to predict molecular properties, which could speed up drug discovery and material development.
system has an underlying understanding of the rules that dictate how building blocks combine to produce valid molecules.
These rules capture the similarities between molecular structures, which helps the system generate new molecules and predict their properties in a data-efficient manner.
machine-learning system that automatically learns the “language” of molecules — what is known as a molecular grammar — using only a small, domain-specific dataset. It uses this grammar to construct viable molecules and predict their properties.
In language theory, one generates words, sentences, or paragraphs based on a set of grammar rules. You can think of a molecular grammar the same way. It is a set of production rules that dictate how to generate molecules or polymers by combining atoms and substructures.
Just like a language grammar, which can generate a plethora of sentences using the same rules, one molecular grammar can represent a vast number of molecules. Molecules with similar structures use the same grammar production rules, and the system learns to understand these similarities.
Since structurally similar molecules often have similar properties, the system uses its underlying knowledge of molecular similarity to predict properties of new molecules more efficiently.
Once we have this grammar as a representation for all the different molecules, we can use it to boost the process of property prediction
The system learns the production rules for a molecular grammar using reinforcement learning — a trial-and-error process where the model is rewarded for behavior that gets it closer to achieving a goal.
But because there could be billions of ways to combine atoms and substructures, the process to learn grammar production rules would be too computationally expensive for anything but the tiniest dataset.
The researchers decoupled the molecular grammar into two parts. The first part, called a metagrammar, is a general, widely applicable grammar they design manually and give the system at the outset. Then it only needs to learn a much smaller, molecule-specific grammar from the domain dataset. This hierarchical approach speeds up the learning process.
This grammar-based representation is very powerful. And because the grammar itself is a very general representation, it can be deployed to different kinds of graph-form data. We are trying to identify other applications beyond chemistry or material science
In the future, they also want to extend their current molecular grammar to include the 3D geometry of molecules and polymers, which is key to understanding the interactions between polymer chains. They are also developing an interface that would show a user the learned grammar production rules and solicit feedback to correct rules that may be wrong, boosting the accuracy of the system.
Molecular engineeringis an emerging field of study concerned with the design and testing of molecular properties, behavior and interactions in order to assemble better materials, systems, and processes for specific functions.
Molecular modeling on GPUsis the technique of using a graphics processing unit (GPU) for molecular simulations.
Molecular modelis a physical model of an atomistic system that represents molecules and their processes.
Molecular dynamicsis a computer simulation method for analyzing the physical movements of atoms and molecules.
Метод классической молекулярной динамикипозволяет с использованием современных ЭВМ рассматривать системы, состоящие из нескольких миллионов атомов на временах порядка нескольких пикосекунд. Применение других подходов (тяжело-атомные, крупно-зернистые (coarse-grained) модели) позволяет увеличить шаг интегрирования и тем самым увеличить доступное для наблюдения время до порядка микросекунд.
Hormoneis a class of signaling molecules in multicellular organisms that are sent to distant organs by complex biological processes to regulate physiology and behavior.
Molecular machineare a class of molecules typically described as an assembly of a discrete number of molecular components intended to produce mechanical movements in response to specific stimuli, mimicking macromolecular devices such as switches and motors.
Молекулярная машинаэто молекулярный компонент, который производит квази-механические движения (выход) в ответ на определенные стимулы (вход).
Molecular assembler"proposed device able to guide chemical reactions by positioning reactive molecules with atomic precision"
Наноассемблерэто разрабатываемое устройство наноразмеров, способное собирать из отдельных атомов или молекул сколь угодно сложные конструкции по вводимому в них плану.
GROMACSis a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids.
CHARMMis the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them.