Computational approaches to the rational design of tubulin-targeting agents

H Pérez-Peña, AC Abel, M Shevelev, AE Prota… - Biomolecules, 2023 - mdpi.com
Microtubules are highly dynamic polymers of α, β-tubulin dimers which play an essential role
in numerous cellular processes such as cell proliferation and intracellular transport, making …

Consequences and opportunities arising due to sparser single-cell RNA-seq datasets

GA Bouland, A Mahfouz, MJT Reinders - Genome biology, 2023 - Springer
With the number of cells measured in single-cell RNA sequencing (scRNA-seq) datasets
increasing exponentially and concurrent increased sparsity due to more zero counts being …

An expedited route to optical and electronic properties at finite temperature via unsupervised learning

F Perrella, F Coppola, N Rega, A Petrone - Molecules, 2023 - mdpi.com
Electronic properties and absorption spectra are the grounds to investigate molecular
electronic states and their interactions with the environment. Modeling and computations are …

[HTML][HTML] Clustering Molecules at a Large Scale: Integrating Spectral Geometry with Deep Learning

Ö Akgüller, MA Balcı, G Cioca - Molecules, 2024 - mdpi.com
This study conducts an in-depth analysis of clustering small molecules using spectral
geometry and deep learning techniques. We applied a spectral geometric approach to …

Identification of bacterial membrane selectivity of Romo1-derived antimicrobial peptide AMPR-22 via molecular dynamics

H Kim, YD Yoo, GY Lee - International Journal of Molecular Sciences, 2022 - mdpi.com
The abuse or misuse of antibiotics has caused the emergence of extensively drug-resistant
(XDR) bacteria, rendering most antibiotics ineffective and increasing the mortality rate of …

quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories

V Mallet, M Nilges, G Bouvier - Bioinformatics, 2021 - academic.oup.com
Abstract Summary We implemented the Self-Organizing Maps algorithm running efficiently
on GPUs, and also provide several clustering methods of the resulting maps. We provide …

MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics

R González-Alemán, D Platero-Rochart… - …, 2022 - academic.oup.com
Motivation The term clustering designates a comprehensive family of unsupervised learning
methods allowing to group similar elements into sets called clusters. Geometrical clustering …

Distinct binding interactions trigger opposite conformational modulations on pathogenic and wildtype Huntingtin exon 1 proteins

J Guan, Z Song, G Wei, Q Qiao - Physical Chemistry Chemical Physics, 2022 - pubs.rsc.org
Abnormal elongation of the polyglutamine tract transforms exon 1 of the Huntingtin protein
(Htt-exon-1) from wildtype to pathogenic form, and causes Huntington's disease. As an …

Discovery of novel microtubule stabilizers targeting taxane binding site by applying molecular docking, molecular dynamics simulation, and anticancer activity testing

H Zhang, HZ Qi, J Mao, HR Zhang, QQ Luo, ML Hu… - Bioorganic …, 2022 - Elsevier
Disruption of the dynamic equilibrium of microtubules can induce cell cycle arrest in G2/M
phase and apoptosis. Hence, discovery of novel tubulin polymerization inhibitors is very …

Diastereoselective synthesis of steroid–[60] fullerene hybrids and theoretical underpinning

D Alonso, D Hernández-Castillo… - The Journal of …, 2020 - ACS Publications
The reaction of C60 with pregnen-20-carboxaldehyde, a biologically active synthetic steroid,
by using a 1, 3-dipolar cycloaddition reaction (Prato's protocol) results in the formation of …