Tertiary alphabet for the observable protein structural universe

De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints

(2016) Robert G. Smock et al.   CELL

A topological and conformational stability alphabet for multipass membrane proteins

(2016) Xiang Feng et al.   Nature Chemical Biology

Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta

(2015) Matthew J. O’Meara et al.   Journal of Chemical Theory and Computation

The Membrane- and Soluble-Protein Helix-Helix Interactome: Similar Geometry via Different Interactions

(2015) Shao-Qing Zhang et al.   STRUCTURE

Tertiary Structural Propensities Reveal Fundamental Sequence/Structure Relationships

(2015) Fan Zheng et al.   STRUCTURE

Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures

(2015) Brinda Vallat et al.   PLoS Computational Biology

A vocabulary of ancient peptides at the origin of folded proteins

(2015) Vikram Alva et al.   eLife

Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures

(2014) Binchen Mao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

CATH: comprehensive structural and functional annotations for genome sequences

(2014) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

Rapid search for tertiary fragments reveals protein sequence-structure relationships

(2014) Jianfu Zhou et al.   PROTEIN SCIENCE

Computational design of water-soluble α-helical barrels

(2014) Andrew R. Thomson et al.   SCIENCE

High thermodynamic stability of parametrically designed helical bundles

(2014) Po-Ssu Huang et al.   SCIENCE

SCOP2 prototype: a new approach to protein structure mining

(2013) Antonina Andreeva et al.   NUCLEIC ACIDS RESEARCH

β-Propeller Blades as Ancestral Peptides in Protein Evolution

(2013) Klaus O. Kopec et al.   PLoS One

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

Modeling Proteins Using a Super-Secondary Structure Library and NMR Chemical Shift Information

(2013) Vilas Menon et al.   STRUCTURE

Protein-Peptide Complex Prediction through Fragment Interaction Patterns

(2013) Erik Verschueren et al.   STRUCTURE

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

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

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field

(2012) Dong Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein design with fragment databases

(2011) Erik Verschueren et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

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

Computational protein design with explicit consideration of surface hydrophobic patches

(2011) Ron Jacak et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces

(2011) G. Grigoryan et al.   SCIENCE

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

(2011) Maxim V. Shapovalov et al.   STRUCTURE

Probing Designability via a Generalized Model of Helical Bundle Geometry

(2010) Gevorg Grigoryan et al.   JOURNAL OF MOLECULAR BIOLOGY

BriX: a database of protein building blocks for structural analysis, modeling and design

(2010) Peter Vanhee et al.   NUCLEIC ACIDS RESEARCH

Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints

(2010) L. L. Porter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Structural Characteristics of Novel Protein Folds

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

Evolutionary Expansion and Specialization of the PDZ Domains

(2009) O. Sakarya et al.   MOLECULAR BIOLOGY AND EVOLUTION

Protein-Peptide Interactions Adopt the Same Structural Motifs as Monomeric Protein Folds

(2009) Peter Vanhee et al.   STRUCTURE

Structural specificity in coiled-coil interactions

(2008) G GRIGORYAN et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments

(2008) Lies Baeten et al.   PLoS Computational Biology