Sequence-structure-function relationships in the microbial protein universe

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Structure-based protein function prediction using graph convolutional networks

(2021) Vladimir Gligorijević et al.   Nature Communications

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

Macromolecular modeling and design in Rosetta: recent methods and frameworks

(2020) Julia Koehler Leman et al.   NATURE METHODS

CATH: increased structural coverage of functional space

(2020) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints

(2019) Joe G. Greener et al.   Nature Communications

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

How type II CRISPR–Cas establish immunity through Cas1–Cas2-mediated spacer integration

(2017) Yibei Xiao et al.   NATURE

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

(2017) Supratim Mukherjee et al.   NATURE BIOTECHNOLOGY

GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison

(2017) Fazle E. Faisal et al.   Scientific Reports

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

The CRISPR-Cas immune system: Biology, mechanisms and applications

(2015) Devashish Rath et al.   BIOCHIMIE

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

(2015) Konstantinos D. Tsirigos et al.   NUCLEIC ACIDS RESEARCH

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

(2014) David T. Jones et al.   BIOINFORMATICS

ECOD: An Evolutionary Classification of Protein Domains

(2014) Hua Cheng et al.   PLoS Computational Biology

A combinatorial approach to graphlet counting

(2013) Tomaž Hočevar et al.   BIOINFORMATICS

EMPeror: a tool for visualizing high-throughput microbial community data

(2013) Yoshiki Vázquez-Baeza et al.   GigaScience

BOCTOPUS: improved topology prediction of transmembrane β barrel proteins

(2012) Sikander Hayat et al.   BIOINFORMATICS

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

(2011) Dominik Gront et al.   PLoS One

Maps of protein structure space reveal a fundamental relationship between protein structure and function

(2011) M. Osadchy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

On the evolutionary origins of “Fold Space Continuity”: A study of topological convergence and divergence in mixed alpha-beta domains

(2010) M.I. Sadowski et al.   JOURNAL OF STRUCTURAL BIOLOGY

FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately

(2010) Inbal Budowski-Tal 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

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

Carbohydrate-binding domains: multiplicity of biological roles

(2009) Daniel Guillén et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The continuity of protein structure space is an intrinsic property of proteins

(2009) J. Skolnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein contact order prediction from primary sequences

(2008) Yi Shi et al.   BMC BIOINFORMATICS

Exploring the structure and function paradigm

(2008) Oliver C. Redfern et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY