All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

Structural basis for outer membrane lipopolysaccharide insertion

(2014) Haohao Dong et al.   NATURE

Structural basis for lipopolysaccharide insertion in the bacterial outer membrane

(2014) Shuai Qiao et al.   NATURE

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns

(2014) Marcin J. Skwark et al.   PLoS Computational Biology

Structural insight into the biogenesis of β-barrel membrane proteins

(2013) Nicholas Noinaj et al.   NATURE

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Conformation-specific labeling of BamA and suppressor analysis suggest a cyclic mechanism for  -barrel assembly in Escherichia coli

(2013) N. W. Rigel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ranking models of transmembrane  -barrel proteins using Z-coordinate predictions

(2012) S. Hayat et al.   BIOINFORMATICS

TMBB-DB: a transmembrane  -barrel proteome database

(2012) T. C. Freeman et al.   BIOINFORMATICS

BOCTOPUS: improved topology prediction of transmembrane β barrel proteins

(2012) Sikander Hayat et al.   BIOINFORMATICS

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Structural Basis for Outer Membrane Sugar Uptake in Pseudomonads

(2012) Bert van den Berg   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural basis for iron piracy by pathogenic Neisseria

(2012) Nicholas Noinaj et al.   NATURE

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

(2012) T. Nugent et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Disulfide Rearrangement Triggered by Translocon Assembly Controls Lipopolysaccharide Export

(2012) S.-S. Chng et al.   SCIENCE

β-Barrel Mobility Underlies Closure of the Voltage-Dependent Anion Channel

(2012) Ulrich Zachariae et al.   STRUCTURE

TMBHMM: A frequency profile based HMM for predicting the topology of transmembrane beta barrel proteins and the exposure status of transmembrane residues

(2011) Nitesh Kumar Singh et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins

(2011) Kenichiro Imai et al.   BMC GENOMICS

Predicting Three-Dimensional Structures of Transmembrane Domains of β-Barrel Membrane Proteins

(2011) Hammad Naveed et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2011) Michael Remmert et al.   NATURE METHODS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A highly accurate statistical approach for the prediction of transmembrane β-barrels

(2010) Thomas C. Freeman et al.   BIOINFORMATICS

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

Targeting mitochondria for cancer therapy

(2010) Simone Fulda et al.   NATURE REVIEWS DRUG DISCOVERY

Common ground for protein translocation: access control for mitochondria and chloroplasts

(2010) Enrico Schleiff et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Characterization of the two-protein complex in Escherichia coli responsible for lipopolysaccharide assembly at the outer membrane

(2010) S.-S. Chng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The porin and the permeating antibiotic: a selective diffusion barrier in Gram-negative bacteria

(2008) Jean-Marie Pagès et al.   NATURE REVIEWS MICROBIOLOGY