The ClusPro web server for protein–protein docking

FRODOCK 2.0: fast protein–protein docking server

(2016) Erney Ramírez-Aportela et al.   BIOINFORMATICS

InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information

(2016) Jinchao Yu et al.   NUCLEIC ACIDS RESEARCH

Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds

(2016) Dzmitry Padhorny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

(2016) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking

(2016) Lim Heo et al.   Scientific Reports

A Web Interface for Easy Flexible Protein-Protein Docking with ATTRACT

(2015) Sjoerd J. de Vries et al.   BIOPHYSICAL JOURNAL

The Impact of Side-Chain Packing on Protein Docking Refinement

(2015) Mohammad Moghadasi et al.   Journal of Chemical Information and Modeling

Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro

(2015) Bing Xia et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells

(2015) Can Küçük et al.   Nature Communications

Methods for SAXS-Based Structure Determination of Biomolecular Complexes

(2014) Sichun Yang   ADVANCED MATERIALS

Reprogramming Acyl Carrier Protein Interactions of an Acyl-CoA Promiscuous trans-Acyltransferase

(2014) Zhixia Ye et al.   CHEMISTRY & BIOLOGY

Generation and Characterization of Small Single Domain Antibodies Inhibiting Human Tumor Necrosis Factor Receptor 1

(2014) Sophie Steeland et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Docking Server for the Identification of Heparin Binding Sites on Proteins

(2014) Scott E. Mottarella et al.   Journal of Chemical Information and Modeling

Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign

(2014) K. Tran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutations in the NOTCH pathway regulator MIB1 cause left ventricular noncompaction cardiomyopathy

(2013) Guillermo Luxán et al.   NATURE MEDICINE

Improved flexible refinement of protein docking in CAPRI rounds 22-27

(2013) Yang Shen   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking, scoring, and affinity prediction in CAPRI

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

How good is automated protein docking?

(2013) Dima Kozakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Application of asymmetric statistical potentials to antibody-protein docking

(2012) R. Brenke et al.   BIOINFORMATICS

Structural basis of bacterial defense against g-type lysozyme-based innate immunity

(2012) S. Leysen et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?

(2012) Rohita Sinha et al.   PLoS One

The Bladder Tumor Suppressor Protein TERE1 (UBIAD1)Modulates Cell Cholesterol: Implications for Tumor Progression

(2011) William J. Fredericks et al.   DNA AND CELL BIOLOGY

Zinc Binding to the Tyr402 and His402 Allotypes of Complement Factor H: Possible Implications for Age-Related Macular Degeneration

(2011) Ruodan Nan et al.   JOURNAL OF MOLECULAR BIOLOGY

Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

(2011) Brian G. Pierce et al.   PLoS One

Structural Insights into the Mechanism of Protein O-Fucosylation

(2011) Erandi Lira-Navarrete et al.   PLoS One

SwarmDock and the Use of Normal Modes in Protein-Protein Docking

(2010) Iain H. Moal et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A Comprehensive Model of the Spectrin Divalent Tetramer Binding Region Deduced Using Homology Modeling and Chemical Cross-linking of a Mini-spectrin

(2010) Donghai Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

The Occluding Loop of Cathepsin B Prevents Its Effective Inhibition by Human Kininogens

(2010) C. Naudin et al.   JOURNAL OF MOLECULAR BIOLOGY

Macromolecular docking restrained by a small angle X-ray scattering profile

(2010) Dina Schneidman-Duhovny et al.   JOURNAL OF STRUCTURAL BIOLOGY

Controlled Assembly of Hydrogenase-CdTe Nanocrystal Hybrids for Solar Hydrogen Production

(2010) Katherine A. Brown et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ligand-Independent Antiapoptotic Function of Estrogen Receptor-β in Lung Cancer Cells

(2010) GuangFeng Zhang et al.   MOLECULAR ENDOCRINOLOGY

The HADDOCK web server for data-driven biomolecular docking

(2010) Sjoerd J de Vries et al.   Nature Protocols

CAPRI targets T29-T42: Proving ground for new docking procedures

(2010) Miriam Eisenstein et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking and scoring protein interactions: CAPRI 2009

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19

(2010) Dima Kozakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 4.0

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

Human immunodeficiency virus type 1 Vpr: oligomerization is an essential feature for its incorporation into virus particles

(2010) Narasimhan J Venkatachari et al.   Virology Journal

Structure and Malonyl CoA-ACP Transacylase Binding ofStreptomyces coelicolorFatty Acid Synthase Acyl Carrier Protein

(2009) Christopher J. Arthur et al.   ACS Chemical Biology

Differential binding of ICln in platelets to integrin-derived activating and inhibitory peptides

(2009) Markus Raab et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Convergence and combination of methods in protein–protein docking

(2009) Sandor Vajda et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Accessibility changes within diphtheria toxin T domain when in the functional molten globule state, as determined using hydrogen/deuterium exchange measurements

(2009) Petr Man et al.   FEBS Journal

Generating Uniform Incremental Grids on SO(3) Using the Hopf Fibration

(2009) Anna Yershova et al.   INTERNATIONAL JOURNAL OF ROBOTICS RESEARCH

Iron–sulfur cluster biosynthesis: characterization of IscU–IscS complex formation and a structural model for sulfide delivery to the [2Fe–2S] assembly site

(2009) Manunya Nuth et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

SUMOylation of nuclear actin

(2009) Wilma A. Hofmann et al.   JOURNAL OF CELL BIOLOGY

Mapping of a Microbial Protein Domain Involved in Binding and Activation of the TLR2/TLR1 Heterodimer

(2009) S. Liang et al.   JOURNAL OF IMMUNOLOGY

Binding Epitopes and Interaction Structure of the Neuroprotective Protease Inhibitor Cystatin C with β-Amyloid Revealed by Proteolytic Excision Mass Spectrometry and Molecular Docking Simulation

(2009) Paulina Juszczyk et al.   JOURNAL OF MEDICINAL CHEMISTRY

Docking of Antizyme to Ornithine Decarboxylase and Antizyme Inhibitor using Experimental Mutant and Double-Mutant Cycle Data

(2009) Ori Cohavi et al.   JOURNAL OF MOLECULAR BIOLOGY

Blockade of Ethanol-Induced Potentiation of Glycine Receptors by a Peptide That Interferes with G   Binding

(2009) L. Guzman et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

Model structure of APOBEC3C reveals a binding pocket modulating ribonucleic acid interaction required for encapsidation

(2009) B. Stauch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Outcome of a Workshop on Applications of Protein Models in Biomedical Research

(2009) Torsten Schwede et al.   STRUCTURE

DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking

(2008) Gwo-Yu Chuang et al.   BIOPHYSICAL JOURNAL

Recent Progress and Future Directions in Protein-Protein Docking

(2008) David Ritchie   CURRENT PROTEIN & PEPTIDE SCIENCE

Functionally Distinct NEAT (NEAr Transporter) Domains within theStaphylococcus aureusIsdH/HarA Protein Extract Heme from Methemoglobin

(2008) Rosemarie M. Pilpa et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Oligomerization of hantaviral nucleocapsid protein: charged residues in the N-terminal coiled-coil domain contribute to intermolecular interactions

(2008) A. Alminaite et al.   JOURNAL OF GENERAL VIROLOGY

Discrimination of near-native structures in protein-protein docking by testing the stability of local minima

(2008) Dima Kozakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An iterative knowledge-based scoring function for protein-protein recognition

(2008) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Principles of flexible protein-protein docking

(2008) Nelly Andrusier et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 3.0

(2008) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS