Macromolecular modeling and design in Rosetta: recent methods and frameworks

JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle… - Nature …, 2020 - nature.com
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …

COVID-19 intranasal vaccines: current progress, advantages, prospects, and challenges

K Dhama, M Dhawan, R Tiwari, TB Emran… - Human vaccines & …, 2022 - Taylor & Francis
Multiple vaccines have recently been developed, and almost all the countries are presently
vaccinating their population to tackle the COVID-19 pandemic. Most of the COVID-19 …

Elucidating solution structures of cyclic peptides using molecular dynamics simulations

J Damjanovic, J Miao, H Huang, YS Lin - Chemical reviews, 2021 - ACS Publications
Protein–protein interactions are vital to biological processes, but the shape and size of their
interfaces make them hard to target using small molecules. Cyclic peptides have shown …

Strategic Feature Selection for Enhanced Scorch Prediction in Flexible Polyurethane Form Manufacturing

F Omoruwou, AA Ojugo… - Journal of Computing …, 2024 - publikasi2.dinus.ac.id
The occurrence of scorch during the production of flexible polyurethane is a significant issue
that negatively impacts foam products' resilience and generally jeopardizes their integrity …

AutoDock CrankPep: combining folding and docking to predict protein–peptide complexes

Y Zhang, MF Sanner - Bioinformatics, 2019 - academic.oup.com
Motivation Protein–peptide interactions mediate a wide variety of cellular and biological
functions. Methods for predicting these interactions have garnered a lot of interest over the …

Investigating protein–peptide interactions using the Schrödinger computational suite

J Bhachoo, T Beuming - Modeling peptide-protein interactions: methods …, 2017 - Springer
The Schrödinger software suite contains a broad array of computational chemistry and
molecular modeling tools that can be used to study the interaction of peptides with proteins …

[HTML][HTML] Activation of targetable inflammatory immune signaling is seen in myelodysplastic syndromes with SF3B1 mutations

GS Choudhary, A Pellagatti, B Agianian, MA Smith… - Elife, 2022 - elifesciences.org
Background: Mutations in the SF3B1 splicing factor are commonly seen in myelodysplastic
syndromes (MDS) and acute myeloid leukemia (AML), yet the specific oncogenic pathways …

Docking small peptides remains a great challenge: an assessment using AutoDock Vina

R Rentzsch, BY Renard - Briefings in Bioinformatics, 2015 - academic.oup.com
There is a growing interest in the mechanisms and the prediction of how flexible peptides
bind proteins, often in a highly selective and conserved manner. While both existing small …

Use of artificial intelligence to enhance phenotypic drug discovery

S Malandraki-Miller, PR Riley - Drug Discovery Today, 2021 - Elsevier
Highlights•This review re-explores the comparison between phenotypic and target-based
drug discovery and outlines how machine learning (ML) can assist the former at the forefront …

[HTML][HTML] Resistance and adaptation of bacteria to non-antibiotic antibacterial agents: physical stressors, nanoparticles, and bacteriophages

S Raza, K Matuła, S Karoń, J Paczesny - Antibiotics, 2021 - mdpi.com
Antimicrobial resistance is a significant threat to human health worldwide, forcing scientists
to explore non-traditional antibacterial agents to support rapid interventions and combat the …