Protein-protein docking: From interaction to interactome

IA Vakser - Biophysical journal, 2014‏ - cell.com
The protein-protein docking problem is one of the focal points of activity in computational
biophysics and structural biology. The three-dimensional structure of a protein-protein …

Hot spots—A review of the protein–protein interface determinant amino‐acid residues

IS Moreira, PA Fernandes… - … : Structure, Function, and …, 2007‏ - Wiley Online Library
Proteins tendency to bind to one another in a highly specific manner forming stable
complexes is fundamental to all biological processes. A better understanding of complex …

[HTML][HTML] Structural genomics of SARS-CoV-2 indicates evolutionary conserved functional regions of viral proteins

S Srinivasan, H Cui, Z Gao, M Liu, S Lu, W Mkandawire… - Viruses, 2020‏ - mdpi.com
During its first two and a half months, the recently emerged 2019 novel coronavirus, SARS-
CoV-2, has already infected over one-hundred thousand people worldwide and has taken …

Dynamic light scattering as a powerful tool for gold nanoparticle bioconjugation and biomolecular binding studies

H Jans, X Liu, L Austin, G Maes, Q Huo - Analytical chemistry, 2009‏ - ACS Publications
Dynamic light scattering (DLS) is an analytical tool used routinely for measuring the
hydrodynamic size of nanoparticles and colloids in a liquid environment. Gold nanoparticles …

Protein–protein interaction and quaternary structure

J Janin, RP Bahadur, P Chakrabarti - Quarterly reviews of biophysics, 2008‏ - cambridge.org
Protein–protein recognition plays an essential role in structure and function. Specific non-
covalent interactions stabilize the structure of macromolecular assemblies, exemplified in …

pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking

TMK Cheng, TL Blundell… - … Structure, Function, and …, 2007‏ - Wiley Online Library
The accurate scoring of rigid‐body docking orientations represents one of the major
difficulties in protein–protein docking prediction. Other challenges are the development of …

Protein–protein interactions in virus–host systems

AF Brito, JW Pinney - Frontiers in microbiology, 2017‏ - frontiersin.org
To study virus–host protein interactions, knowledge about viral and host protein
architectures and repertoires, their particular evolutionary mechanisms, and information on …

Protein structure fitting and refinement guided by cryo-EM density

M Topf, K Lasker, B Webb, H Wolfson, W Chiu, A Sali - Structure, 2008‏ - cell.com
For many macromolecular assemblies, both a cryo-electron microscopy map and atomic
structures of its component proteins are available. Here we describe a method for fitting and …

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 …

Protein interaction networks from yeast to human

P Bork, LJ Jensen, C Von Mering, AK Ramani… - Current opinion in …, 2004‏ - Elsevier
Protein interaction networks summarize large amounts of protein–protein interaction data,
both from individual, small-scale experiments and from automated high-throughput screens …