Folding Membrane Proteins by Deep Transfer Learning Sheng Wang, Zhen Li, Yizhou Yu, Jinbo Xu  Cell Systems  Volume 5, Issue 3, Pages 202-211.e3 (September 2017) DOI: 10.1016/j.cels.2017.09.001 Copyright © 2017 Elsevier Inc. Terms and Conditions

Cell Systems 2017 5, 202-211.e3DOI: (10.1016/j.cels.2017.09.001) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure 1 Overview of Our Deep Learning Model for MP Contact Prediction Where L Is the Sequence Length of One MP under Prediction Cell Systems 2017 5, 202-211.e3DOI: (10.1016/j.cels.2017.09.001) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure 2 Contact Prediction and 3D Modeling Accuracy on the 510 Membrane Proteins Top L/5 long-range accuracy (A), medium-range accuracy (B), and TMscore of the best of top 5 3D models (C) generated by our three models Mixed (cyan), NonMP-only (purple), MP-only (green), CCMpred (blue), and MetaPSICOV (red) with respect to ln(Meff). (D) Summary results of all tested methods in terms of modeling accuracy. Column “#<XÅ” lists the number of MPs whose 3D models have RMSD ≤X Å. Column “#TM>Y” lists the number of MPs whose 3D models have TMscore ≥Y. RMSD¯ (TMsco¯) shows the average RMSD (TMscore) of all 510 MPs. TBM (MP) and TBM (NonMP) stands for template-based modeling with membrane proteins as templates and without membrane proteins as templates, respectively. Cell Systems 2017 5, 202-211.e3DOI: (10.1016/j.cels.2017.09.001) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure 3 Quality Comparison of the Best of the Top Five Contact-Assisted Models Generated by Our Two Methods, CCMpred and MetaPSICOV (A) Mixed versus CCMpred; (B) Mixed versus MetaPSICOV; (C) NonMP versus CCMpred; (D) NonMP versus MetaPSICOV. Cell Systems 2017 5, 202-211.e3DOI: (10.1016/j.cels.2017.09.001) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure 4 Case Study of One CAMEO Target 5h35E (A) The long- and medium-range contact prediction accuracy of our methods, MetaPSICOV, CCMpred, and EVfold (web server). (B–D) The overlap between the native contact map and contact maps predicted by our method, CCMpred, MetaPSICOV, and EVfold. Top L predicted all-range contacts are displayed. A gray, red, and green dot represents a native contact, a correct prediction, and a wrong prediction, respectively. (E) The superimposition between our predicted model (in red) and the native structure (in blue). Cell Systems 2017 5, 202-211.e3DOI: (10.1016/j.cels.2017.09.001) Copyright © 2017 Elsevier Inc. Terms and Conditions

Figure 5 3D Modeling Accuracy with Respect to the Number of Effective Sequence Homologs (A) TMscore with respect to ln(Neff), based upon the 354 multi-pass membrane proteins in PDB. (B) ln(Neff) distribution of the 354 multi-pass MPs in PDB. (C) ln(Neff) distribution of the 2,215 reviewed human multi-pass MPs. Cell Systems 2017 5, 202-211.e3DOI: (10.1016/j.cels.2017.09.001) Copyright © 2017 Elsevier Inc. Terms and Conditions