The value of protein structure classification information-Surveying the scientific literature

CATH: comprehensive structural and functional annotations for genome sequences

(2014) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

On the Universe of Protein Folds

(2013) Rachel Kolodny et al.   Annual Review of Biophysics

Small-angle X-ray scattering constraints and local geometry like secondary structures can construct a coarse-grained protein model at amino acid residue resolution

(2013) Yasumasa Morimoto et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

ThreaDom: extracting protein domain boundary information from multiple threading alignments

(2013) Zhidong Xue et al.   BIOINFORMATICS

High-quality protein backbone reconstruction from alpha carbons using Gaussian mixture models

(2013) Benjamin L. Moore et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

SCOP2 prototype: a new approach to protein structure mining

(2013) Antonina Andreeva et al.   NUCLEIC ACIDS RESEARCH

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

Rebelling for a Reason: Protein Structural “Outliers”

(2013) Gandhimathi Arumugam et al.   PLoS One

Capturing protein sequence-structure specificity using computational sequence design

(2013) Paul Mach et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The four-transmembrane protein IP39 of Euglena forms strands by a trimeric unit repeat

(2013) Hiroshi Suzuki et al.   Nature Communications

N-Terminal Domains in Two-Domain Proteins Are Biased to Be Shorter and Predicted to Fold Faster Than Their C-Terminal Counterparts

(2013) Etai Jacob et al.   Cell Reports

Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes

(2013) Syed Abbas Bukhari et al.   PLoS Computational Biology

Viral Capsid Proteins Are Segregated in Structural Fold Space

(2013) Shanshan Cheng et al.   PLoS Computational Biology

Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies

(2013) Hannah Edwards et al.   PLoS Computational Biology

Deconstruction of Activity-Dependent Covalent Modification of Heme in Human Neutrophil Myeloperoxidase by Multistage Mass Spectrometry (MS4)

(2012) Kieran F. Geoghegan et al.   BIOCHEMISTRY

Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms

(2012) Dapeng Zhang et al.   BIOINFORMATICS

A holistic in silico approach to predict functional sites in protein structures

(2012) Joan Segura et al.   BIOINFORMATICS

Identification of Domains in Protein Structures from the Analysis of Intramolecular Interactions

(2012) Alessandro Genoni et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Classification of protein functional surfaces using structural characteristics

(2012) Y. Y. Tseng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of oligomeric state through geometric coupling of protein interfaces

(2012) T. Perica et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In vivo translation rates can substantially delay the cotranslational folding of the Escherichia coli cytosolic proteome

(2012) P. Ciryam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three-dimensional domain swapping in the protein structure space

(2012) Yongqi Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

(2012) M. S. Vijayabaskar et al.   PLoS Computational Biology

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

(2012) Nicholas Furnham et al.   PLoS Computational Biology

Fast large-scale clustering of protein structures using Gauss integrals

(2011) Tim Harder et al.   BIOINFORMATICS

PASS2 version 4: An update to the database of structure-based sequence alignments of structural domain superfamilies

(2011) A. Gandhimathi et al.   NUCLEIC ACIDS RESEARCH

PSCDB: a database for protein structural change upon ligand binding

(2011) T. Amemiya et al.   NUCLEIC ACIDS RESEARCH

Structural and functional analysis of the archaeal endonuclease Nob1

(2011) Thomas Veith et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

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

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

Protein-protein docking benchmark version 4.0

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

Searching protein structure databases with DaliLite v.3

(2008) L. Holm et al.   BIOINFORMATICS

The Jpred 3 secondary structure prediction server

(2008) C. Cole et al.   NUCLEIC ACIDS RESEARCH

The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies

(2008) A. L. Cuff et al.   NUCLEIC ACIDS RESEARCH