Protein structure determination using metagenome sequence data

Structural basis for amino acid export by DMT superfamily transporter YddG

(2016) Hirotoshi Tsuchiya et al.   NATURE

Crystal structure of an Fe-S cluster-containing fumarate hydratase enzyme fromLeishmania majorreveals a unique protein fold

(2016) Patricia R. Feliciano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta

(2016) Sergey Ovchinnikov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural basis of lipoprotein signal peptidase II action and inhibition by the antibiotic globomycin

(2016) L. Vogeley et al.   SCIENCE

Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases

(2016) Schara Safarian et al.   SCIENCE

Crystal structure of E. coli lipoprotein diacylglyceryl transferase

(2016) Guotao Mao et al.   Nature Communications

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

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

Crystal structures of a double-barrelled fluoride ion channel

(2015) Randy B. Stockbridge et al.   NATURE

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Sikander Hayat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Origin of Consistent Protein Structure Refinement from Structural Averaging

(2015) Hahnbeom Park et al.   STRUCTURE

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

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

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

(2015) Sergey Ovchinnikov et al.   eLife

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

(2014) Stefan Seemayer et al.   BIOINFORMATICS

3Dmol.js: molecular visualization with WebGL

(2014) N. Rego et al.   BIOINFORMATICS

GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity

(2014) Noël Malod-Dognin et al.   BIOINFORMATICS

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation

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

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

(2014) Jianzhu Ma et al.   PLoS Computational Biology

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

Improved low-resolution crystallographic refinement with Phenix and Rosetta

(2013) Frank DiMaio et al.   NATURE METHODS

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz et al.   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

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

Discriminative modelling of context-specific amino acid substitution probabilities

(2012) Christof Angermüller et al.   BIOINFORMATICS

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

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

Genomics-aided structure prediction

(2012) J. I. Sulkowska 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

D³ Data-Driven Documents

(2011) M. Bostock et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

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

Fast overlapping of protein contact maps by alignment of eigenvectors

(2010) Pietro Di Lena et al.   BIOINFORMATICS

Protein structure comparison using iterated double dynamic programming

(2010) William R. Taylor   PROTEIN SCIENCE

Learning generative models for protein fold families

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

A simple and fast heuristic for protein structure comparison

(2008) David A Pelta et al.   BMC BIOINFORMATICS

A Bioinformatician's Guide to Metagenomics

(2008) V. Kunin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS