Rapid search for tertiary fragments reveals protein sequence-structure relationships

A Structural Portrait of the PDZ Domain Family

(2014) Andreas Ernst et al.   JOURNAL OF MOLECULAR BIOLOGY

Proof of principle for epitope-focused vaccine design

(2014) Bruno E. Correia et al.   NATURE

A Real-Time All-Atom Structural Search Engine for Proteins

(2014) Gabriel Gonzalez et al.   PLoS Computational Biology

A Yellow Fluorescent Protein with Reduced Chloride Sensitivity Engineered by Loop-Insertion

(2013) Junyi Liang et al.   CHEMBIOCHEM

Template-based structure modeling of protein–protein interactions

(2013) Andras Szilagyi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Ballast: A Ball-based Algorithm for Structural Motifs

(2013) Lu He et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Assessment of template-based protein structure predictions in CASP10

(2013) Yuanpeng J. Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

A Probabilistic Fragment-Based Protein Structure Prediction Algorithm

(2012) David Simoncini et al.   PLoS One

Rigid substructure search

(2011) D. Shirvanyants et al.   BIOINFORMATICS

Protein design with fragment databases

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

Protein sequence comparison and fold recognition: progress and good-practice benchmarking

(2011) Johannes Söding et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

(2011) Po-Ssu Huang et al.   PLoS One

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

(2011) G. Grigoryan et al.   SCIENCE

Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

(2011) M. L. Azoitei et al.   SCIENCE

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

The LabelHash algorithm for substructure matching

(2010) Mark Moll et al.   BMC BIOINFORMATICS

Calibur: a tool for clustering large numbers of protein decoys

(2010) Shuai Cheng Li et al.   BMC BIOINFORMATICS

PDZ domains and their binding partners: structure, specificity, and modification

(2010) Ho-Jin Lee et al.   Cell Communication and Signaling

Searching Protein 3-D Structures in Linear Time

(2010) Tetsuo Shibuya   JOURNAL OF COMPUTATIONAL BIOLOGY

Probing Designability via a Generalized Model of Helical Bundle Geometry

(2010) Gevorg Grigoryan et al.   JOURNAL OF MOLECULAR 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

π-Turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence

(2010) K.R. Rajashankar et al.   PROTEIN SCIENCE

Structural Characteristics of Novel Protein Folds

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

Advances and pitfalls of protein structural alignment

(2009) Hitomi Hasegawa et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Integrated search and alignment of protein structures

(2008) A. Sacan et al.   BIOINFORMATICS

Protein structure alignment considering phenotypic plasticity

(2008) G. Csaba et al.   BIOINFORMATICS

The BCL-2 protein family: opposing activities that mediate cell death

(2007) Richard J. Youle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY