Large-scale determination of previously unsolved protein structures using evolutionary information

Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4

(2015) Sagar Antala et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Tara Oceans studies plankton at planetary scale

(2015) P. Bork et al.   SCIENCE

Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors

(2015) Thomas A. Hopf et al.   Nature Communications

CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations

(2014) Stefan Seemayer et al.   BIOINFORMATICS

Proposed Carrier Lipid-binding Site of Undecaprenyl Pyrophosphate Phosphatase fromEscherichia coli

(2014) Hsin-Yang Chang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation

(2014) Pengfei Tian et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families

(2014) Jimin Pei et al.   PROTEIN SCIENCE

A structural model of the active ribosome-bound membrane protein insertase YidC

(2014) Stephan Wickles et al.   eLife

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

(2014) Sergey Ovchinnikov et al.   eLife

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

Analysis of two domains with novel RNA-processing activities throws light on the complex evolution of ribosomal RNA biogenesis

(2014) A. Maxwell Burroughs et al.   Frontiers in Genetics

SATP (YaaH), a succinate–acetate transporter protein inEscherichia coli

(2013) Joana Sá-Pessoa et al.   BIOCHEMICAL JOURNAL

A two-domain elevator mechanism for sodium/proton antiport

(2013) Chiara Lee et al.   NATURE

Mechanism of farnesylated CAAX protein processing by the intramembrane protease Rce1

(2013) Ioannis Manolaridis et al.   NATURE

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

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

Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation

(2013) S. Matsumoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

One contact for every twelve residues allows robust and accurate topology-level protein structure modeling

(2013) David E. Kim et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

INVERTED TOPOLOGIES IN MEMBRANE PROTEINS: A MINI-REVIEW

(2013) Amanda M Duran et al.   Computational and Structural Biotechnology Journal

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB

(2012) Q. Xu et al.   BIOINFORMATICS

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Phosphatidylglycerol::Prolipoprotein Diacylglyceryl Transferase (Lgt) of Escherichia coli Has Seven Transmembrane Segments, and Its Essential Residues Are Embedded in the Membrane

(2012) J. Pailler et al.   JOURNAL OF BACTERIOLOGY

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

Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

(2012) O. F. Lange et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics-aided structure prediction

(2012) J. I. Sulkowska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The cytochrome bd respiratory oxygen reductases

(2011) Vitaliy B. Borisov et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures

(2011) T. Muth et al.   BIOINFORMATICS

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

(2011) David T. Jones 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

CREST - a large and diverse superfamily of putative transmembrane hydrolases

(2011) Jimin Pei et al.   Biology Direct

Expansion of Type II CAAX Proteases Reveals Evolutionary Origin of γ-Secretase Subunit APH-1

(2011) Jimin Pei et al.   JOURNAL OF MOLECULAR BIOLOGY

Improved molecular replacement by density- and energy-guided protein structure optimization

(2011) Frank DiMaio et al.   NATURE

Antiparallel EmrE exports drugs by exchanging between asymmetric structures

(2011) Emma A. Morrison et al.   NATURE

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

(2011) Michael Remmert et al.   NATURE METHODS

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

(2011) Sidhartha Chaudhury et al.   PLoS One

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

The integral membrane FtsW protein and peptidoglycan synthase PBP3 form a subcomplex in Escherichia coli

(2010) C. Fraipont et al.   MICROBIOLOGY-SGM

Common structural features of mapeg-a widespread superfamily of membrane associated proteins with highly divergent functions in eicosanoid and glutathione metabolism

(2010) Per-Johan Jakobsson et al.   PROTEIN SCIENCE

Learning generative models for protein fold families

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

Structure prediction for CASP8 with all-atom refinement using Rosetta

(2009) Srivatsan Raman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers

(2008) Stephen K. Burley et al.   STRUCTURE