Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions

P Tompa, M Fuxreiter - Trends in biochemical sciences, 2008‏ - cell.com
The notion that all protein functions are determined through macromolecular interactions is
the driving force behind current efforts that aim to solve the structures of all cellular …

Predicting protein function from sequence and structure

D Lee, O Redfern, C Orengo - Nature reviews molecular cell biology, 2007‏ - nature.com
While the number of sequenced genomes continues to grow, experimentally verified
functional annotation of whole genomes remains patchy. Structural genomics projects are …

Contacts-based prediction of binding affinity in protein–protein complexes

A Vangone, AMJJ Bonvin - elife, 2015‏ - elifesciences.org
Almost all critical functions in cells rely on specific protein–protein interactions.
Understanding these is therefore crucial in the investigation of biological systems. Despite …

Interactome3D: adding structural details to protein networks

R Mosca, A Céol, P Aloy - Nature methods, 2013‏ - nature.com
Network-centered approaches are increasingly used to understand the fundamentals of
biology. However, the molecular details contained in the interaction networks, often …

FireDock: a web server for fast interaction refinement in molecular docking

E Mashiach, D Schneidman-Duhovny… - Nucleic acids …, 2008‏ - academic.oup.com
Structural details of protein–protein interactions are invaluable for understanding and
deciphering biological mechanisms. Computational docking methods aim to predict the …

Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry

F Herzog, A Kahraman, D Boehringer, R Mak… - Science, 2012‏ - science.org
The identification of proximate amino acids by chemical cross-linking and mass
spectrometry (XL-MS) facilitates the structural analysis of homogeneous protein complexes …

Transient protein–protein interactions

SE Acuner Ozbabacan, HB Engin… - … , Design & Selection, 2011‏ - academic.oup.com
Transient complexes are crucial for diverse biological processes such as biochemical
pathways and signaling cascades in the cell. Here, we give an overview of the transient …

Protein–protein interactions: detection, reliability assessment and applications

X Peng, J Wang, W Peng, FX Wu… - Briefings in …, 2017‏ - academic.oup.com
Protein–protein interactions (PPIs) participate in all important biological processes in living
organisms, such as catalyzing metabolic reactions, DNA replication, DNA transcription …

Relating three-dimensional structures to protein networks provides evolutionary insights

PM Kim, LJ Lu, Y **a, MB Gerstein - Science, 2006‏ - science.org
Most studies of protein networks operate on a high level of abstraction, neglecting structural
and chemical aspects of each interaction. Here, we characterize interactions by using atomic …

Recent progress and future directions in protein-protein docking

DW Ritchie - Current protein and peptide science, 2008‏ - ingentaconnect.com
This article gives an overview of recent progress in protein-protein docking and it identifies
several directions for future research. Recent results from the CAPRI blind docking …