Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategy

Abstract

The following sentence on page 1722 is incorrect: Using this clustering approach, we identified 159 a-helical protein chains in 37 families corresponding to 354 protein pairs (Supporting Information Table S1), plus 68 b-barrels in 8 families corresponding to 319 alignments (Supporting Information Table S2), for a total of 673 alignments.The correct sentence should read: Using this clustering approach, we identified 152 a-helical protein chains in 40 families corresponding to 354 protein pairs (Supporting Information Table S1), plus 68 b-barrels in 8 families corresponding to 319 alignments (Supporting Information Table S2), for a total of 673 alignments.

Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms

“…The TM regions of these channels were aligned using Fr-TM-Align (Pandit and Skolnick, 2008;Zhang and Skolnick, 2005), which aligns structures pairwise by optimizing for the global template-modeling-score (TM-score), a measure of backbone fold similarity that is independent of protein length (see Methods). As a fragment-based alignment method, Fr-TM-Align is effective even in cases with large conformational differences (Stamm and Forrest, 2015).…”

“…To obtain a structure-based, sequence-agnostic sequence alignment, structures were first aligned pairwise using Fr-TM-Align version 1.0, a fragment-based alignment approach that aligns residues based on patterns of secondary structure (Pandit and Skolnick, 2008). Fr-TM-Align has been tested on membrane proteins and is robust even to large conformational changes (Stamm and Forrest, 2015). As with other methods, the aligned structures are iteratively aligned and scored for alignment match before the alignment with the best pairwise TM-score is chosen.…”

Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data

“…The variety of available methods for 3D genome structure determination and their likely complementary strengths and weaknesses also suggest the possibility to apply such methods simultaneously in order to obtain a consensus solution based on suitable criteria. Similar strategies have been proposed, for example, to improve the reliability of protein-ligand predictions, 128,129 protein structure alignments, 130 protein structure comparison, 131 and protein secondary structure prediction.…”

EncoMPASS: an online database for analyzing structure and symmetry in membrane proteins

“…To address these issues, we created the Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry (EncoMPASS). Expanding on the offline, manually-curated membrane protein structure classification database HOMEP (15), the EncoMPASS database is automated and uses accurate structure and sequence alignments to relate membrane protein structures. Instead of building a hierarchical classification in the style of e.g.…”