Evolutionary-guided de novo structure prediction of self-associated transmembrane helical proteins with near-atomic accuracy

A frequent, GxxxG-mediated, transmembrane association motif is optimized for the formation of interhelical C -H hydrogen bonds

(2014) B. K. Mueller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues

(2014) Kuang-Yui M. Chen et al.   PLoS Computational Biology

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Architecture and Membrane Interactions of the EGF Receptor

(2013) Anton Arkhipov et al.   CELL

Conformational Coupling across the Plasma Membrane in Activation of the EGF Receptor

(2013) Nicholas F. Endres et al.   CELL

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

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

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

Coevolutionary signals across protein lineages help capture multiple protein conformations

(2013) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tryptophan at the transmembrane-cytosolic junction modulates thrombopoietin receptor dimerization and activation

(2013) J.-P. Defour et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of FGFR3 Transmembrane Domain Dimer: Implications for Signaling and Human Pathologies

(2013) Eduard V. Bocharov et al.   STRUCTURE

Structural and thermodynamic insight into the process of “weak” dimerization of the ErbB4 transmembrane domain by solution NMR

(2012) Eduard V. Bocharov et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution

(2012) Sarel J. Fleishman et al.   CELL

Dimeric structure of transmembrane domain of amyloid precursor protein in micellar environment

(2012) Kirill D. Nadezhdin et al.   FEBS LETTERS

Hydrophobic Matching Controls the Tilt and Stability of the Dimeric Platelet-derived Growth Factor Receptor (PDGFR) β Transmembrane Segment

(2012) Claudia Muhle-Goll et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Homotypic Interaction and Amino Acid Distribution of Unilaterally Conserved Transmembrane Helices

(2012) Christian Lothar Ried et al.   JOURNAL OF MOLECULAR BIOLOGY

Multistate Organization of Transmembrane Helical Protein Dimers Governed by the Host Membrane

(2012) Anton A. Polyansky et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Naturally evolved G protein-coupled receptors adopt metastable conformations

(2012) K.-Y. M. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis

(2012) A. E. Dago et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial structure and dimer–monomer equilibrium of the ErbB3 transmembrane domain in DPC micelles

(2011) K.S. Mineev et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

A Photon-Free Approach to Transmembrane Protein Structure Determination

(2011) Cinque S. Soto et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2011) Michael Remmert et al.   NATURE METHODS

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

Structural topology of phospholamban pentamer in lipid bilayers by a hybrid solution and solid-state NMR method

(2011) R. Verardi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Left-Handed Dimer of EphA2 Transmembrane Domain: Helix Packing Diversity among Receptor Tyrosine Kinases

(2010) Eduard V. Bocharov et al.   BIOPHYSICAL JOURNAL

New insights into the mechanisms of hematopoietic cell transformation by activated receptor tyrosine kinases

(2010) F. Toffalini et al.   BLOOD

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Spatial Structure of the Transmembrane Domain Heterodimer of ErbB1 and ErbB2 Receptor Tyrosine Kinases

(2010) Konstantin S. Mineev et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Evidence for Loose Linkage between Ligand Binding and Kinase Activation in the Epidermal Growth Factor Receptor

(2010) C. Lu et al.   MOLECULAR AND CELLULAR BIOLOGY

The structural basis for intramembrane assembly of an activating immunoreceptor complex

(2010) Matthew E Call et al.   NATURE IMMUNOLOGY

Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus

(2010) R. Acharya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Learning generative models for protein fold families

(2010) Sivaraman Balakrishnan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Transmembrane helix-helix interactions involved in ErbB receptor signaling

(2010) Florian Cymer et al.   Cell Adhesion & Migration

Structural Basis for Dimerization of the BNIP3 Transmembrane Domain,

(2009) Endah S. Sulistijo et al.   BIOCHEMISTRY

Mechanism for Activation of the EGF Receptor Catalytic Domain by the Juxtamembrane Segment

(2009) Natalia Jura et al.   CELL

The structure of the integrin αIIbβ3 transmembrane complex explains integrin transmembrane signalling

(2009) Tong-Lay Lau et al.   EMBO JOURNAL

The Structure of a Receptor with Two Associating Transmembrane Domains on the Cell Surface: Integrin αIIbβ3

(2009) Jieqing Zhu et al.   MOLECULAR CELL

Solution structure and functional analysis of the influenza B proton channel

(2009) Junfeng Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Prediction of membrane protein structures with complex topologies using limited constraints

(2009) P. Barth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous prediction of protein folding and docking at high resolution

(2009) Rhiju Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interaction and conformational dynamics of membrane-spanning protein helices

(2009) Dieter Langosch et al.   PROTEIN SCIENCE

OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar

(2008) Håkan Viklund et al.   BIOINFORMATICS

Graphical Models of Residue Coupling in Protein Families

(2008) J. Thomas et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Spatial Structure and pH-dependent Conformational Diversity of Dimeric Transmembrane Domain of the Receptor Tyrosine Kinase EphA1

(2008) Eduard V. Bocharov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Spatial Structure of the Dimeric Transmembrane Domain of the Growth Factor Receptor ErbB2 Presumably Corresponding to the Receptor Active State

(2008) Eduard V. Bocharov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural basis for the function and inhibition of an influenza virus proton channel

(2008) Amanda L. Stouffer et al.   NATURE

Cell-surface protein-protein interaction analysis with time-resolved FRET and snap-tag technologies: application to GPCR oligomerization

(2008) Damien Maurel et al.   NATURE METHODS

Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking

(2008) H. Madaoui et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein-Protein Interactions in the Membrane: Sequence, Structural, and Biological Motifs

(2008) David T. Moore et al.   STRUCTURE