相关论文: Rapid Exploration of Assembly Chemical Space of Mo…
There is a lack of scalable quantitative measures of reactivity for functional groups in organic chemistry. Measuring reactivity experimentally is costly and time-consuming and does not scale to the astronomical size of chemical space. In…
Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
Determining the complexity of molecules has important applications from molecular design to understanding the history of the process that led to the formation of the molecule. Currently, it is not possible to experimentally determine,…
The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by the relentless developments of computer architectures and algorithms. This explosion in the number and extent (in size and time) of MD…
We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…
Aligning theoretical atomistic structural models of materials with available experimental data presents a significant challenge for disordered systems. The configurational space to navigate is vast, and faithful realizations require large…
Evaluating the (dis)similarity of crystalline, disordered and molecular compounds is a critical step in the development of algorithms to navigate automatically the configuration space of complex materials. For instance, a structural…
Searching for novel molecules with desired chemical properties is crucial in drug discovery. Existing work focuses on developing neural models to generate either molecular sequences or chemical graphs. However, it remains a big challenge to…
Finding the common structural features of two molecules is a fundamental task in cheminformatics. Most drugs are small molecules, which can naturally be interpreted as graphs. Hence, the task is formalized as maximum common subgraph…
Conjugated organic molecules represent an important area of materials chemistry for both fundamental scientific exploration and technological applications. Using a genetic algorithm to computationally screen up to ~25-50 million molecules…
We use the Galaxy And Mass Assembly (GAMA) survey to measure the local Universe mass dependent merger fraction and merger rate using galaxy pairs and the CAS structural method, which identifies highly asymmetric merger candidate galaxies.…
Molecular machine learning has gained popularity with the advancements of geometric deep learning. In parallel, retrieval-augmented generation has become a principled approach commonly used with language models. However, the optimal…
Assembly theory has received considerable attention in the recent past. Here we analyze the formal framework of this model and show that assembly pathways coincide with certain minimal hyperpaths in B-hypergraphs. This makes it possible to…
Crystal Structure Prediction (CSP) of molecular crystals plays a central role in applications, such as pharmaceuticals and organic electronics. CSP is challenging and computationally expensive due to the need to explore a large search space…
The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the…
In drug discovery, knowledge of the graph structure of chemical compounds is essential. Many thousands of scientific articles in chemistry and pharmaceutical sciences have investigated chemical compounds, but in cases the details of the…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
The problem of finding dense components of a graph is a widely explored area in data analysis, with diverse applications in fields and branches of study including community mining, spam detection, computer security and bioinformatics. This…
Metabolomics complements investigation of the genome, transcriptome, and proteome of an organism. Today, the vast majority of metabolites remain unknown, in particular for non-model organisms. Mass spectrometry is one of the predominant…
A multitude of measures have been proposed to quantify the similarity between protein 3-D structure. Among these measures, contact map overlap (CMO) maximization deserved sustained attention during past decade because it offers a fine…