Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction

S Wan, AP Bhati, SJ Zasada… - Interface focus, 2020 - royalsocietypublishing.org
A central quantity of interest in molecular biology and medicine is the free energy of binding
of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding …

[HTML][HTML] Artificial intelligence (AI) in rare diseases: is the future brighter?

S Brasil, C Pascoal, R Francisco, V dos Reis Ferreira… - Genes, 2019 - mdpi.com
The amount of data collected and managed in (bio) medicine is ever-increasing. Thus, there
is a need to rapidly and efficiently collect, analyze, and characterize all this information …

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

L Casalino, AC Dommer, Z Gaieb… - … Journal of High …, 2021 - journals.sagepub.com
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC
resources to explore the time-dependent dynamics of molecular systems. We use this …

Supercomputer-based ensemble docking drug discovery pipeline with application to COVID-19

A Acharya, R Agarwal, MB Baker… - Journal of chemical …, 2020 - ACS Publications
We present a supercomputer-driven pipeline for in silico drug discovery using enhanced
sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use …

Deep learning for rare disease: A sco** review

J Lee, C Liu, J Kim, Z Chen, Y Sun, JR Rogers… - Journal of biomedical …, 2022 - Elsevier
Although individually rare, collectively more than 7,000 rare diseases affect about 10% of
patients. Each of the rare diseases impacts the quality of life for patients and their families …

Using GANs with adaptive training data to search for new molecules

AE Blanchard, C Stanley, D Bhowmik - Journal of cheminformatics, 2021 - Springer
The process of drug discovery involves a search over the space of all possible chemical
compounds. Generative Adversarial Networks (GANs) provide a valuable tool towards …

Targeting neuronal lysosomal dysfunction caused by β-glucocerebrosidase deficiency with an enzyme-based brain shuttle construct

A Gehrlein, V Udayar, N Anastasi, ML Morella… - Nature …, 2023 - nature.com
Mutations in glucocerebrosidase cause the lysosomal storage disorder Gaucher's disease
and are the most common risk factor for Parkinson's disease. Therapies to restore the …

Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites

E Cho, M Rosa, R Anjum, S Mehmood… - Journal of Chemical …, 2021 - ACS Publications
β-coronavirus (CoVs) alone has been responsible for three major global outbreaks in the
21st century. The current crisis has led to an urgent requirement to develop therapeutics …

Structural insights into the lead identification of sub-type selective PDE4B inhibitors from plant bioactive molecule analogues

B Sharma, R Purohit - Journal of Molecular Liquids, 2023 - Elsevier
Abstract Phosphodiesterase-4B (PDE4B), a sub-type of PDE4, is highly expressed in the
brain and associated with schizophrenia, neuroinflammation, and cognition. A selective …

Manifold learning in atomistic simulations: a conceptual review

J Rydzewski, M Chen, O Valsson - Machine Learning: Science …, 2023 - iopscience.iop.org
Analyzing large volumes of high-dimensional data requires dimensionality reduction: finding
meaningful low-dimensional structures hidden in their high-dimensional observations. Such …