Emerging methods in protein co-evolution
Co-evolution is a fundamental component of the theory of evolution and is essential for
understanding the relationships between species in complex ecological networks. A wide …
understanding the relationships between species in complex ecological networks. A wide …
On the binding affinity of macromolecular interactions: daring to ask why proteins interact
PL Kastritis, AMJJ Bonvin - Journal of The Royal Society …, 2013 - royalsocietypublishing.org
Interactions between proteins are orchestrated in a precise and time-dependent manner,
underlying cellular function. The binding affinity, defined as the strength of these …
underlying cellular function. The binding affinity, defined as the strength of these …
Uncovering disease-disease relationships through the incomplete interactome
INTRODUCTION A disease is rarely a straightforward consequence of an abnormality in a
single gene, but rather reflects the interplay of multiple molecular processes. The …
single gene, but rather reflects the interplay of multiple molecular processes. The …
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 …
biophysics and structural biology. The three-dimensional structure of a protein-protein …
Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes
The present review focuses on the evolution of proteins and the impact of amino acid
mutations on function from a structural perspective. Proteins evolve under the law of natural …
mutations on function from a structural perspective. Proteins evolve under the law of natural …
Analyzing protein–protein interaction networks
The advent of the “omics” era in biology research has brought new challenges and requires
the development of novel strategies to answer previously intractable questions. Molecular …
the development of novel strategies to answer previously intractable questions. Molecular …
Protein modeling: what happened to the “protein structure gap”?
T Schwede - Structure, 2013 - cell.com
Computational modeling of three-dimensional macromolecular structures and complexes
from their sequence has been a long-standing vision in structural biology. Over the last 2 …
from their sequence has been a long-standing vision in structural biology. Over the last 2 …
Optimized atomic statistical potentials: assessment of protein interfaces and loops
GQ Dong, H Fan, D Schneidman-Duhovny… - …, 2013 - academic.oup.com
Motivation: Statistical potentials have been widely used for modeling whole proteins and
their parts (eg sidechains and loops) as well as interactions between proteins, nucleic acids …
their parts (eg sidechains and loops) as well as interactions between proteins, nucleic acids …
Structure of the activating IL-1 receptor signaling complex
Abstract Interleukin-1 (IL-1)-family cytokines are mediators of innate and adaptive immunity.
They exert proinflammatory effects by binding a primary receptor that recruits a receptor …
They exert proinflammatory effects by binding a primary receptor that recruits a receptor …
Towards a detailed atlas of protein–protein interactions
Highlights•We review current resources that organize experimental knowledge of the
interaction space.•We present the latest efforts in the prediction of interactions and the …
interaction space.•We present the latest efforts in the prediction of interactions and the …