MP-T: improving membrane protein alignment for structure prediction

Comprehensive comparison of graph based multiple protein sequence alignment strategies

(2012) Ilya Plyusnin et al.   BMC BIOINFORMATICS

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

(2012) Jia-Ming Chang et al.   BMC BIOINFORMATICS

Environment specific substitution tables improve membrane protein alignment

(2011) J. R. Hill et al.   BIOINFORMATICS

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

(2011) Y. Yang et al.   BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

(2011) Julie D. Thompson et al.   PLoS One

Critical assessment of methods of protein structure prediction (CASP)-round IX

(2011) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Study of the Evolution of Inverted-Topology Repeats from LeuT-Fold Transporters Using AlignMe

(2010) Kamil Khafizov et al.   BIOCHEMISTRY

MEDELLER: homology-based coordinate generation for membrane proteins

(2010) Sebastian Kelm et al.   BIOINFORMATICS

MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities

(2010) Y. Liu et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

iMembrane: homology-based membrane-insertion of proteins

(2009) Sebastian Kelm et al.   BIOINFORMATICS

pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination

(2009) Anna Lobley et al.   BIOINFORMATICS

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins

(2008) W. Pirovano et al.   BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly

(2008) Kathryn A. Scott et al.   STRUCTURE