[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) …
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 …
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 …
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 …
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 …
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 …
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 …
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 …
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
Recent advances in computational power and algorithms have enabled molecular dynamics
(MD) simulations to reach greater time scales. However, for observing conformational …
(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 …
environment, may adversely affect the endocrine system. Exploring the interactions between …