[HTML][HTML] StructureMan: A structure manipulation tool to study large scale biomolecular interactions

Y Xian, Y Xie, SM Silva, CB Karki, W Qiu… - Frontiers in molecular …, 2021 - frontiersin.org
Studying biomolecular interactions is a crucial but challenging task. Due to their large
scales, many biomolecular interactions are difficult to be simulated via all atom models. An …

The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions

B Jiménez-García, J Roel-Touris… - Nucleic Acids …, 2023 - academic.oup.com
Computational docking is an instrumental method of the structural biology toolbox.
Specifically, integrative modeling software, such as LightDock, arise as complementary and …

[HTML][HTML] Information-driven modeling of biomolecular complexes

CW van Noort, RV Honorato, AMJJ Bonvin - Current Opinion in Structural …, 2021 - Elsevier
Proteins play crucial roles in every cellular process by interacting with each other, nucleic
acids, metabolites, and other molecules. The resulting assemblies can be very large and …

[HTML][HTML] Experiments and simulations: a pas de deux to unravel biological function

M Topf, E Rosta, GR Bowman… - Frontiers in Molecular …, 2021 - frontiersin.org
Understanding the molecular mechanisms used by biological systems to perform their
functions is often essential to rationally target associated diseases. In many cases, the …

An overview of recent advances in structural bioinformatics of protein–protein interactions and a guide to their principles

G Sudha, R Nussinov, N Srinivasan - Progress in biophysics and molecular …, 2014 - Elsevier
Rich data bearing on the structural and evolutionary principles of protein–protein
interactions are paving the way to a better understanding of the regulation of function in the …

A structural perspective on protein–protein interactions

RB Russell, F Alber, P Aloy, FP Davis, D Korkin… - Current opinion in …, 2004 - Elsevier
Structures of macromolecular complexes are necessary for a mechanistic description of
biochemical and cellular processes. They can be solved by experimental methods, such as …

Structural prediction of protein–protein interactions by docking: Application to biomedical problems

D Barradas-Bautista, M Rosell, C Pallara… - Advances in protein …, 2018 - Elsevier
A huge amount of genetic information is available thanks to the recent advances in
sequencing technologies and the larger computational capabilities, but the interpretation of …

[HTML][HTML] The HADDOCK2. 2 web server: user-friendly integrative modeling of biomolecular complexes

GCP Van Zundert, J Rodrigues, M Trellet… - Journal of molecular …, 2016 - Elsevier
The prediction of the quaternary structure of biomolecular macromolecules is of paramount
importance for fundamental understanding of cellular processes and drug design. In the era …

[HTML][HTML] Identifying and visualizing macromolecular flexibility in structural biology

M Palamini, A Canciani, F Forneris - Frontiers in molecular …, 2016 - frontiersin.org
Structural biology comprises a variety of tools to obtain atomic resolution data for the
investigation of macromolecules. Conventional structural methodologies including …

Multiscale Structural and Biophysical Studies of Protein-Compound Interactions

SJ Trudeau - 2024 - academiccommons.columbia.edu
The recognition of small organic compounds and metabolites is essential for living systems,
enabling the cell to sense environmental stimuli and respond appropriately. Developing …