High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling

Deep architectures for protein contact map prediction

(2012) Pietro Di Lena et al.   BIOINFORMATICS

Crystal structure of the channelrhodopsin light-gated cation channel

(2012) Hideaki E. Kato et al.   NATURE

Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation

(2012) Michael Hohl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

Predicting Residue-Residue Contacts and Helix-Helix Interactions in Transmembrane Proteins Using an Integrative Feature-Based Random Forest Approach

(2011) Xiao-Feng Wang et al.   PLoS One

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

(2011) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving Protein Structure Prediction Using Multiple Sequence-Based Contact Predictions

(2011) Sitao Wu et al.   STRUCTURE

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

(2010) Lukas Burger et al.   PLoS Computational Biology

Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm

(2010) Timothy Nugent et al.   PLoS Computational Biology

Predicting helix–helix interactions from residue contacts in membrane proteins

(2009) Allan Lo et al.   BIOINFORMATICS

Transmembrane protein topology prediction using support vector machines

(2009) Timothy Nugent et al.   BMC BIOINFORMATICS

Learning from Imbalanced Data

(2009) Haibo He et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

A comprehensive assessment of sequence-based and template-based methods for protein contact prediction

(2008) Sitao Wu et al.   BIOINFORMATICS

MemBrain: Improving the Accuracy of Predicting Transmembrane Helices

(2008) Hongbin Shen et al.   PLoS One

Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks

(2008) Angelika Fuchs et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS