[HTML][HTML] Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods

JM Krieger, P Doruker, AL Scott, D Perahia… - Current opinion in …, 2020 - Elsevier
… 1 5 , Pemra Doruker 1 5 , Ana Ligia Scott 2 5 , David Perahia 3 , Ivet Bahar 1 … Ana Ligia
Scott: Formal analysis, Methodology, Visualization, Writing - original draft, … Perahia, LPB Scott

[HTML][HTML] Sampling of protein conformational space using hybrid simulations: A critical assessment of recent methods

…, ZL Dahmani, MGS Costa, E Balog, AL Scott… - Frontiers in molecular …, 2022 - frontiersin.org
Recent years have seen several hybrid simulation methods for exploring the conformational
space of proteins and their complexes or assemblies. These methods often combine fast …

[HTML][HTML] Structural dynamics of DPP-4 and its influence on the projection of bioactive ligands

…, AN Lima, D Perahia, MA Miteva, AL Scott… - Molecules, 2018 - mdpi.com
Dipeptidyl peptidase-4 (DPP-4) is a target to treat type II diabetes mellitus. Therefore, it is
important to understand the structural aspects of this enzyme and its interaction with drug …

PINK1 interacts with VCP/p97 and activates PKA to promote NSFL1C/p47 phosphorylation and dendritic arborization in neurons

…, E Steer, PA Otero, NW Bateman, MH Cheng, AL Scott… - eneuro, 2018 - eneuro.org
While PTEN-induced kinase 1 (PINK1) is well characterized for its role in mitochondrial
homeostasis, much less is known concerning its ability to prevent synaptodendritic degeneration. …

Interaction between 1-pyrenesulfonic acid and albumin: Moving inside the protein

…, AN Lima, PT de Resende Lara, AL Scott… - … Acta Part A: Molecular …, 2019 - Elsevier
Due to the high sensitivity to alterations in microenvironment polarity of macromolecules,
pyrene and its derivatives have long been applied in biosciences. Human serum albumin (HSA)…

[HTML][HTML] Molecular modelling of the HCMV IL-10 protein isoforms and analysis of their interaction with the human IL-10 receptor

…, HBCR Batista, E Poole, M Nevels, EA Philot, AL Scott… - Plos one, 2022 - journals.plos.org
The human cytomegalovirus (HCMV) UL111A gene encodes several homologs of the cellular
interleukin 10 (cIL-10). Alternative splicing in the UL111A region produces two relatively …

Predicting regions prone to protein aggregation based on SVM algorithm

CA Moreira, EA Philot, AN Lima, AL Scott - Applied Mathematics and …, 2019 - Elsevier
The phenomenon of protein aggregation has been associated with several neurodegenerative
diseases, such as Parkinson's and Alzheimer's. Computational tools have been used to …

[HTML][HTML] Methyl divanillate: redox properties and binding affinity with albumin of an antioxidant and potential NADPH oxidase inhibitor

DN De Vasconcelos, AN Lima, EA Philot, AL Scott… - RSC …, 2019 - pubs.rsc.org
Vanillic acid is a widely used food additive (flavouring agent, JECFA number: 959) with
many reported beneficial biological effects. The same is true for its ester derivative (methyl …

[HTML][HTML] Unveiling functional motions based on point mutations in biased signaling systems: A normal mode study on nerve growth factor bound to TrkA

PT Resende-Lara, D Perahia, AL Scott, ASK Braz - Plos one, 2020 - journals.plos.org
Many receptors elicit signal transduction by activating multiple intracellular pathways. This
transduction can be triggered by a non-specific ligand, which simultaneously activates all the …

Virtual screening and in vitro assays of novel hits as promising DPP-4 inhibitors

…, AN Lima, LM Pires, RA Dos Santos, AL Scott… - Biochimie, 2022 - Elsevier
Diabetes is a metabolic disorder that presents hyperglycemia and vascular complications
due to the non-production of insulin or its inappropriate use by the body. One of the strategies …