AIMC Topic: Molecular Dynamics Simulation

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Discovery of SARS-CoV-2 papain-like protease inhibitors through machine learning and molecular simulation approaches.

Drug discoveries & therapeutics
The papain-like protease (PLpro), a cysteine protease found in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), plays a crucial role in viral replication by cleaving the viral polyproteins and interfering with the host's innate immune re...

Iterative enhancement of cutinase thermostability by multiple strategies based on combined directed evolution and computationally assisted design.

Bioresource technology
Cutinase exhibits versatile biocatalytic potential in polymer degradation, textile processing, and industrial biocatalysis, where enhancing the thermal stability under extreme conditions is essential for practical applications. To enhance the thermal...

Molecular dynamics-driven drug discovery.

Physical chemistry chemical physics : PCCP
Molecular dynamics (MD) simulation is an important tool and has a wide range of applications in many scientific fields, including drug discovery. Herein, focusing on drug discovery, the early compound discovery stage in particular, we discuss some of...

Coordinated Residue Motions at the Enzyme-Substrate Interface Promote DNA Translocation in Polymerases.

Journal of the American Chemical Society
The translocation of DNA in polymerase (Pol) enzymes is a critical step for Pol-mediated nucleic acid polymerization, essential for storing and transmitting genetic information in all living organisms. During this process, the newly elongated double-...

The continuous evolution of biomolecular force fields.

Structure (London, England : 1993)
Biomolecular force fields have continuously evolved to improve their accuracy and broaden their applications in biological and therapeutic discoveries. The rapid adaptation of advanced computational technology, in particular the recent deep learning ...

Next-generation cancer therapeutics: unveiling the potential of liposome-based nanoparticles through bioinformatics.

Mikrochimica acta
Cancer remains one of the most deadly diseases in the world, requiring constant growth and improvements in therapeutic strategies. Traditional cancer treatments, such as chemotherapy, radiotherapy, and surgery, have limitations like off-target releas...

Engineered multi-domain lipid nanoparticles for targeted delivery.

Chemical Society reviews
Engineered lipid nanoparticles (LNPs) represent a breakthrough in targeted drug delivery, enabling precise spatiotemporal control essential to treat complex diseases such as cancer and genetic disorders. However, the complexity of the delivery proces...

Enzymatic carbon-fluorine bond cleavage by human gut microbes.

Proceedings of the National Academy of Sciences of the United States of America
Fluorinated compounds are used for agrochemical, pharmaceutical, and numerous industrial applications, resulting in global contamination. In many molecules, fluorine is incorporated to enhance the half-life and improve bioavailability. Fluorinated co...

Unraveling the ecotoxicity of micro(nano)plastics loaded with environmental pollutants using ensemble machine learning.

Journal of hazardous materials
Micro(nano)plastics are ubiquitous and pose a severe threat to the environment and human health. Despite increasing research, most existing studies have focused on the toxicity of micro(nano)plastics as individual pollutants. Furthermore, fragmented ...

Smart Reaction Templating: A Graph-Based Method for Automated Molecular Dynamics Input Generation.

Journal of chemical information and modeling
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and postreaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that automates the gener...