An Integrated Framework Advancing Membrane Protein Modeling and Design

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

(2015) Y. Wang et al.   Nature Communications

Deciphering Regulatory Mechanism of the Juxtamembrane Region in Thrombopoietin Receptor Activation

(2015) Shao-Qing Zhang et al.   BIOPHYSICAL JOURNAL

Tethered Protein Display Identifies a Novel Kir3.2 (GIRK2) Regulator from Protein Scaffold Libraries

(2014) Sviatoslav N. Bagriantsev et al.   ACS Chemical Neuroscience

Conformational Dynamics at the Inner Gate of KcsA during Activation

(2014) Raymond E. Hulse et al.   BIOCHEMISTRY

Interfacially active peptides and proteins

(2014) William C. Wimley et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

PconsFold: improved contact predictions improve protein models

(2014) Mirco Michel et al.   BIOINFORMATICS

Highly Efficient Macromolecule-Sized Poration of Lipid Bilayers by a Synthetically Evolved Peptide

(2014) Gregory Wiedman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rebuilding a macromolecular membrane complex at the atomic scale: Case of the Kir6.2 potassium channel coupled to the muscarinic acetylcholine receptor M2

(2014) Nicolas Sapay et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

De novo design of a transmembrane Zn2+-transporting four-helix bundle

(2014) Nathan H. Joh et al.   SCIENCE

Protein-Protein Docking with Dynamic Residue Protonation States

(2014) Krishna Praneeth Kilambi et al.   PLoS Computational Biology

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

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

Charge asymmetry in the proteins of the outer membrane

(2013) Joanna S. G. Slusky et al.   BIOINFORMATICS

Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel

(2013) M. B. Ulmschneider 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

Simultaneous prediction of protein secondary structure and transmembrane spans

(2013) Julia Koehler Leman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

BCL::MP-Fold: Folding Membrane Proteins through Assembly of Transmembrane Helices

(2013) Brian E. Weiner et al.   STRUCTURE

Mechanisms of molecular transport through the urea channel of Helicobacter pylori

(2013) Reginald McNulty et al.   Nature Communications

Rapid Calculation of Protein pKa Values Using Rosetta

(2012) Krishna Praneeth Kilambi et al.   BIOPHYSICAL JOURNAL

Co-translational association of cell-free expressed membrane proteins with supplied lipid bilayers

(2012) Christian Roos et al.   MOLECULAR MEMBRANE BIOLOGY

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

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

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

(2011) David T. Jones et al.   BIOINFORMATICS

Computational design of membrane proteins

(2011) Alessandro Senes   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Crystal structure of metarhodopsin II

(2011) Hui-Woog Choe et al.   NATURE

OPM database and PPM web server: resources for positioning of proteins in membranes

(2011) Mikhail A. Lomize et al.   NUCLEIC ACIDS RESEARCH

Modeling Symmetric Macromolecular Structures in Rosetta3

(2011) Frank DiMaio et al.   PLoS One

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

(2011) Sarel J. Fleishman et al.   PLoS One

Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2

(2011) Sidhartha Chaudhury et al.   PLoS One

Real-Time PyMOL Visualization for Rosetta and PyRosetta

(2011) Evan H. Baugh et al.   PLoS One

Structural basis for gating charge movement in the voltage sensor of a sodium channel

(2011) V. Yarov-Yarovoy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A knowledge-based potential highlights unique features of membrane α-helical and β-barrel protein insertion and folding

(2011) Daniel Hsieh et al.   PROTEIN SCIENCE

MEDELLER: homology-based coordinate generation for membrane proteins

(2010) Sebastian Kelm et al.   BIOINFORMATICS

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

(2010) Michael D. Tyka et al.   JOURNAL OF MOLECULAR BIOLOGY

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

(2010) Elizabeth H. Kellogg et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

iMembrane: homology-based membrane-insertion of proteins

(2009) Sebastian Kelm et al.   BIOINFORMATICS

Properties and identification of human protein drug targets

(2009) Tala M. Bakheet et al.   BIOINFORMATICS

Broad-Spectrum Antimicrobial Peptides by Rational Combinatorial Design and High-Throughput Screening: The Importance of Interfacial Activity

(2009) Ramesh Rathinakumar et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Improving consensus structure by eliminating averaging artifacts

(2009) Dukka B KC   BMC STRUCTURAL BIOLOGY

How Translocons Select Transmembrane Helices

(2008) Stephen H. White et al.   Annual Review of Biophysics

Computationally Designed Peptide Inhibitors of Protein−Protein Interactions in Membranes†

(2008) Gregory A. Caputo et al.   BIOCHEMISTRY

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

(2008) Håkan Viklund et al.   BIOINFORMATICS

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

Membrane lipids: where they are and how they behave

(2008) Gerrit van Meer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Membrane proteins and membrane proteomics

(2008) Sandra Tan et al.   PROTEOMICS