Molecular mechanics force fields enable atomistic simulations of complex systems that are too large for a quantum mechanical treatment. Simulation accuracy depends on the parameters employed in the fo...

Nature Chemistry - It is 100 years since the initial development of quantum mechanics, and not only did it bring with it a greater understanding of the world around us, it also introduced a new...

Machine Learning Interatomic Potentials (MLIPs), trained with Quantum Mechanics data, can model potential energy surfaces for molecular systems with very high accuracy and extreme speedups compared to...

Invent novel deep learning techniques for models of (bio)molecular structure, dynamics, reactivity and function. Design, implement, and iterate on model architectures and training algorithms (e.g., di...

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

Annual conference on Free Energy Methods in Drug Discovery

Amylose and cellulose are important biopolymers with diverse applications in biotechnology and materials science. Understanding their structural, dynamic, and solvation properties at the molecular level is critical for harnessing their potential. This study investigates the electronic and structural properties of single-chain cellulose and single- and double-chain amylose in aqueous solution using molecular dynamics simulations with both nonpolarizable (CHARMM) and polarizable (Drude) force fields. CHARMM simulations show stable hydrogen bonding between amylose and water, higher glucose ring dipole moments, increased rigidity, adoption of chair conformations, and less variation in dihedral angles. In contrast, Drude simulations captured dynamic electronic polarization, enhanced conformational flexibility, and resulted in heterogeneous inter- and intramolecular hydrogen bonds. For cellulose, structural and solvation behaviors were largely similar between CHARMM and Drude. These findings highlight molecular interactions and solvation dynamics of amylose and cellulose, with potential relevance in materials science and biotechnology.

Accurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, hav...

Since it was unveiled in 2020, Google DeepMind's game-changing AI tool has helped researchers all over the world to predict the 3D structures of hundreds of millions of proteins.

HADDOCK3 is the next generation integrative modelling software in the long-lasting HADDOCK project. It represents a complete rethinking and rewriting of the HADDOCK2.X series, implementing a new way…

Patrick Walters, the chief scientist of OpenADMET, discusses an ambitious open-science project aimed at figuring out how to avoid pharmacokinetic and toxicity traps in small-molecule drug discovery.

De novo binder discovery is unpredictable and inefficient due to a lack of quantitative understanding of protein-protein interaction (PPI) sequence-function landscapes. Here, we use our PANCS-Binder t...

Noncovalent interactions (NCIs) are fundamental to the structure, stability, and function of proteins. These interactions form complex networks that control how different protein regions relate to eac...

YouTube video by ProteinDesignStudio