Related papers: Graph Transformation for Enzymatic Mechanisms
The molecular energies of chemical systems have been successfully calculated on quantum computers, however, more attention has been paid to the dynamic process of chemical reactions in practical application, especially in catalyst design,…
We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First,…
It is well known that Drug Design is often a costly process both in terms of time and economic effort. While good Quantitative Structure-Activity Relationship models (QSAR) can help predicting molecular properties without the need to…
Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical…
It is increasingly realized that taking stochastic effects into account is important in order to study biological cells. However, the corresponding mathematical formulation, the chemical master equation (CME), suffers from the curse of…
Rapid discovery of new reactions and molecules in recent years has been facilitated by the advancements in high throughput screening, accessibility to a much more complex chemical design space, and the development of accurate molecular…
We consider possible designs and experimental realiza-tions in synthesized rather than naturally occurring bio-chemical systems of a selection of basic bio-inspired information processing steps. These include feed-forward loops, which have…
Transformers generate valid and diverse chemical structures, but little is known about the mechanisms that enable these models to capture the rules of molecular representation. We present a mechanistic analysis of autoregressive…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
The existing literature on stochastic simulation of chemical reaction networks has a tendency to move as quickly as possible to the abstract formulation of the stochastic dynamics in terms of probabilities based on the concept of the…
The chemistry of an astrophysical environment is closely coupled to its dynamics, the latter often found to be complex. Hence, to properly model these environments a 3D context is necessary. However, solving chemical kinetics within a 3D…
Analyzing qualitative behaviors of biochemical reactions using its associated network structure has proven useful in diverse branches of biology. As an extension of our previous work, we introduce a graph-based framework to calculate steady…
Retrosynthesis prediction is a fundamental problem in organic synthesis, where the task is to identify precursor molecules that can be used to synthesize a target molecule. A key consideration in building neural models for this task is…
Enumerating chemical graphs satisfying given constraints is a fundamental problem in mathematical and computational chemistry, and plays an essential part in a recently proposed framework for the inverse QSAR/QSPR. In this paper,…
Understanding how biochemical systems settle into stable states, such as how protein concentrations reach equilibrium, is central to explaining cellular behavior and designing synthetic biological circuits. However, existing analytical…
Atomistic simulations are essential tools in chemistry and materials science, accelerating the discovery of novel catalysts, energy storage materials, and pharmaceuticals. However, running these simulations remains challenging due to the…
Relational tables, where each row corresponds to an entity and each column corresponds to an attribute, have been the standard for tables in relational databases. However, such a standard cannot be taken for granted when dealing with tables…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
Enzymes are genetically encoded biocatalysts capable of accelerating chemical reactions. How can we automatically design functional enzymes? In this paper, we propose EnzyGen, an approach to learn a unified model to design enzymes across…