Is it reliable to use common molecular docking methods for comparing the binding affinities of enantiomer pairs for their protein target?

D Ramírez, J Caballero - International journal of molecular sciences, 2016 - mdpi.com
Molecular docking is a computational chemistry method which has become essential for the
rational drug design process. In this context, it has had great impact as a successful tool for …

Computational studies of snake venom toxins

PG Ojeda, D Ramírez, J Alzate-Morales, J Caballero… - Toxins, 2017 - mdpi.com
Most snake venom toxins are proteins, and participate to envenomation through a diverse
array of bioactivities, such as bleeding, inflammation, and pain, cytotoxic, cardiotoxic or …

Study of the differential activity of thrombin inhibitors using docking, QSAR, molecular dynamics, and MM-GBSA

K Mena-Ulecia, W Tiznado, J Caballero - PLoS One, 2015 - journals.plos.org
Non-peptidic thrombin inhibitors (TIs; 177 compounds) with diverse groups at motifs P1
(such as oxyguanidine, amidinohydrazone, amidine, amidinopiperidine), P2 (such as …

Quantitative and label-free detection of protein kinase A activity based on surface-enhanced raman spectroscopy with gold nanostars

S He, YME Kyaw, EKM Tan, L Bekale… - Analytical …, 2018 - ACS Publications
The activity of extracellular protein kinase A (PKA) is known to be a biomarker for cancer.
However, conventional PKA assays based on colorimetric, radioactive, and fluorometric …

Virtual Screening of Novel 24-Dehydroxysterol Reductase (DHCR24) Inhibitors and the Biological Evaluation of Irbesartan in Cholesterol-Lowering Effect

H Wang, Z Lu, Y Li, T Liu, L Zhao, T Gao, X Lu, B Gao - Molecules, 2023 - mdpi.com
Hyperlipidemia is a risk factor for the development of fatty liver and cardiovascular diseases
such as atherosclerosis and coronary heart disease, and hence, cholesterol-lowering drugs …

Curcumin specifically binds to the human calcium–calmodulin-dependent protein kinase IV: Fluorescence and molecular dynamics simulation studies

N Hoda, H Naz, E Jameel, A Shandilya… - Journal of …, 2016 - Taylor & Francis
Calcium–calmodulin-dependent protein kinase IV (CAMK4) plays significant role in the
regulation of calcium-dependent gene expression, and thus, it is involved in varieties of …

[HTML][HTML] Computational methods applied to rational drug design

D Ramírez - The Open Medicinal Chemistry Journal, 2016 - ncbi.nlm.nih.gov
Due to the synergic relationship between medical chemistry, bioinformatics and molecular
simulation, the development of new accurate computational tools for small molecules drug …

Recent advances in computational models for the study of protein–peptide interactions

D Kilburg, E Gallicchio - Advances in protein chemistry and structural …, 2016 - Elsevier
We review computational models and software tools in current use for the study of protein–
peptide interactions. Peptides and peptide derivatives are growing in interest as therapeutic …

Impact of plasma oxidation on structural features of human epidermal growth factor

M Yusupov, JW Lackmann, J Razzokov… - Plasma Processes …, 2018 - Wiley Online Library
We perform computer simulations supported by experiments to investigate the oxidation of
an important signaling protein, that is, human epidermal growth factor (hEGF), caused by …

Mycobacterium tuberculosis serine/threonine protein kinases: Structural information for the design of their specific ATP-competitive inhibitors

J Caballero, A Morales-Bayuelo… - Journal of Computer …, 2018 - Springer
In the last decades, human protein kinases (PKs) have been relevant as targets in the
development of novel therapies against many diseases, but the study of Mycobacterium …