MP-T: improving membrane protein alignment for structure prediction

Abstract

All source code, alignments and models are available at http://www.stats.ox.ac.uk/proteins/resources

A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling

“…For this reason, we tested three algorithms of pairwise alignment using their results as an input for each method of model building. Two of the alignment methods are specifically constructed for membrane proteins, MP-T 10 and AlignMe 11 , and the third one, MUSTER 12 , gains its quality from evolutionary predictions. The latter algorithm is a built-in algorithm of I-TASSER suite and its results were used only for this method of structure prediction.…”

Characterizing the Structure, Function, and Evolution of Human Solute Carrier (SLC) Transporters Using Computational Approaches

“…They include profile-profile alignment and fold recognition methods that rely on observed or predicted structural information (e.g., HHpred (Soding et al 2005)), multiple sequence alignment methods (e.g., MAFFT (Katoh and Toh 2008)), as well as methods that combine these approaches (e.g., Promals3D (Pei et al 2008)). Several alignment methods have been specifically optimized to align membrane proteins (Khafizov et al 2010;Hill and Deane 2013;Pirovano et al 2008;Chang et al 2012) (Table 2.1). Two recent developments include (1) alignment of membrane proteins (AlignMe), which is a user-friendly program that uses information such as residue Type gives type of the prediction method; "S" and "P" correspond to a web server and a computer program, respectively c URL provides the Internet address for the service d…”

“…Reference gives the primary literature describing the method hydrophobicity and predicted secondary structure to align sequences or hydropathy profiles of membrane proteins (Khafizov et al 2010;Stamm et al 2013) and (2) membrane protein threader (MP-T), which is a sequence-structure alignment method based on multiple sequence alignment (Hill and Deane 2013). MP-T uses predicted and observed information such as accessible surface area, membrane positioning, as well as secondary structure derived from homologs of the target protein.…”

Structure Prediction of Transmembrane Proteins

“…Aligning transmembrane sequences used to be a long-standing unsolved problem, but by now numerous TMP sequence aligner methods have been developed, e.g. AlignMe [140] and MP-T [53]. According to Forrest et al [38], comparative modeling of TMPs has been estimated to obtain accuracy as high as that of soluble proteins if the alignment for TMPs achieves the accuracy of its soluble protein counterpart.…”

“…A web server for homology modeling of TMPs named Memoir [34] is a pipeline utilizing iMembrane [65], a membrane protein annotator using CGDB [21] coarse-grained database; MP-T [53] target-template aligner; Medeller [66], a coordinate generator and FREAD [22], a loop modeler. Memoir does not search for a homologue template, therefore it needs this as an input parameter and does not provide any information on the reliability of the resulting structures.…”