Modeling the Dynamics of Protein–Protein Interfaces, How and Why?

E Karaca, C Prévost, S Sacquin-Mora - Molecules, 2022 - mdpi.com
Protein–protein assemblies act as a key component in numerous cellular processes. Their
accurate modeling at the atomic level remains a challenge for structural biology. To address …

[HTML][HTML] Computer aided drug design in the development of proteolysis targeting chimeras

TM Tunjic, N Weber, M Brunsteiner - Computational and Structural …, 2023 - Elsevier
Proteolysis targeting chimeras represent a class of drug molecules with a number of
attractive properties, most notably a potential to work for targets that, so far, have been in …

Wastewater purification from drug (BEN) and poison (MAL) by graphene oxide/guar gum/CuO (GOGC): a novel MD simulation of carbon nanocomposite architecting …

AR Akbarzadeh, MS Esmaeili, S Parvaz… - Diamond and Related …, 2023 - Elsevier
In this study, the synthesized nanocomposite was evaluated novel graphene oxide/guar
gum/CuO (GOGC) adsorbent. For higher adsorption efficiency and antibacterial properties …

Pinobanksin from peony seed husk: A flavonoid with the potential to inhibit the proliferation of SH‐SY5Y

WT Chen, YY Zhang, Q Qiang, LL Zou… - Food Science & …, 2024 - Wiley Online Library
Pinobanksin, as one of the flavonoids, has powerful biological activities but has been under‐
recognized. In this study, we optimized the extraction method of phragmites from peony seed …

[HTML][HTML] Unveiling the molecular activity of HIV towards the CD4: A study based on subtype C via docking and dynamics approach

SK Mishra, N Kumar, Z Tóth, YAB Jardan… - Journal of Genetic …, 2025 - Elsevier
Abstract Background Acquired Immunodeficiency Syndrome (AIDS) is a critical global health
issue caused by the human immunodeficiency virus (HIV). It has different strains and …

Using selectively scaled molecular dynamics simulations to assess ligand poses in rna aptamers

Y Liu, AT Frank - Journal of Chemical Theory and Computation, 2022 - ACS Publications
Predicting the structure (or pose) of RNA-ligand complexes is an important problem in RNA
structural biology. Although one could use computational docking to rapidly sample putative …

Binding Kinetics Toolkit for Analyzing Transient Molecular Conformations and Computing Free Energy Landscapes

T Ruzmetov, R Montes, J Sun, SH Chen… - The Journal of …, 2022 - ACS Publications
Understanding ligand binding kinetics and thermodynamics, which involves investigating
the free, transient, and final complex conformations, is important in fundamental studies and …

Investigating Riboswitch-Containing Complexes via Molecular Dynamics Simulations

Y Liu - 2024 - deepblue.lib.umich.edu
Riboswitches are important structural elements that are predominantly found in bacteria,
regulating the expression of downstream genes in response to the binding of ligands. There …

Bacterial spot of tomato and pepper: insights into host-pathogen interactions

ML Malvino - 2021 - ideals.illinois.edu
The Solanaceae family, containing approximately 100 genera and 2,500 species, is the third
most valuable crop family in the world, and the most valuable vegetable crop. Some of the …

Profiling Unbinding Events to Identify Near-Native RNA-Ligand Poses

Y Liu, AT Frank - bioRxiv, 2022 - biorxiv.org
Predicting the structure (or pose) of RNA-ligand complexes is an important problem in RNA
structural biology and drug discovery. Although one could use molecular docking …