[HTML][HTML] Assessment of mutations on RBD in the Spike protein of SARS-CoV-2 Alpha, Delta and Omicron variants

CHS da Costa, CAB de Freitas, CN Alves… - Scientific Reports, 2022 - nature.com
The severe acute respiratory syndrome (SARS) coronavirus 2 (CoV-2) variant Omicron
spread more rapid than the other variants of SARS-CoV-2 virus. Mutations on the Spike (S) …

[HTML][HTML] Variability in docking success rates due to dataset preparation

CR Corbeil, CI Williams, P Labute - Journal of computer-aided molecular …, 2012 - Springer
The results of cognate docking with the prepared Astex dataset provided by the organizers
of the “Docking and Scoring: A Review of Docking Programs” session at the 241st ACS …

Survey of the year 2008: applications of isothermal titration calorimetry

RJ Falconer, A Penkova, I Jelesarov… - Journal of molecular …, 2010 - Wiley Online Library
Isothermal titration calorimetry (ITC) is a fast, accurate and label‐free method for measuring
the thermodynamics and binding affinities of molecular associations in solution. Because the …

[HTML][HTML] Solvated interaction energy: from small-molecule to antibody drug design

EO Purisima, CR Corbeil, F Gaudreault… - Frontiers in Molecular …, 2023 - frontiersin.org
Scoring functions are ubiquitous in structure-based drug design as an aid to predicting
binding modes and estimating binding affinities. Ideally, a scoring function should be …

Exploring the potentiality of natural products from essential oils as inhibitors of odorant-binding proteins: A structure-and ligand-based virtual screening approach to …

KS da Costa, JM Galúcio, CHS da Costa… - ACS …, 2019 - ACS Publications
Odorant-binding proteins (OBPs) are the main olfactory proteins of mosquitoes, and their
structures have been widely explored to develop new repellents. In the present study, we …

Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein–protein interface

A Metz, C Pfleger, H Kopitz… - Journal of chemical …, 2012 - ACS Publications
Protein–protein interfaces are considered difficult targets for small-molecule protein–protein
interaction modulators (PPIMs). Here, we present for the first time a computational strategy …

Huprine–tacrine heterodimers as anti-amyloidogenic compounds of potential interest against Alzheimer's and prion diseases

C Galdeano, E Viayna, I Sola, X Formosa… - Journal of medicinal …, 2012 - ACS Publications
A family of huprine–tacrine heterodimers has been developed to simultaneously block the
active and peripheral sites of acetylcholinesterase (AChE). Their dual site binding for AChE …

[HTML][HTML] Identification mechanism of BACE1 on inhibitors probed by using multiple separate molecular dynamics simulations and comparative calculations of binding …

Y Wang, F Yang, D Yan, Y Zeng, B Wei, J Chen, W He - Molecules, 2023 - mdpi.com
β-amyloid cleaving enzyme 1 (BACE1) is regarded as an important target of drug design
toward the treatment of Alzheimer's disease (AD). In this study, three separate molecular …

DeepWEST: Deep learning of kinetic models with the Weighted Ensemble Simulation Toolkit for enhanced sampling

AA Ojha, S Thakur, SH Ahn… - Journal of chemical theory …, 2023 - ACS Publications
Recent advances in computational power and algorithms have enabled molecular dynamics
(MD) simulations to reach greater time scales. However, for observing conformational …

Structural and energetic basis of interaction between human estrogen-related receptor γ and environmental endocrine disruptors from multiple molecular dynamics …

L Chen, X Huang, Y Li, B Zhao, M Liang… - Journal of Hazardous …, 2023 - Elsevier
Environmental endocrine disruptors (EEDs), a class of molecules that are widespread in our
environment, may adversely affect the endocrine system. Exploring the interactions between …