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 …
[HTML][HTML] Forces stabilizing proteins
CN Pace, JM Scholtz, GR Grimsley - FEBS letters, 2014 - Elsevier
The goal of this article is to summarize what has been learned about the major forces
stabilizing proteins since the late 1980s when site-directed mutagenesis became possible …
stabilizing proteins since the late 1980s when site-directed mutagenesis became possible …
Accurate design of megadalton-scale two-component icosahedral protein complexes
Nature provides many examples of self-and co-assembling protein-based molecular
machines, including icosahedral protein cages that serve as scaffolds, enzymes, and …
machines, including icosahedral protein cages that serve as scaffolds, enzymes, and …
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 …
Understanding these is therefore crucial in the investigation of biological systems. Despite …
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
MF Lensink, G Brysbaert, T Mauri… - Proteins: Structure …, 2021 - Wiley Online Library
We present the results for CAPRI Round 50, the fourth joint CASP‐CAPRI protein assembly
prediction challenge. The Round comprised a total of twelve targets, including six dimers …
prediction challenge. The Round comprised a total of twelve targets, including six dimers …
Computational design of self-assembling protein nanomaterials with atomic level accuracy
We describe a general computational method for designing proteins that self-assemble to a
desired symmetric architecture. Protein building blocks are docked together symmetrically to …
desired symmetric architecture. Protein building blocks are docked together symmetrically to …
Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition
MF Lensink, S Velankar… - … : Structure, Function, and …, 2017 - Wiley Online Library
We present the sixth report evaluating the performance of methods for predicting the atomic
resolution structures of protein complexes offered as targets to the community‐wide initiative …
resolution structures of protein complexes offered as targets to the community‐wide initiative …
Critical assessment of methods for predicting the 3D structure of proteins and protein complexes
SJ Wodak, S Vajda, MF Lensink… - Annual review of …, 2023 - annualreviews.org
Advances in a scientific discipline are often measured by small, incremental steps. In this
review, we report on two intertwined disciplines in the protein structure prediction field …
review, we report on two intertwined disciplines in the protein structure prediction field …
Molecular docking as a popular tool in drug design, an in silico travel
New molecular modeling approaches, driven by rapidly improving computational platforms,
have allowed many success stories for the use of computer-assisted drug design in the …
have allowed many success stories for the use of computer-assisted drug design in the …
Principles and overview of sampling methods for modeling macromolecular structure and dynamics
T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …
how macromolecules carry out their functions in the cell. Significant advances have been …