Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes

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

Arbitrary protein−protein docking targets biologically relevant interfaces

(2012) Juliette Martin et al.   BMC Biophysics

Towards the prediction of protein interaction partners using physical docking

(2011) M. N. Wass et al.   Molecular Systems Biology

InterEvol database: exploring the structure and evolution of protein complex interfaces

(2011) Guilhem Faure et al.   NUCLEIC ACIDS RESEARCH

Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions

(2011) M. Heo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A structure-based benchmark for protein-protein binding affinity

(2011) Panagiotis L. Kastritis et al.   PROTEIN SCIENCE

Accounting for conformational changes during protein–protein docking

(2010) Martin Zacharias   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein binding specificity versus promiscuity

(2010) Gideon Schreiber et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

(2010) Panagiotis L. Kastritis et al.   JOURNAL OF PROTEOME RESEARCH

Protein–protein docking tested in blind predictions: the CAPRI experiment

(2010) Joël Janin   Molecular BioSystems

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

(2010) T. Ando et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and refinement of encounter complexes for protein-protein docking: Taking account of macromolecular crowding

(2010) Xiaofan Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking by structural similarity at protein-protein interfaces

(2010) Rohita Sinha et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

(2010) Sean R. McGuffee et al.   PLoS Computational Biology

The courtship of proteins: Understanding the encounter complex

(2009) Marcellus Ubbink   FEBS LETTERS

Improving the Accuracy of an Affinity Prediction Method by Using Statistics on Shape Complementarity between Proteins

(2009) Tatsuya Yoshikawa et al.   Journal of Chemical Information and Modeling

From Dedicated Grid to Volunteer Grid: Large Scale Execution of a Bioinformatics Application

(2009) Viktors Bertis et al.   Journal of Grid Computing

The Negatome database: a reference set of non-interacting protein pairs

(2009) Pawel Smialowski et al.   NUCLEIC ACIDS RESEARCH

Present and future challenges and limitations in protein-protein docking

(2009) Carles Pons et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins

(2009) Peter Májek et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

DOCKGROUND protein-protein docking decoy set

(2008) S. Liu et al.   BIOINFORMATICS

Identification of Protein Interaction Partners and Protein–Protein Interaction Sites

(2008) Sophie Sacquin-Mora et al.   JOURNAL OF MOLECULAR BIOLOGY

Constraints imposed by non-functional protein–protein interactions on gene expression and proteome size

(2008) Jingshan Zhang et al.   Molecular Systems Biology

Protein-protein interaction networks and biology—what's the connection?

(2008) Luke Hakes et al.   NATURE BIOTECHNOLOGY

Replica exchange simulations of transient encounter complexes in protein-protein association

(2008) Y. C. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA