Defining the limits of homology modeling in information-driven protein docking

Solvated protein-protein docking using Kyte-Doolittle-based water preferences

(2013) Panagiotis L. Kastritis et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

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

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

Advances in integrative modeling of biomolecular complexes

(2012) Ezgi Karaca et al.   METHODS

KoBaMIN: a knowledge-based minimization web server for protein structure refinement

(2012) J. P. G. L. M. Rodrigues et al.   NUCLEIC ACIDS RESEARCH

Templates are available to model nearly all complexes of structurally characterized proteins

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

Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network

(2012) Sjoerd J. L. van Wijk et al.   PLoS Computational Biology

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

(2011) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanism of activation of methyltransferases involved in translation by the Trm112 ‘hub’ protein

(2011) Dominique Liger et al.   NUCLEIC ACIDS RESEARCH

CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK

(2011) Sjoerd J. de Vries et al.   PLoS One

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

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

Next challenges in protein-protein docking: from proteome to interactome and beyond

(2011) Adrien S.J. Melquiond et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Toward the estimation of the absolute quality of individual protein structure models

(2010) Pascal Benkert et al.   BIOINFORMATICS

Predicting the accuracy of protein-ligand docking on homology models

(2010) Annalisa Bordogna et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Putting an N-terminal end to the Clostridium thermocellum xylanase Xyn10B story: Crystal structure of the CBM22-1–GH10 modules complexed with xylohexaose

(2010) Shabir Najmudin et al.   JOURNAL OF STRUCTURAL BIOLOGY

The HADDOCK web server for data-driven biomolecular docking

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

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction

(2010) N. A. G. Meenan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Blind predictions of protein interfaces by docking calculations in CAPRI

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

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The Ternary Structure of the Double-headed Arrowhead Protease Inhibitor API-A Complexed with Two Trypsins Reveals a Novel Reactive Site Conformation

(2009) Rui Bao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fast and accurate automatic structure prediction with HHpred

(2009) Andrea Hildebrand et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evolution and dynamics of protein interactions and networks

(2008) Emmanuel D Levy et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

How well can the accuracy of comparative protein structure models be predicted?

(2008) David Eramian et al.   PROTEIN SCIENCE

An in Vivo Map of the Yeast Protein Interactome

(2008) K. Tarassov et al.   SCIENCE