Integrative computational modeling of protein interactions

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

On the Universe of Protein Folds

(2013) Rachel Kolodny et al.   Annual Review of Biophysics

InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution

(2013) Jessica Andreani et al.   BIOINFORMATICS

pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring

(2013) Brian Jiménez-García et al.   BIOINFORMATICS

The scoring of poses in protein-protein docking: current capabilities and future directions

(2013) Iain H Moal et al.   BMC BIOINFORMATICS

Evaluating template-based and template-free protein-protein complex structure prediction

(2013) T. Vreven et al.   BRIEFINGS IN BIOINFORMATICS

Molecular origins of binding affinity: seeking the Archimedean point

(2013) Panagiotis L Kastritis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Scoring functions for protein–protein interactions

(2013) Iain H Moal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex

(2013) Janosch Hennig et al.   JOURNAL OF BIOMOLECULAR NMR

A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking

(2013) Mikael Trellet et al.   PLoS One

Improving ranking of models for protein complexes with side chain modeling and atomic potentials

(2013) Shruthi Viswanath et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models

(2013) Anna Vangone et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction

(2013) Li C. Xue et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Flexible docking and refinement with a coarse-grained protein model using ATTRACT

(2013) Sjoerd de Vries et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2013) J. P. G. L. M. Rodrigues et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking, scoring, and affinity prediction in CAPRI

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

Protein docking using case-based reasoning

(2013) Anisah W. Ghoorah et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

How good is automated protein docking?

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

On the binding affinity of macromolecular interactions: daring to ask why proteins interact

(2012) P. L. Kastritis et al.   Journal of the Royal Society Interface

Advances in integrative modeling of biomolecular complexes

(2012) Ezgi Karaca et al.   METHODS

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

ATTRACT-EM: A New Method for the Computational Assembly of Large Molecular Machines Using Cryo-EM Maps

(2012) Sjoerd J. de Vries et al.   PLoS One

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

Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis

(2012) A. E. Dago et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling

(2012) N. Kalisman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scoring protein interaction decoys using exposed residues (SPIDER): A novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues

(2012) Raed Khashan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

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

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

(2011) Shiyong Liu et al.   BMC BIOINFORMATICS

HomPPI: a class of sequence homology based protein-protein interface prediction methods

(2011) Li C Xue et al.   BMC BIOINFORMATICS

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Mechanism of nitric oxide synthase regulation: Electron transfer and interdomain interactions

(2011) Changjian Feng   COORDINATION CHEMISTRY REVIEWS

Protein–protein HADDocking using exclusively pseudocontact shifts

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

Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein−Protein Docking

(2011) Carles Pons et al.   Journal of Chemical Information and Modeling

MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map

(2011) E. Tjioe et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Dominique Liger et al.   NUCLEIC ACIDS RESEARCH

PredUs: a web server for predicting protein interfaces using structural neighbors

(2011) Q. C. Zhang 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

Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2

(2011) Sidhartha Chaudhury et al.   PLoS One

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

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

Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data

(2011) Shandar Ahmad et al.   PLoS One

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

(2011) Thom Vreven et al.   PROTEIN SCIENCE

Prescont: Predicting protein-protein interfaces utilizing four residue properties

(2011) Hermann Zellner et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

SymmRef: A flexible refinement method for symmetric multimers

(2011) Efrat Mashiach-Farkash et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Biomolecular modeling and simulation: a field coming of age

(2011) Tamar Schlick et al.   QUARTERLY REVIEWS OF BIOPHYSICS

A Multidomain Flexible Docking Approach to Deal with Large Conformational Changes in the Modeling of Biomolecular Complexes

(2011) Ezgi Karaca et al.   STRUCTURE

Protein-Protein Complex Structure Predictions by Multimeric Threading and Template Recombination

(2011) Srayanta Mukherjee et al.   STRUCTURE

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

Unmet challenges of structural genomics

(2010) Maksymilian Chruszcz et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Accounting for conformational changes during protein–protein docking

(2010) Martin Zacharias   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

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

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

Solution Structure of the 128 kDa Enzyme I Dimer fromEscherichia coliand Its 146 kDa Complex with HPr Using Residual Dipolar Couplings and Small- and Wide-Angle X-ray Scattering

(2010) Charles D. Schwieters et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Building Macromolecular Assemblies by Information-driven Docking

(2010) Ezgi Karaca et al.   MOLECULAR & CELLULAR PROTEOMICS

HexServer: an FFT-based protein docking server powered by graphics processors

(2010) G. Macindoe et al.   NUCLEIC ACIDS RESEARCH

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

(2010) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

An integrated suite of fast docking algorithms

(2010) Efrat Mashiach et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions

(2010) Sjoerd J. de Vries 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

Progress and challenges in predicting protein-protein interaction sites

(2009) I. Ezkurdia et al.   BRIEFINGS IN BIOINFORMATICS

Ion mobility mass spectrometry of proteins and proteinassemblies

(2009) Charlotte Uetrecht et al.   CHEMICAL SOCIETY REVIEWS

Convergence and combination of methods in protein–protein docking

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

Nature of the protein universe

(2009) M. Levitt   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Proteins Get in Touch: Interface Prediction in the Study of Biomolecular Complexes

(2008) Sjoerd de Vries et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

The RosettaDock server for local protein-protein docking

(2008) S. Lyskov et al.   NUCLEIC ACIDS RESEARCH

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

(2008) Yuedong Yang et al.   PROTEIN SCIENCE