Beating the Best: Improving on AlphaFold2 at Protein Structure Prediction

by   Abbi Abdel-Rehim, et al.

The goal of Protein Structure Prediction (PSP) problem is to predict a protein's 3D structure (confirmation) from its amino acid sequence. The problem has been a 'holy grail' of science since the Noble prize-winning work of Anfinsen demonstrated that protein conformation was determined by sequence. A recent and important step towards this goal was the development of AlphaFold2, currently the best PSP method. AlphaFold2 is probably the highest profile application of AI to science. Both AlphaFold2 and RoseTTAFold (another impressive PSP method) have been published and placed in the public domain (code models). Stacking is a form of ensemble machine learning ML in which multiple baseline models are first learnt, then a meta-model is learnt using the outputs of the baseline level model to form a model that outperforms the base models. Stacking has been successful in many applications. We developed the ARStack PSP method by stacking AlphaFold2 and RoseTTAFold. ARStack significantly outperforms AlphaFold2. We rigorously demonstrate this using two sets of non-homologous proteins, and a test set of protein structures published after that of AlphaFold2 and RoseTTAFold. As more high quality prediction methods are published it is likely that ensemble methods will increasingly outperform any single method.


page 6

page 7

page 8

page 9


PSP: Million-level Protein Sequence Dataset for Protein Structure Prediction

Proteins are essential component of human life and their structures are ...

Leveraging Sequence Embedding and Convolutional Neural Network for Protein Function Prediction

The capability of accurate prediction of protein functions and propertie...

End-to-End Optimized Pipeline for Prediction of Protein Folding Kinetics

Protein folding is the intricate process by which a linear sequence of a...

ProteinNet: a standardized data set for machine learning of protein structure

Rapid progress in deep learning has spurred its application to bioinform...

MAS2HP: A Multi Agent System to predict protein structure in 2D HP model

Protein Structure Prediction (PSP) is an unsolved problem in the field o...

Subcellular Protein Localisation in the Human Protein Atlas using Ensembles of Diverse Deep Architectures

Automated visual localisation of subcellular proteins can accelerate our...

Decoy Selection for Protein Structure Prediction Via Extreme Gradient Boosting and Ranking

Identifying one or more biologically-active/native decoys from millions ...

Please sign up or login with your details

Forgot password? Click here to reset