AcconPred: Predicting Solvent Accessibility and Contact Number Simultaneously by a Multitask Learning Framework under the Conditional Neural Fields Model

BioMed Research International
Jianzhu Ma, Sheng Wang

Abstract

The solvent accessibility of protein residues is one of the driving forces of protein folding, while the contact number of protein residues limits the possibilities of protein conformations. The de novo prediction of these properties from protein sequence is important for the study of protein structure and function. Although these two properties are certainly related with each other, it is challenging to exploit this dependency for the prediction. We present a method AcconPred for predicting solvent accessibility and contact number simultaneously, which is based on a shared weight multitask learning framework under the CNF (conditional neural fields) model. The multitask learning framework on a collection of related tasks provides more accurate prediction than the framework trained only on a single task. The CNF method not only models the complex relationship between the input features and the predicted labels, but also exploits the interdependency among adjacent labels. Trained on 5729 monomeric soluble globular protein datasets, AcconPred could reach 0.68 three-state accuracy for solvent accessibility and 0.75 correlation for contact number. Tested on the 105 CASP11 domain datasets for solvent accessibility, AcconPred could r...Continue Reading

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Citations

Aug 1, 2015·International Journal of Molecular Sciences·Sheng WangQingming Tang
Jan 26, 2016·Journal of Chemical Information and Modeling·Bian LiJens Meiler
Apr 27, 2016·Nucleic Acids Research·Sheng WangJinbo Xu
May 20, 2016·Molecular BioSystems·Vidya Rajendran
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Jan 29, 2019·Database : the Journal of Biological Databases and Curation·Piyush AgrawalGajendra P S Raghava
Oct 20, 2021·Journal of Chemical Theory and Computation·Daniel MulnaesHolger Gohlke

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Methods Mentioned

BETA
protein folding

Software Mentioned

RaptorX
PSIPRED
AcconPred
ACCpro5
DSSP
SPINE
SANN
HHpred
SS8
BLAST

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