
Fixed-backbone protein sequence design aims to generate new sequences for specific protein structures.
Current methods face limitations in sequence diversity and experimental validation, hindering functional protein design.

Purpose of the Study:

To address limitations in existing protein sequence design methods.
To develop a novel model for enhanced protein sequence design with improved diversity and functional validation.
To create new enzymes with improved catalytic activity and substrate selectivity.

Main Methods:

Developed the Graphormer-based Protein Design (GPD) model, utilizing Transformer architecture on graph-based protein structures.
Incorporated Gaussian noise and sequence random masks into node features to boost sequence recovery and diversity.
Applied GPD to design CalB hydrolase, generating nine artificial variants.

Main Results:

The GPD model demonstrated superior performance over the state-of-the-art ProteinMPNN model, particularly in sequence diversity.
Designed CalB hydrolase variants exhibited a 1.7-fold increase in catalytic activity compared to wild-type.
The designed proteins showed strong substrate selectivity for p-nitrophenyl acetate with varying carbon chain lengths (C2-C16).

Conclusions:

The GPD method significantly improves fixed-backbone protein sequence design, offering enhanced sequence diversity.
The successful de novo design of CalB hydrolase with increased catalytic activity and selectivity demonstrates GPD's potential.
GPD is a promising tool for the de novo design of industrial enzymes and protein therapeutics.