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Updated: Oct 16, 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

Fast activation maximization for molecular sequence design.

Johannes Linder¹, Georg Seelig^2,3

¹Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA. jlinder2@cs.washington.edu.

BMC Bioinformatics

|October 21, 2021

Summary

This summary is machine-generated.

Fast SeqProp accelerates molecular design by optimizing DNA and protein sequences using machine learning. This new method significantly improves convergence speed and finds better solutions for sequence optimization tasks.

Keywords:

Activation maximization DNA Deep learning Design Gradient ascent Neural network Optimization Protein RNA Sequence design

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Area of Science:

Computational biology
Machine learning in molecular design

Background:

Machine learning models are increasingly used for DNA and protein sequence optimization.
Activation maximization is a design strategy for differentiable models but suffers from vanishing gradients and poor convergence.

Purpose of the Study:

To introduce Fast SeqProp, an improved activation maximization method for efficient sequence optimization.
To overcome limitations of existing methods, such as vanishing gradients and skewed parameters.

Main Methods:

Fast SeqProp combines straight-through approximation with normalization.
It optimizes sequences using gradient ascent with a differentiable predictor.

Main Results:

Fast SeqProp achieves up to 100-fold faster convergence compared to prior methods.
The method finds improved fitness optima for DNA and protein sequence design.
Demonstrated on six deep learning predictors, including a protein structure predictor.

Conclusions:

Fast SeqProp is a reliable and efficient method for general-purpose sequence optimization.
The method is widely applicable across various deep learning models and can incorporate regularization.
Fast SeqProp can aid in developing novel molecules, drug therapies, and vaccines.