KAUST DepartmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Computational Bioscience Research Center (CBRC)
MetadataShow full item record
AbstractComputational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here, we describe a high-throughput deep transfer learning method that first predicts MP contacts by learning from non-MPs and then predicts 3D structure models using the predicted contacts as distance restraints. Tested on 510 non-redundant MPs, our method has contact prediction accuracy at least 0.18 better than existing methods, predicts correct folds for 218 MPs, and generates 3D models with root-mean-square deviation (RMSD) less than 4 and 5 Å for 57 and 108 MPs, respectively. A rigorous blind test in the continuous automated model evaluation project shows that our method predicted high-resolution 3D models for two recent test MPs of 210 residues with RMSD ∼2 Å. We estimated that our method could predict correct folds for 1,345–1,871 reviewed human multi-pass MPs including a few hundred new folds, which shall facilitate the discovery of drugs targeting at MPs.
CitationWang S, Li Z, Yu Y, Xu J (2017) Folding Membrane Proteins by Deep Transfer Learning. Cell Systems 5: 202–211.e3. Available: http://dx.doi.org/10.1016/j.cels.2017.09.001.
SponsorsThis work is supported by NIH grant R01GM089753 to J.X. and National Science Foundation grant DBI-1564955 to J.X. The authors are also grateful to the support of Nvidia and the computational resources provided by XSEDE. An early version of this paper was submitted to and peer reviewed at the 2017 Annual International Conference on Research in Computational Molecular Biology (RECOMB). The manuscript was revised and then independently further reviewed at Cell Systems.
- PredMP: a web server for de novo prediction and visualization of membrane proteins.
- Authors: Wang S, Fei S, Wang Z, Li Y, Xu J, Zhao F, Gao X
- Issue date: 2018 Aug 4
- Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.
- Authors: Wang S, Sun S, Li Z, Zhang R, Xu J
- Issue date: 2017 Jan
- High-resolution structure prediction of <i>β</i>-barrel membrane proteins.
- Authors: Tian W, Lin M, Tang K, Liang J, Naveed H
- Issue date: 2018 Feb 13
- Ab initio modeling of small proteins by iterative TASSER simulations.
- Authors: Wu S, Skolnick J, Zhang Y
- Issue date: 2007 May 8
- CONFOLD: Residue-residue contact-guided ab initio protein folding.
- Authors: Adhikari B, Bhattacharya D, Cao R, Cheng J
- Issue date: 2015 Aug