Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels

Global harmful algal bloom status reporting

(2021) Gustaaf Hallegraeff et al.   HARMFUL ALGAE

Root Digger: a root placement program for phylogenetic trees

(2021) Ben Bettisworth et al.   BMC BIOINFORMATICS

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

Microbial Rhodopsins: The Last Two Decades

(2021) Andrey Rozenberg et al.   Annual Review of Microbiology

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

Cryo-EM structure and dynamics of the green-light absorbing proteorhodopsin

(2021) Stephan Hirschi et al.   Nature Communications

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations

(2020) Sree Ganesh Balasubramani et al.   JOURNAL OF CHEMICAL PHYSICS

Structural and functional characterization of the bestrophin-2 anion channel

(2020) Aaron P. Owji et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Lateral Gene Transfer of Anion-Conducting Channelrhodopsins between Green Algae and Giant Viruses

(2020) Andrey Rozenberg et al.   CURRENT BIOLOGY

Zinc Binding to Heliorhodopsin

(2020) Masanori Hashimoto et al.   Journal of Physical Chemistry Letters

Molecular mechanisms of gating in the calcium-activated chloride channel bestrophin

(2019) Alexandria N Miller et al.   eLife

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Structure and mechanisms of sodium-pumping KR2 rhodopsin

(2019) Kirill Kovalev et al.   Science Advances

HH-suite3 for fast remote homology detection and deep protein annotation

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

Enzymerhodopsins: novel photoregulated catalysts for optogenetics

(2019) Shatanik Mukherjee et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Crystal structure of heliorhodopsin

(2019) Wataru Shihoya et al.   NATURE

Thylakoid localized bestrophin-like proteins are essential for the CO2 concentrating mechanism of Chlamydomonas reinhardtii

(2019) Ananya Mukherjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

One thousand plant transcriptomes and the phylogenomics of green plants

(2019)   NATURE

Unique structure and function of viral rhodopsins

(2019) Dmitry Bratanov et al.   Nature Communications

X-ray Crystallographic Structure and Oligomerization of Gloeobacter Rhodopsin

(2019) Takefumi Morizumi et al.   Scientific Reports

Retinal Proteins: Photochemistry and Optogenetics

(2019) Hideki Kandori   BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution

(2019) Chuan Tian et al.   Journal of Chemical Theory and Computation

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees

(2018) Uyen Mai et al.   BMC GENOMICS

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

A global ocean atlas of eukaryotic genes

(2018) Quentin Carradec et al.   Nature Communications

Real-space refinement in PHENIX for cryo-EM and crystallography

(2018) Pavel V. Afonine et al.   Acta Crystallographica Section D-Structural Biology

Two-component cyclase opsins of green algae are ATP-dependent and light-inhibited guanylyl cyclases

(2018) Yuehui Tian et al.   BMC BIOLOGY

Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions

(2018) Timothy G. Stephens et al.   Scientific Reports

New tools for automated high-resolution cryo-EM structure determination in RELION-3

(2018) Jasenko Zivanov et al.   eLife

Absorption and Emission Spectroscopic Investigation of Thermal Dynamics and Photo-Dynamics of the Rhodopsin Domain of the Rhodopsin-Guanylyl Cyclase from the Nematophagous Fungus Catenaria anguillulae

(2017) Alfons Penzkofer et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams et al.   PROTEIN SCIENCE

The form and function of channelrhodopsin

(2017) Karl Deisseroth et al.   SCIENCE

Software update: the ORCA program system, version 4.0

(2017) Frank Neese   Wiley Interdisciplinary Reviews-Computational Molecular Science

Whole-cell Patch-clamp Recordings for Electrophysiological Determination of Ion Selectivity in Channelrhodopsins

(2017) Christiane Grimm et al.   Jove-Journal of Visualized Experiments

Fast and accurate branch lengths estimation for phylogenomic trees

(2016) Manuel Binet et al.   BMC BIOINFORMATICS

CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules

(2016) Antonin Pavelka et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics

(2016) Jan Janouškovec et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct regions that control ion selectivity and calcium-dependent activation in the bestrophin ion channel

(2016) George Vaisey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A voltage-dependent chloride channel fine-tunes photosynthesis in plants

(2016) Andrei Herdean et al.   Nature Communications

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

DiffLogo: a comparative visualization of sequence motifs

(2015) Martin Nettling et al.   BMC BIOINFORMATICS

Plastid Genome-Based Phylogeny Pinpointed the Origin of the Green-Colored Plastid in the Dinoflagellate Lepidodinium chlorophorum

(2015) Ryoma Kamikawa et al.   Genome Biology and Evolution

Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage

(2015) Ansgar Gruber et al.   PLANT JOURNAL

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Optogenetic manipulation of cGMP in cells and animals by the tightly light-regulated guanylyl-cyclase opsin CyclOp

(2015) Shiqiang Gao et al.   Nature Communications

Sequence, Structure and Ligand Binding Evolution of Rhodopsin-Like G Protein-Coupled Receptors: A Crystal Structure-Based Phylogenetic Analysis

(2015) Steffen Wolf et al.   PLoS One

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Structure and insights into the function of a Ca2+-activated Cl− channel

(2014) Veronica Kane Dickson et al.   NATURE

Structure and selectivity in bestrophin ion channels

(2014) T. Yang et al.   SCIENCE

ModelOMatic: Fast and Automated Model Selection between RY, Nucleotide, Amino Acid, and Codon Substitution Models

(2014) Simon Whelan et al.   SYSTEMATIC BIOLOGY

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms

(2013) Oliver P. Ernst et al.   CHEMICAL REVIEWS

Quantifying the local resolution of cryo-EM density maps

(2013) Alp Kucukelbir et al.   NATURE METHODS

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

A light-driven sodium ion pump in marine bacteria

(2013) Keiichi Inoue et al.   Nature Communications

ChemShell-a modular software package for QM/MM simulations

(2013) Sebastian Metz et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Characterisation of AnBEST1, a functional anion channel in the plasma membrane of the filamentous fungus, Aspergillus nidulans

(2011) Stephen K. Roberts et al.   FUNGAL GENETICS AND BIOLOGY

Transfer-PCR (TPCR): A highway for DNA cloning and protein engineering

(2011) Ariel Erijman et al.   JOURNAL OF STRUCTURAL BIOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

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

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Bestrophins and retinopathies

(2010) Qinghuan Xiao et al.   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

electronic Ligand Builder and Optimization Workbench(eLBOW): a tool for ligand coordinate and restraint generation

(2009) Nigel W. Moriarty et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Molecular Physiology of Bestrophins: Multifunctional Membrane Proteins Linked to Best Disease and Other Retinopathies

(2008) H. Criss Hartzell et al.   PHYSIOLOGICAL REVIEWS