Fine tuned exploration of evolutionary relationships within the protein universe

MANET 3.0: Hierarchy and modularity in evolving metabolic networks

(2019) Fizza Mughal et al.   PLoS One

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Basic units of protein structure, folding, and function

(2017) Igor N. Berezovsky et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

The RING 2.0 web server for high quality residue interaction networks

(2016) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

Impact of structure space continuity on protein fold classification

(2016) Jinrui Xu et al.   Scientific Reports

The early history and emergence of molecular functions and modular scale-free network behavior

(2016) M. Fayez Aziz et al.   Scientific Reports

The Pfam protein families database: towards a more sustainable future

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

Graph theoretic network analysis reveals protein pathways underlying cell death following neurotropic viral infection

(2015) Sourish Ghosh et al.   Scientific Reports

A vocabulary of ancient peptides at the origin of folded proteins

(2015) Vikram Alva et al.   eLife

Global view of the protein universe

(2014) S. Nepomnyachiy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing the effect of dynamics on the closed-loop protein-folding hypothesis

(2013) S. V. Chintapalli et al.   Journal of the Royal Society Interface

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

(2013) Naomi K. Fox et al.   NUCLEIC ACIDS RESEARCH

Maximum Allowed Solvent Accessibilites of Residues in Proteins

(2013) Matthew Z. Tien et al.   PLoS One

Probing the protein space for extending the detection of weak homology folds

(2012) Danilo Gullotto et al.   JOURNAL OF THEORETICAL BIOLOGY

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

(2012) Martin Christen Frølund Thomsen et al.   NUCLEIC ACIDS RESEARCH

The Enzymatic and Metabolic Capabilities of Early Life

(2012) Aaron David Goldman et al.   PLoS One

Distinct activities of several RNase J proteins in methanogenic archaea

(2011) Shiri Levy et al.   RNA Biology

Prototypes of elementary functional loops unravel evolutionary connections between protein functions

(2010) Alexander Goncearenco et al.   BIOINFORMATICS

The evolution and functional repertoire of translation proteins following the origin of life

(2010) Aaron D Goldman et al.   Biology Direct

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

(2010) A. L. Cuff et al.   NUCLEIC ACIDS RESEARCH

Structural Characteristics of Novel Protein Folds

(2010) Narcis Fernandez-Fuentes et al.   PLoS Computational Biology

Nothing about protein structure classification makes sense except in the light of evolution

(2009) Ruben E Valas et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Is protein classification necessary? Toward alternative approaches to function annotation

(2009) Donald Petrey et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Discrete–continuous duality of protein structure space

(2009) Ruslan I Sadreyev et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

A galaxy of folds

(2009) Vikram Alva et al.   PROTEIN SCIENCE

Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures

(2009) Alberto Pascual-García et al.   PLoS Computational Biology

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure

(2008) Grzegorz Koczyk et al.   NUCLEIC ACIDS RESEARCH

Network ‘Small-World-Ness’: A Quantitative Method for Determining Canonical Network Equivalence

(2008) Mark D. Humphries et al.   PLoS One

Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function

(2002) Iddo Friedberg et al.   PROTEIN SCIENCE