Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications
Proteins are dynamical entities that undergo a plethora of conformational changes,
accomplishing their biological functions. Molecular dynamics simulation and normal mode …
accomplishing their biological functions. Molecular dynamics simulation and normal mode …
[HTML][HTML] Use of computational biochemistry for elucidating molecular mechanisms of nitric oxide synthase
Nitric oxide (NO) is an essential signaling molecule in the regulation of multiple cellular
processes. It is endogenously synthesized by NO synthase (NOS) as the product of L …
processes. It is endogenously synthesized by NO synthase (NOS) as the product of L …
An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass
J Salamanca Viloria, MF Allega, M Lambrughi… - Scientific reports, 2017 - nature.com
Proteins are highly dynamic entities attaining a myriad of different conformations. Protein
side chains change their states during dynamics, causing clashes that are propagated at …
side chains change their states during dynamics, causing clashes that are propagated at …
The Molecular Mechanism of P2Y1 Receptor Activation
Human purinergic G protein‐coupled receptor P2Y1 (P2Y1R) is activated by adenosine 5′‐
diphosphate (ADP) to induce platelet activation and thereby serves as an important …
diphosphate (ADP) to induce platelet activation and thereby serves as an important …
Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology
Streptococcus pyogenes (Group A streptococcus; GAS) is an important human pathogen
responsible for mild to severe, life-threatening infections. GAS expresses a wide range of …
responsible for mild to severe, life-threatening infections. GAS expresses a wide range of …
Computational and biochemical analysis of type IV pilus dynamics and stability
Y Karami, A López-Castilla, A Ori, JL Thomassin… - Structure, 2021 - cell.com
Summary Type IV pili (T4P) are distinctive dynamic filaments at the surface of many bacteria
that can rapidly extend and retract and withstand strong forces. T4P are important virulence …
that can rapidly extend and retract and withstand strong forces. T4P are important virulence …
“Infostery” analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations
Characterizing a protein mutational landscape is a very challenging problem in Biology.
Many disease-associated mutations do not seem to produce any effect on the global shape …
Many disease-associated mutations do not seem to produce any effect on the global shape …
[HTML][HTML] Cysteine hyperoxidation rewires communication pathways in the nucleosome and destabilizes the dyad
Gene activity is tightly controlled by reversible chemical modifications called epigenetic
marks, which are of various types and modulate gene accessibility without affecting the DNA …
marks, which are of various types and modulate gene accessibility without affecting the DNA …
Histone H3 as a redox switch in the nucleosome core particle: insights from molecular modeling
Y Karami, R Gonzalez Aleman, M Duch, Y Qiu… - bioRxiv, 2024 - biorxiv.org
Histones post-translational modifications are major regulators of the chromatin dynamics.
Understanding the structural signature of these marks in the nucleosome context is of major …
Understanding the structural signature of these marks in the nucleosome context is of major …
E-Biothon: an experimental platform for BioInformatics
M Daydé, B Depardon, A Franc… - 2015 Computer …, 2015 - ieeexplore.ieee.org
The E-Biothon platform [1] is an experimental Cloud platform to help speed up and advance
research in biology, health and environment. It is based on a Blue Gene/P system and a web …
research in biology, health and environment. It is based on a Blue Gene/P system and a web …