Performance of ZDOCK and IRAD in CAPRI rounds 28-34

Structure of UBE2Z Enzyme Provides Functional Insight into Specificity in the FAT10 Protein Conjugation Machinery

(2015) Julien Schelpe et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structures of the Ultra-High-Affinity Protein–Protein Complexes of Pyocins S2 and AP41 and Their Cognate Immunity Proteins from Pseudomonas aeruginosa

(2015) Amar Joshi et al.   JOURNAL OF MOLECULAR BIOLOGY

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

(2015) Thom Vreven et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanism of UCH-L5 Activation and Inhibition by DEUBAD Domains in RPN13 and INO80G

(2015) Danny D. Sahtoe et al.   MOLECULAR CELL

Text Mining for Protein Docking

(2015) Varsha D. Badal et al.   PLoS Computational Biology

Investigations into the auto-FAT10ylation of the bispecific E2 conjugating enzyme UBA6-specific E2 enzyme 1

(2014) Annette Aichem et al.   FEBS Journal

Information-driven modeling of large macromolecular assemblies using NMR data

(2014) Hugo van Ingen et al.   JOURNAL OF MAGNETIC RESONANCE

Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome

(2014) Robert K. McGinty et al.   NATURE

On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys

(2013) Ezgi Karaca et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Stabilization of an Unusual Salt Bridge in Ubiquitin by the Extra C-Terminal Domain of the Proteasome-Associated Deubiquitinase UCH37 as a Mechanism of Its Exo Specificity

(2013) Marie E. Morrow et al.   BIOCHEMISTRY

Structure and dynamics of human Nedd4-1 WW3 in complex with the αENaC PY motif

(2013) Romel Bobby et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Exploring Angular Distance in Protein-Protein Docking Algorithms

(2013) Thom Vreven et al.   PLoS One

How to Use Not-Always-Reliable Binding Site Information in Protein-Protein Docking Prediction

(2013) Lin Li et al.   PLoS One

Structural mechanisms of PriA-mediated DNA replication restart

(2013) B. Bhattacharyya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Performance of ZDOCK in CAPRI rounds 20-26

(2013) Thom Vreven et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Binding interface prediction by combining protein-protein docking results

(2013) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Blind prediction of interfacial water positions in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural Insights into the Conformation and Oligomerization of E2∼Ubiquitin Conjugates

(2012) Richard C. Page et al.   BIOCHEMISTRY

A method for integrative structure determination of protein-protein complexes

(2012) Dina Schneidman-Duhovny et al.   BIOINFORMATICS

A common ancestry for BAP1 and Uch37 regulators

(2012) Luis Sanchez-Pulido et al.   BIOINFORMATICS

Structure of the Ultra-High-Affinity Colicin E2 DNase–Im2 Complex

(2012) Justyna Aleksandra Wojdyla et al.   JOURNAL OF MOLECULAR BIOLOGY

Fitting Multimeric Protein Complexes into Electron Microscopy Maps Using 3D Zernike Descriptors

(2012) Juan Esquivel-Rodríguez et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Human Ubiquitin Conjugating Enzyme (E2)-HECT E3 Ligase Structure-function Screen

(2012) Yi Sheng et al.   MOLECULAR & CELLULAR PROTEOMICS

Prediction of protein-protein binding free energies

(2012) Thom Vreven et al.   PROTEIN SCIENCE

Structural Basis of High-Affinity Nuclear Localization Signal Interactions with Importin-α

(2012) Mary Marfori et al.   TRAFFIC

Recognition of UbcH5c and the nucleosome by the Bmi1/Ring1b ubiquitin ligase complex

(2011) Matthew L Bentley et al.   EMBO JOURNAL

The structural basis of Edc3- and Scd6-mediated activation of the Dcp1:Dcp2 mRNA decapping complex

(2011) Simon A Fromm et al.   EMBO JOURNAL

Protein–protein HADDocking using exclusively pseudocontact shifts

(2011) Christophe Schmitz et al.   JOURNAL OF BIOMOLECULAR NMR

Integrating atom-based and residue-based scoring functions for protein-protein docking

(2011) Thom Vreven et al.   PROTEIN SCIENCE

Structural characterization of human Uch37

(2011) Sethe E. Burgie et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Binding Specificity ofEscherichia coliSingle-Stranded DNA Binding Protein for the χ Subunit of DNA pol III Holoenzyme and PriA Helicase

(2010) Alexander G. Kozlov et al.   BIOCHEMISTRY

Structural Characterization of Protein–Protein Complexes by Integrating Computational Docking with Small-angle Scattering Data

(2010) Carles Pons et al.   JOURNAL OF MOLECULAR BIOLOGY

Design, Production and Molecular Structure of a New Family of Artificial Alpha-helicoidal Repeat Proteins (αRep) Based on Thermostable HEAT-like Repeats

(2010) Agathe Urvoas et al.   JOURNAL OF MOLECULAR BIOLOGY

Crystal Structures of Nucleosome Core Particles Containing the ‘601’ Strong Positioning Sequence

(2010) Dileep Vasudevan et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure of Proteasome Ubiquitin Receptor hRpn13 and Its Activation by the Scaffolding Protein hRpn2

(2010) Xiang Chen et al.   MOLECULAR CELL

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19

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

Determining macromolecular assembly structures by molecular docking and fitting into an electron density map

(2010) Keren Lasker et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

USE1 is a bispecific conjugating enzyme for ubiquitin and FAT10, which FAT10ylates itself in cis

(2010) Annette Aichem et al.   Nature Communications

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions

(2008) D. W. Ritchie et al.   BIOINFORMATICS

Six Classes of Nuclear Localization Signals Specific to Different Binding Grooves of Importin α

(2008) Shunichi Kosugi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A combination of rescoring and refinement significantly improves protein docking performance

(2008) Brian Pierce et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS