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

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

A new statistical framework to assess structural alignment quality using information compression

(2014) J. H. Collier et al.   BIOINFORMATICS

Systematic Detection of Internal Symmetry in Proteins Using CE-Symm

(2014) Douglas Myers-Turnbull et al.   JOURNAL OF MOLECULAR BIOLOGY

Alignment of Helical Membrane Protein Sequences Using AlignMe

(2013) Marcus Stamm et al.   PLoS One

CAD-score: A new contact area difference-based function for evaluation of protein structural models

(2013) Kliment Olechnovič et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

(Pseudo-)Symmetrical Transport

(2013) L. R. Forrest   SCIENCE

Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments

(2012) A. W. Slater et al.   BIOINFORMATICS

MP-T: improving membrane protein alignment for structure prediction

(2012) Jamie R. Hill et al.   BIOINFORMATICS

Evolutionary inaccuracy of pairwise structural alignments

(2012) M. I. Sadowski et al.   BIOINFORMATICS

Improved model quality assessment using ProQ2

(2012) Arjun Ray et al.   BMC BIOINFORMATICS

PDBTM: Protein Data Bank of transmembrane proteins after 8 years

(2012) Dániel Kozma et al.   NUCLEIC ACIDS RESEARCH

The Alternating-Access Mechanism of MFS Transporters Arises from Inverted-Topology Repeats

(2011) Sebastian Radestock et al.   JOURNAL OF MOLECULAR BIOLOGY

Detecting internally symmetric protein structures

(2010) Changhoon Kim et al.   BMC BIOINFORMATICS

Dali server: conservation mapping in 3D

(2010) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

Protein structure comparison using iterated double dynamic programming

(2010) William R. Taylor   PROTEIN SCIENCE

Structures of membrane proteins

(2010) Kutti R. Vinothkumar et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

(2009) Shashi Pandit et al.   BMC BIOINFORMATICS

Transmembrane protein topology prediction using support vector machines

(2009) Timothy Nugent et al.   BMC BIOINFORMATICS

Advances and pitfalls of protein structural alignment

(2009) Hitomi Hasegawa et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Biophysical dissection of membrane proteins

(2009) Stephen H. White   NATURE

TOPCONS: consensus prediction of membrane protein topology

(2009) A. Bernsel et al.   NUCLEIC ACIDS RESEARCH

Accuracy analysis of multiple structure alignments

(2009) Christoph Berbalk et al.   PROTEIN SCIENCE

Protein structure alignment considering phenotypic plasticity

(2008) G. Csaba et al.   BIOINFORMATICS

TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model

(2008) Mallika Veeramalai et al.   BMC BIOINFORMATICS

Matt: Local Flexibility Aids Protein Multiple Structure Alignment

(2008) Matthew Menke et al.   PLoS Computational Biology

Mechanism for alternating access in neurotransmitter transporters

(2008) L. R. Forrest et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Common occurrence of internal repeat symmetry in membrane proteins

(2007) Sungwon Choi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison

(2002) Angel R. Ortiz et al.   PROTEIN SCIENCE