Please use this identifier to cite or link to this item: http://localhost/handle/Hannan/186974
Title: Deep Conditional Random Field Approach to Transmembrane Topology Prediction and Application to GPCR Three-Dimensional Structure Modeling
Authors: Hongjie Wu;Kun Wang;Liyao Lu;Yu Xue;Qiang Lyu;Min Jiang
Year: 2017
Publisher: IEEE
Abstract: Transmembrane proteins play important roles in cellular energy production, signal transmission, and metabolism. Many shallow machine learning methods have been applied to transmembrane topology prediction, but the performance was limited by the large size of membrane proteins and the complex biological evolution information behind the sequence. In this paper, we proposed a novel deep approach based on conditional random fields named as dCRF-TM for predicting the topology of transmembrane proteins. Conditional random fields take into account more complicated interrelation between residue labels in full-length sequence than HMM and SVM-based methods. Three widely-used datasets were employed in the benchmark. DCRF-TM had the accuracy 95 percent over helix location prediction and the accuracy 78 percent over helix number prediction. DCRF-TM demonstrated a more robust performance on large size proteins (>350 residues) against 11 state-of-the-art predictors. Further dCRF-TM was applied to ab initio modeling three-dimensional structures of seven-transmembrane receptors, also known as G protein-coupled receptors. The predictions on 24 solved G protein-coupled receptors and unsolved vasopressin V2 receptor illustrated that dCRF-TM helped abGPCR-I-TASSER to improve TM-score 34.3 percent rather than using the random transmembrane definition. Two out of five predicted models caught the experimental verified disulfide bonds in vasopressin V2 receptor.
URI: http://localhost/handle/Hannan/186974
volume: 14
issue: 5
More Information: 1106,
1114
Appears in Collections:2017

Files in This Item:
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7552547.pdf1.14 MBAdobe PDF
Title: Deep Conditional Random Field Approach to Transmembrane Topology Prediction and Application to GPCR Three-Dimensional Structure Modeling
Authors: Hongjie Wu;Kun Wang;Liyao Lu;Yu Xue;Qiang Lyu;Min Jiang
Year: 2017
Publisher: IEEE
Abstract: Transmembrane proteins play important roles in cellular energy production, signal transmission, and metabolism. Many shallow machine learning methods have been applied to transmembrane topology prediction, but the performance was limited by the large size of membrane proteins and the complex biological evolution information behind the sequence. In this paper, we proposed a novel deep approach based on conditional random fields named as dCRF-TM for predicting the topology of transmembrane proteins. Conditional random fields take into account more complicated interrelation between residue labels in full-length sequence than HMM and SVM-based methods. Three widely-used datasets were employed in the benchmark. DCRF-TM had the accuracy 95 percent over helix location prediction and the accuracy 78 percent over helix number prediction. DCRF-TM demonstrated a more robust performance on large size proteins (>350 residues) against 11 state-of-the-art predictors. Further dCRF-TM was applied to ab initio modeling three-dimensional structures of seven-transmembrane receptors, also known as G protein-coupled receptors. The predictions on 24 solved G protein-coupled receptors and unsolved vasopressin V2 receptor illustrated that dCRF-TM helped abGPCR-I-TASSER to improve TM-score 34.3 percent rather than using the random transmembrane definition. Two out of five predicted models caught the experimental verified disulfide bonds in vasopressin V2 receptor.
URI: http://localhost/handle/Hannan/186974
volume: 14
issue: 5
More Information: 1106,
1114
Appears in Collections:2017

Files in This Item:
File SizeFormat 
7552547.pdf1.14 MBAdobe PDF
Title: Deep Conditional Random Field Approach to Transmembrane Topology Prediction and Application to GPCR Three-Dimensional Structure Modeling
Authors: Hongjie Wu;Kun Wang;Liyao Lu;Yu Xue;Qiang Lyu;Min Jiang
Year: 2017
Publisher: IEEE
Abstract: Transmembrane proteins play important roles in cellular energy production, signal transmission, and metabolism. Many shallow machine learning methods have been applied to transmembrane topology prediction, but the performance was limited by the large size of membrane proteins and the complex biological evolution information behind the sequence. In this paper, we proposed a novel deep approach based on conditional random fields named as dCRF-TM for predicting the topology of transmembrane proteins. Conditional random fields take into account more complicated interrelation between residue labels in full-length sequence than HMM and SVM-based methods. Three widely-used datasets were employed in the benchmark. DCRF-TM had the accuracy 95 percent over helix location prediction and the accuracy 78 percent over helix number prediction. DCRF-TM demonstrated a more robust performance on large size proteins (>350 residues) against 11 state-of-the-art predictors. Further dCRF-TM was applied to ab initio modeling three-dimensional structures of seven-transmembrane receptors, also known as G protein-coupled receptors. The predictions on 24 solved G protein-coupled receptors and unsolved vasopressin V2 receptor illustrated that dCRF-TM helped abGPCR-I-TASSER to improve TM-score 34.3 percent rather than using the random transmembrane definition. Two out of five predicted models caught the experimental verified disulfide bonds in vasopressin V2 receptor.
URI: http://localhost/handle/Hannan/186974
volume: 14
issue: 5
More Information: 1106,
1114
Appears in Collections:2017

Files in This Item:
File SizeFormat 
7552547.pdf1.14 MBAdobe PDF