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BY 4.0 license Open Access Published by De Gruyter Open Access May 29, 2019

AngularQA: Protein Model Quality Assessment with LSTM Networks

  • Matthew Conover , Max Staples , Dong Si , Miao Sun and Renzhi Cao EMAIL logo


Quality Assessment (QA) plays an important role in protein structure prediction. Traditional multimodel QA method usually suffer from searching databases or comparing with other models for making predictions, which usually fail when the poor quality models dominate the model pool. We propose a novel protein single-model QA method which is built on a new representation that converts raw atom information into a series of carbon-alpha (Cα) atoms with side-chain information, defined by their dihedral angles and bond lengths to the prior residue. An LSTM network is used to predict the quality by treating each amino acid as a time-step and consider the final value returned by the LSTM cells. To the best of our knowledge, this is the first time anyone has attempted to use an LSTM model on the QA problem; furthermore, we use a new representation which has not been studied for QA. In addition to angles, we make use of sequence properties like secondary structure parsed from protein structure at each time-step without using any database, which is different than all existed QA methods. Our model achieves an overall correlation of 0.651 on the CASP12 testing dataset. Our experiment points out new directions for QA problem and our method could be widely used for protein structure prediction problem. The software is freely available at GitHub:


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Received: 2018-09-09
Accepted: 2019-05-01
Published Online: 2019-05-29

© 2019 Matthew Conover et al., published by De Gruyter

This work is licensed under the Creative Commons Attribution 4.0 Public License.

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